Daily Papers

The simplified molecular-input line-entry system (SMILES) is the most popular representation of chemical compounds. Therefore, many SMILES-based molecular property prediction models have been developed. In particular, transformer-based models show promising performance because the model utilizes a massive chemical dataset for self-supervised learning. However, there is no transformer-based model to overcome the inherent limitations of SMILES, which result from the generation process of SMILES. In this study, we grammatically parsed SMILES to obtain connectivity between substructures and their type, which is called the grammatical knowledge of SMILES. First, we pretrained the transformers with substructural tokens, which were parsed from SMILES. Then, we used the training strategy 'same compound model' to better understand SMILES grammar. In addition, we injected knowledge of connectivity and type into the transformer with knowledge adapters. As a result, our representation model outperformed previous compound representations for the prediction of molecular properties. Finally, we analyzed the attention of the transformer model and adapters, demonstrating that the proposed model understands the grammar of SMILES.

Compound AI systems that combine multiple LLM calls, such as self-refine and multi-agent-debate, achieve strong performance on many AI tasks. We address a core question in optimizing compound systems: for each LLM call or module in the system, how should one decide which LLM to use? We show that these LLM choices have a large effect on quality, but the search space is exponential. We propose LLMSelector, an efficient framework for model selection in compound systems, which leverages two key empirical insights: (i) end-to-end performance is often monotonic in how well each module performs, with all other modules held fixed, and (ii) per-module performance can be estimated accurately by an LLM. Building upon these insights, LLMSelector iteratively selects one module and allocates to it the model with the highest module-wise performance, as estimated by an LLM, until no further gain is possible. LLMSelector is applicable to any compound system with a bounded number of modules, and its number of API calls scales linearly with the number of modules, achieving high-quality model allocation both empirically and theoretically. Experiments with popular compound systems such as multi-agent debate and self-refine using LLMs such as GPT-4o, Claude 3.5 Sonnet and Gemini 1.5 show that LLMSelector confers 5%-70% accuracy gains compared to using the same LLM for all modules.

Recent developments in natural language representations have been accompanied by large and expensive models that leverage vast amounts of general-domain text through self-supervised pre-training. Due to the cost of applying such models to down-stream tasks, several model compression techniques on pre-trained language representations have been proposed (Sun et al., 2019; Sanh, 2019). However, surprisingly, the simple baseline of just pre-training and fine-tuning compact models has been overlooked. In this paper, we first show that pre-training remains important in the context of smaller architectures, and fine-tuning pre-trained compact models can be competitive to more elaborate methods proposed in concurrent work. Starting with pre-trained compact models, we then explore transferring task knowledge from large fine-tuned models through standard knowledge distillation. The resulting simple, yet effective and general algorithm, Pre-trained Distillation, brings further improvements. Through extensive experiments, we more generally explore the interaction between pre-training and distillation under two variables that have been under-studied: model size and properties of unlabeled task data. One surprising observation is that they have a compound effect even when sequentially applied on the same data. To accelerate future research, we will make our 24 pre-trained miniature BERT models publicly available.

We, team AImsterdam, summarize our submission to the fastMRI challenge (Zbontar et al., 2018). Our approach builds on recent advances in invertible learning to infer models as presented in Putzky and Welling (2019). Both, our single-coil and our multi-coil model share the same basic architecture.

The cascade of 2D geometric transformations were exploited to model relations between entities in a knowledge graph (KG), leading to an effective KG embedding (KGE) model, CompoundE. Furthermore, the rotation in the 3D space was proposed as a new KGE model, Rotate3D, by leveraging its non-commutative property. Inspired by CompoundE and Rotate3D, we leverage 3D compound geometric transformations, including translation, rotation, scaling, reflection, and shear and propose a family of KGE models, named CompoundE3D, in this work. CompoundE3D allows multiple design variants to match rich underlying characteristics of a KG. Since each variant has its own advantages on a subset of relations, an ensemble of multiple variants can yield superior performance. The effectiveness and flexibility of CompoundE3D are experimentally verified on four popular link prediction datasets.

We present Compound Conditioned ControlNet, C3Net, a novel generative neural architecture taking conditions from multiple modalities and synthesizing multimodal contents simultaneously (e.g., image, text, audio). C3Net adapts the ControlNet architecture to jointly train and make inferences on a production-ready diffusion model and its trainable copies. Specifically, C3Net first aligns the conditions from multi-modalities to the same semantic latent space using modality-specific encoders based on contrastive training. Then, it generates multimodal outputs based on the aligned latent space, whose semantic information is combined using a ControlNet-like architecture called Control C3-UNet. Correspondingly, with this system design, our model offers an improved solution for joint-modality generation through learning and explaining multimodal conditions instead of simply taking linear interpolations on the latent space. Meanwhile, as we align conditions to a unified latent space, C3Net only requires one trainable Control C3-UNet to work on multimodal semantic information. Furthermore, our model employs unimodal pretraining on the condition alignment stage, outperforming the non-pretrained alignment even on relatively scarce training data and thus demonstrating high-quality compound condition generation. We contribute the first high-quality tri-modal validation set to validate quantitatively that C3Net outperforms or is on par with first and contemporary state-of-the-art multimodal generation. Our codes and tri-modal dataset will be released.

We introduce Masked Trajectory Models (MTM) as a generic abstraction for sequential decision making. MTM takes a trajectory, such as a state-action sequence, and aims to reconstruct the trajectory conditioned on random subsets of the same trajectory. By training with a highly randomized masking pattern, MTM learns versatile networks that can take on different roles or capabilities, by simply choosing appropriate masks at inference time. For example, the same MTM network can be used as a forward dynamics model, inverse dynamics model, or even an offline RL agent. Through extensive experiments in several continuous control tasks, we show that the same MTM network -- i.e. same weights -- can match or outperform specialized networks trained for the aforementioned capabilities. Additionally, we find that state representations learned by MTM can significantly accelerate the learning speed of traditional RL algorithms. Finally, in offline RL benchmarks, we find that MTM is competitive with specialized offline RL algorithms, despite MTM being a generic self-supervised learning method without any explicit RL components. Code is available at https://github.com/facebookresearch/mtm

The democratization of machine learning systems has made the process of fine-tuning accessible to practitioners, leading to a wide range of open-source models fine-tuned on specialized tasks and datasets. Recent work has proposed to merge such models to combine their functionalities. However, prior approaches are usually restricted to models that are fine-tuned from the same base model. Furthermore, the final merged model is typically required to be of the same size as the original models. In this work, we propose a new two-step algorithm to merge models -- termed PLeaS -- which relaxes these constraints. First, leveraging the Permutation symmetries inherent in the two models, PLeaS partially matches nodes in each layer by maximizing alignment. Next, PLeaS computes the weights of the merged model as a layer-wise Least Squares solution to minimize the approximation error between the features of the merged model and the permuted features of the original models. PLeaS allows a practitioner to merge two models sharing the same architecture into a single performant model of a desired size, even when the two original models are fine-tuned from different base models. We also demonstrate how our method can be extended to address a challenging scenario where no data is available from the fine-tuning domains. We demonstrate our method to merge ResNet and ViT models trained with shared and different label spaces, and show improvement over the state-of-the-art merging methods of up to 15 percentage points for the same target compute while merging models trained on DomainNet and fine-grained classification tasks. Our code is open-sourced at https://github.com/SewoongLab/PLeaS-Merging .

Large language models (LLMs) appear to bias their survey answers toward certain values. Nonetheless, some argue that LLMs are too inconsistent to simulate particular values. Are they? To answer, we first define value consistency as the similarity of answers across (1) paraphrases of one question, (2) related questions under one topic, (3) multiple-choice and open-ended use-cases of one question, and (4) multilingual translations of a question to English, Chinese, German, and Japanese. We apply these measures to a few large (>=34b), open LLMs including llama-3, as well as gpt-4o, using eight thousand questions spanning more than 300 topics. Unlike prior work, we find that models are relatively consistent across paraphrases, use-cases, translations, and within a topic. Still, some inconsistencies remain. Models are more consistent on uncontroversial topics (e.g., in the U.S., "Thanksgiving") than on controversial ones ("euthanasia"). Base models are both more consistent compared to fine-tuned models and are uniform in their consistency across topics, while fine-tuned models are more inconsistent about some topics ("euthanasia") than others ("women's rights") like our human subjects (n=165).

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing, reducing the failure rate, and streamlining clinical trials. In this work, we make an initial attempt towards enabling ChatGPT-like capabilities on drug molecule graphs, by developing a prototype system DrugChat. DrugChat works in a similar way as ChatGPT. Users upload a compound molecule graph and ask various questions about this compound. DrugChat will answer these questions in a multi-turn, interactive manner. The DrugChat system consists of a graph neural network (GNN), a large language model (LLM), and an adaptor. The GNN takes a compound molecule graph as input and learns a representation for this graph. The adaptor transforms the graph representation produced by the GNN into another representation that is acceptable to the LLM. The LLM takes the compound representation transformed by the adaptor and users' questions about this compound as inputs and generates answers. All these components are trained end-to-end. To train DrugChat, we collected instruction tuning datasets which contain 10,834 drug compounds and 143,517 question-answer pairs. The code and data is available at https://github.com/UCSD-AI4H/drugchat

Cancer is the second leading cause of death, with chemotherapy as one of the primary forms of treatment. As a result, researchers are turning to drug combination therapy to decrease drug resistance and increase efficacy. Current methods of drug combination screening, such as in vivo and in vitro, are inefficient due to stark time and monetary costs. In silico methods have become increasingly important for screening drugs, but current methods are inaccurate and generalize poorly to unseen anticancer drugs. In this paper, I employ a geometric deep-learning model utilizing a graph attention network that is equivariant to 3D rotations, translations, and reflections with structural motifs. Additionally, the gene expression of cancer cell lines is utilized to classify synergistic drug combinations specific to each cell line. I compared the proposed geometric deep learning framework to current state-of-the-art (SOTA) methods, and the proposed model architecture achieved greater performance on all 12 benchmark tasks performed on the DrugComb dataset. Specifically, the proposed framework outperformed other SOTA methods by an accuracy difference greater than 28%. Based on these results, I believe that the equivariant graph attention network's capability of learning geometric data accounts for the large performance improvements. The model's ability to generalize to foreign drugs is thought to be due to the structural motifs providing a better representation of the molecule. Overall, I believe that the proposed equivariant geometric deep learning framework serves as an effective tool for virtually screening anticancer drug combinations for further validation in a wet lab environment. The code for this work is made available online at: https://github.com/WeToTheMoon/EGAT_DrugSynergy.

Intelligent agents must be generalists - showing the ability to quickly adapt and generalize to varying tasks. Within the framework of reinforcement learning (RL), model-based RL algorithms learn a task-agnostic dynamics model of the world, in principle allowing them to generalize to arbitrary rewards. However, one-step models naturally suffer from compounding errors, making them ineffective for problems with long horizons and large state spaces. In this work, we propose a novel class of models - generalized occupancy models (GOMs) - that retain the generality of model-based RL while avoiding compounding error. The key idea behind GOMs is to model the distribution of all possible long-term outcomes from a given state under the coverage of a stationary dataset, along with a policy that realizes a particular outcome from the given state. These models can then quickly be used to select the optimal action for arbitrary new tasks, without having to redo policy optimization. By directly modeling long-term outcomes, GOMs avoid compounding error while retaining generality across arbitrary reward functions. We provide a practical instantiation of GOMs using diffusion models and show its efficacy as a new class of transferable models, both theoretically and empirically across a variety of simulated robotics problems. Videos and code at https://weirdlabuw.github.io/gom/.

In a compound AI system, components such as an LLM call, a retriever, a code interpreter, or tools are interconnected. The system's behavior is primarily driven by parameters such as instructions or tool definitions. Recent advancements enable end-to-end optimization of these parameters using an LLM. Notably, leveraging an LLM as an optimizer is particularly efficient because it avoids gradient computation and can generate complex code and instructions. This paper presents a survey of the principles and emerging trends in LLM-based optimization of compound AI systems. It covers archetypes of compound AI systems, approaches to LLM-based end-to-end optimization, and insights into future directions and broader impacts. Importantly, this survey uses concepts from program analysis to provide a unified view of how an LLM optimizer is prompted to optimize a compound AI system. The exhaustive list of paper is provided at https://github.com/linyuhongg/LLM-based-Optimization-of-Compound-AI-Systems.

Using the weights of trained Neural Network (NN) models as data modality has recently gained traction as a research field - dubbed Weight Space Learning (WSL). Multiple recent works propose WSL methods to analyze models, evaluate methods, or synthesize weights. Weight space learning methods require populations of trained models as datasets for development and evaluation. However, existing collections of models - called `model zoos' - are unstructured or follow a rudimentary definition of diversity. In parallel, work rooted in statistical physics has identified phases and phase transitions in NN models. Models are homogeneous within the same phase but qualitatively differ from one phase to another. We combine the idea of `model zoos' with phase information to create a controlled notion of diversity in populations. We introduce 12 large-scale zoos that systematically cover known phases and vary over model architecture, size, and datasets. These datasets cover different modalities, such as computer vision, natural language processing, and scientific ML. For every model, we compute loss landscape metrics and validate full coverage of the phases. With this dataset, we provide the community with a resource with a wide range of potential applications for WSL and beyond. Evidence suggests the loss landscape phase plays a role in applications such as model training, analysis, or sparsification. We demonstrate this in an exploratory study of the downstream methods like transfer learning or model weights averaging.

Scaling laws predict the loss of a target machine learning model by extrapolating from easier-to-train models with fewer parameters or smaller training sets. This provides an efficient way for practitioners and researchers alike to compare pretraining decisions involving optimizers, datasets, and model architectures. Despite the widespread use of scaling laws to model the dynamics of language model training, there has been little work on understanding how to best estimate and interpret them. We collect (and release) a large-scale dataset containing losses and downstream evaluations for 485 previously published pretrained models. We use these to estimate more than 1000 scaling laws, then derive a set of best practices for estimating scaling laws in new model families. We find that fitting scaling laws to intermediate checkpoints of training runs (and not just their final losses) substantially improves accuracy, and that -- all else equal -- estimates of performance are generally most accurate when derived from other models of similar sizes. However, because there is a significant degree of variability across model seeds, training multiple small models is sometimes more useful than training a single large one. Moreover, while different model families differ scaling behavior, they are often similar enough that a target model's behavior can be predicted from a single model with the same architecture, along with scaling parameter estimates derived from other model families.

Diffusion models are relatively easy to train but require many steps to generate samples. Consistency models are far more difficult to train, but generate samples in a single step. In this paper we propose Multistep Consistency Models: A unification between Consistency Models (Song et al., 2023) and TRACT (Berthelot et al., 2023) that can interpolate between a consistency model and a diffusion model: a trade-off between sampling speed and sampling quality. Specifically, a 1-step consistency model is a conventional consistency model whereas we show that a infty-step consistency model is a diffusion model. Multistep Consistency Models work really well in practice. By increasing the sample budget from a single step to 2-8 steps, we can train models more easily that generate higher quality samples, while retaining much of the sampling speed benefits. Notable results are 1.4 FID on Imagenet 64 in 8 step and 2.1 FID on Imagenet128 in 8 steps with consistency distillation. We also show that our method scales to a text-to-image diffusion model, generating samples that are very close to the quality of the original model.

In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure in the form of a SMILES sequence, gene expression profiles of tumors and prior knowledge on intracellular interactions from protein-protein interaction networks. We demonstrate that our multiscale convolutional attention-based (MCA) encoder significantly outperforms a baseline model trained on Morgan fingerprints, a selection of encoders based on SMILES as well as previously reported state of the art for multimodal drug sensitivity prediction (R2 = 0.86 and RMSE = 0.89). Moreover, the explainability of our approach is demonstrated by a thorough analysis of the attention weights. We show that the attended genes significantly enrich apoptotic processes and that the drug attention is strongly correlated with a standard chemical structure similarity index. Finally, we report a case study of two receptor tyrosine kinase (RTK) inhibitors acting on a leukemia cell line, showcasing the ability of the model to focus on informative genes and submolecular regions of the two compounds. The demonstrated generalizability and the interpretability of our model testify its potential for in-silico prediction of anticancer compound efficacy on unseen cancer cells, positioning it as a valid solution for the development of personalized therapies as well as for the evaluation of candidate compounds in de novo drug design.

Tangent Model Composition (TMC) is a method to combine component models independently fine-tuned around a pre-trained point. Component models are tangent vectors to the pre-trained model that can be added, scaled, or subtracted to support incremental learning, ensembling, or unlearning. Component models are composed at inference time via scalar combination, reducing the cost of ensembling to that of a single model. TMC improves accuracy by 4.2% compared to ensembling non-linearly fine-tuned models at a 2.5x to 10x reduction of inference cost, growing linearly with the number of component models. Each component model can be forgotten at zero cost, with no residual effect on the resulting inference. When used for continual fine-tuning, TMC is not constrained by sequential bias and can be executed in parallel on federated data. TMC outperforms recently published continual fine-tuning methods almost uniformly on each setting -- task-incremental, class-incremental, and data-incremental -- on a total of 13 experiments across 3 benchmark datasets, despite not using any replay buffer. TMC is designed for composing models that are local to a pre-trained embedding, but could be extended to more general settings.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

In deep learning, models typically reuse the same parameters for all inputs. Mixture of Experts (MoE) defies this and instead selects different parameters for each incoming example. The result is a sparsely-activated model -- with outrageous numbers of parameters -- but a constant computational cost. However, despite several notable successes of MoE, widespread adoption has been hindered by complexity, communication costs and training instability -- we address these with the Switch Transformer. We simplify the MoE routing algorithm and design intuitive improved models with reduced communication and computational costs. Our proposed training techniques help wrangle the instabilities and we show large sparse models may be trained, for the first time, with lower precision (bfloat16) formats. We design models based off T5-Base and T5-Large to obtain up to 7x increases in pre-training speed with the same computational resources. These improvements extend into multilingual settings where we measure gains over the mT5-Base version across all 101 languages. Finally, we advance the current scale of language models by pre-training up to trillion parameter models on the "Colossal Clean Crawled Corpus" and achieve a 4x speedup over the T5-XXL model.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Generative models for materials, especially inorganic crystals, hold potential to transform the theoretical prediction of novel compounds and structures. Advancement in this field depends critically on robust benchmarks and minimal, information-rich datasets that enable meaningful model evaluation. This paper critically examines common datasets and reported metrics for a crystal structure prediction taskx2014generating the most likely structures given the chemical composition of a material. We focus on three key issues: First, materials datasets should contain unique crystal structures; for example, we show that the widely-utilized carbon-24 dataset only contains approx40% unique structures. Second, materials datasets should not be split randomly if polymorphs of many different compositions are numerous, which we find to be the case for the perov-5 dataset. Third, benchmarks can mislead if used uncritically, e.g., reporting a match rate metric without considering the structural variety exhibited by identical building blocks. To address these oft-overlooked issues, we introduce several fixes. We provide revised versions of the carbon-24 dataset: one with duplicates removed, one deduplicated and split by number of atoms N, and two containing only identical structures but with different unit cells. We also propose a new split for the perov-5 dataset which ensures polymorphs are grouped within each split subset, setting a more sensible standard for benchmarking model performance. Finally, we present METRe and cRMSE, new model evaluation metrics that can correct existing issues with the match rate metric.

Pretrained neural networks have attracted significant interest in chemistry and small molecule drug design. Embeddings from these models are widely used for molecular property prediction, virtual screening, and small data learning in molecular chemistry. This study presents the most extensive comparison of such models to date, evaluating 25 models across 25 datasets. Under a fair comparison framework, we assess models spanning various modalities, architectures, and pretraining strategies. Using a dedicated hierarchical Bayesian statistical testing model, we arrive at a surprising result: nearly all neural models show negligible or no improvement over the baseline ECFP molecular fingerprint. Only the CLAMP model, which is also based on molecular fingerprints, performs statistically significantly better than the alternatives. These findings raise concerns about the evaluation rigor in existing studies. We discuss potential causes, propose solutions, and offer practical recommendations.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

In this work we analyze strategies for convolutional neural network scaling; that is, the process of scaling a base convolutional network to endow it with greater computational complexity and consequently representational power. Example scaling strategies may include increasing model width, depth, resolution, etc. While various scaling strategies exist, their tradeoffs are not fully understood. Existing analysis typically focuses on the interplay of accuracy and flops (floating point operations). Yet, as we demonstrate, various scaling strategies affect model parameters, activations, and consequently actual runtime quite differently. In our experiments we show the surprising result that numerous scaling strategies yield networks with similar accuracy but with widely varying properties. This leads us to propose a simple fast compound scaling strategy that encourages primarily scaling model width, while scaling depth and resolution to a lesser extent. Unlike currently popular scaling strategies, which result in about O(s) increase in model activation w.r.t. scaling flops by a factor of s, the proposed fast compound scaling results in close to O(s) increase in activations, while achieving excellent accuracy. This leads to comparable speedups on modern memory-limited hardware (e.g., GPU, TPU). More generally, we hope this work provides a framework for analyzing and selecting scaling strategies under various computational constraints.

Model merging aims to combine multiple fine-tuned models into a single set of weights that performs well across all source tasks. While prior work has shown that merging can approximate the performance of individual fine-tuned models for each task, it largely overlooks scenarios where models are compressed into low-rank representations, either through low-rank adaptation (LoRA) or post-training singular value decomposition (SVD). We first demonstrate that applying conventional merging methods to low-rank weights leads to severe performance degradation in the merged model. Motivated by this phenomenon, we propose a fundamentally different approach: instead of collapsing all adapters into one set of weights, we construct a compact basis (e.g., an equivalent of holding two or more models) from which original task-specific models can be recovered via linear combination. This reframes merging as generating a reconstruction-capable model space rather than producing a single merged model. Crucially, this allows us to ``revert'' to each individual model when needed, recognizing that no merged model can consistently outperform one specialized for its task. Building on this insight, we introduce our method, Reversible Model Merging (RMM), an efficient, data-free, and flexible method that provides a closed-form solution for selecting the optimal basis of model weights and task-specific coefficients for linear combination. Extensive experiments across diverse datasets and model scales demonstrate that RMM consistently outperforms existing merging approaches, preserving the performance of low-rank compressed models by a significant margin.

While fine-tuning pretrained models has become common practice, these models often underperform outside their specific domains. Recently developed model merging techniques enable the direct integration of multiple models, each fine-tuned for distinct tasks, into a single model. This strategy promotes multitasking capabilities without requiring retraining on the original datasets. However, existing methods fall short in addressing potential conflicts and complex correlations between tasks, especially in parameter-level adjustments, posing a challenge in effectively balancing parameter competition across various tasks. This paper introduces an innovative technique named PCB-Merging (Parameter Competition Balancing), a lightweight and training-free technique that adjusts the coefficients of each parameter for effective model merging. PCB-Merging employs intra-balancing to gauge parameter significance within individual tasks and inter-balancing to assess parameter similarities across different tasks. Parameters with low importance scores are dropped, and the remaining ones are rescaled to form the final merged model. We assessed our approach in diverse merging scenarios, including cross-task, cross-domain, and cross-training configurations, as well as out-of-domain generalization. The experimental results reveal that our approach achieves substantial performance enhancements across multiple modalities, domains, model sizes, number of tasks, fine-tuning forms, and large language models, outperforming existing model merging methods. The code is publicly available at: https://github.com/duguodong7/pcb-merging.

It is a common belief that large language models (LLMs) are better than smaller-sized ones. However, larger models also require significantly more time and compute during inference. This begs the question: what happens when both models operate under the same budget? (e.g., compute, run-time). To address this question, we analyze code generation LLMs of various sizes and make comparisons such as running a 70B model once vs. generating five outputs from a 13B model. We consider a standard unit-test setup, which can be used to select the correct output from the smaller model. Our findings reveal that the repeated use of smaller models can yield consistent improvements, with gains of up to 15% across five tasks. On the other hand, in scenarios where unit-tests are unavailable, a ranking-based selection of candidates from the smaller model falls short of the performance of a single output from larger ones. Our results highlight the potential of using smaller models instead of larger ones, and the importance of studying approaches for ranking LLM outputs.

Machine learning models are often used to inform real world risk assessment tasks: predicting consumer default risk, predicting whether a person suffers from a serious illness, or predicting a person's risk to appear in court. Given multiple models that perform almost equally well for a prediction task, to what extent do predictions vary across these models? If predictions are relatively consistent for similar models, then the standard approach of choosing the model that optimizes a penalized loss suffices. But what if predictions vary significantly for similar models? In machine learning, this is referred to as predictive multiplicity i.e. the prevalence of conflicting predictions assigned by near-optimal competing models. In this paper, we present a framework for measuring predictive multiplicity in probabilistic classification (predicting the probability of a positive outcome). We introduce measures that capture the variation in risk estimates over the set of competing models, and develop optimization-based methods to compute these measures efficiently and reliably for convex empirical risk minimization problems. We demonstrate the incidence and prevalence of predictive multiplicity in real-world tasks. Further, we provide insight into how predictive multiplicity arises by analyzing the relationship between predictive multiplicity and data set characteristics (outliers, separability, and majority-minority structure). Our results emphasize the need to report predictive multiplicity more widely.

Model merging aims to combine multiple expert models into a more capable single model, offering benefits such as reduced storage and serving costs, improved generalization, and support for decentralized model development. Despite its promise, previous studies have primarily focused on merging a few small models. This leaves many unanswered questions about the effect of scaling model size and how it interplays with other key factors -- like the base model quality and number of expert models -- , to affect the merged model's performance. This work systematically evaluates the utility of model merging at scale, examining the impact of these different factors. We experiment with merging fully fine-tuned models using 4 popular merging methods -- Averaging, Task~Arithmetic, Dare, and TIES -- across model sizes ranging from 1B-64B parameters and merging up to 8 different expert models. We evaluate the merged models on both held-in tasks, i.e., the expert's training tasks, and zero-shot generalization to unseen held-out tasks. Our experiments provide several new insights about model merging at scale and the interplay between different factors. First, we find that merging is more effective when experts are created from strong base models, i.e., models with good zero-shot performance. Second, larger models facilitate easier merging. Third merging consistently improves generalization capabilities. Notably, when merging 8 large expert models, the merged models often generalize better compared to the multitask trained models. Fourth, we can better merge more expert models when working with larger models. Fifth, different merging methods behave very similarly at larger scales. Overall, our findings shed light on some interesting properties of model merging while also highlighting some limitations. We hope that this study will serve as a reference point on large-scale merging for upcoming research.

The fine-tuning of deep pre-trained models has revealed compositional properties, with multiple specialized modules that can be arbitrarily composed into a single, multi-task model. However, identifying the conditions that promote compositionality remains an open issue, with recent efforts concentrating mainly on linearized networks. We conduct a theoretical study that attempts to demystify compositionality in standard non-linear networks through the second-order Taylor approximation of the loss function. The proposed formulation highlights the importance of staying within the pre-training basin to achieve composable modules. Moreover, it provides the basis for two dual incremental training algorithms: the one from the perspective of multiple models trained individually, while the other aims to optimize the composed model as a whole. We probe their application in incremental classification tasks and highlight some valuable skills. In fact, the pool of incrementally learned modules not only supports the creation of an effective multi-task model but also enables unlearning and specialization in certain tasks. Code available at https://github.com/aimagelab/mammoth.

Linear structural equation models are multivariate statistical models encoded by mixed graphs. In particular, the set of covariance matrices for distributions belonging to a linear structural equation model for a fixed mixed graph G=(V, D,B) is parameterized by a rational function with parameters for each vertex and edge in G. This rational parametrization naturally allows for the study of these models from an algebraic and combinatorial point of view. Indeed, this point of view has led to a collection of results in the literature, mainly focusing on questions related to identifiability and determining relationships between covariances (i.e., finding polynomials in the Gaussian vanishing ideal). So far, a large proportion of these results has focused on the case when D, the directed part of the mixed graph G, is acyclic. This is due to the fact that in the acyclic case, the parametrization becomes polynomial and there is a description of the entries of the covariance matrices in terms of a finite sum. We move beyond the acyclic case and give a closed form expression for the entries of the covariance matrices in terms of the one-connections in a graph obtained from D through some small operations. This closed form expression then allows us to show that if G is simple, then the parametrization map is generically finite-to-one. Finally, having a closed form expression for the covariance matrices allows for the development of an algorithm for systematically exploring possible polynomials in the Gaussian vanishing ideal.

When manipulating three-dimensional data, it is possible to ensure that rotational and translational symmetries are respected by applying so-called SE(3)-equivariant models. Protein structure prediction is a prominent example of a task which displays these symmetries. Recent work in this area has successfully made use of an SE(3)-equivariant model, applying an iterative SE(3)-equivariant attention mechanism. Motivated by this application, we implement an iterative version of the SE(3)-Transformer, an SE(3)-equivariant attention-based model for graph data. We address the additional complications which arise when applying the SE(3)-Transformer in an iterative fashion, compare the iterative and single-pass versions on a toy problem, and consider why an iterative model may be beneficial in some problem settings. We make the code for our implementation available to the community.

In the era of large language models, model merging is a promising way to combine multiple task-specific models into a single multitask model without extra training. However, two challenges remain: (a) interference between different models and (b) heterogeneous data during testing. Traditional model merging methods often show significant performance gaps compared to fine-tuned models due to these issues. Additionally, a one-size-fits-all model lacks flexibility for diverse test data, leading to performance degradation. We show that both shared and exclusive task-specific knowledge are crucial for merging performance, but directly merging exclusive knowledge hinders overall performance. In view of this, we propose Twin-Merging, a method that encompasses two principal stages: (1) modularizing knowledge into shared and exclusive components, with compression to reduce redundancy and enhance efficiency; (2) dynamically merging shared and task-specific knowledge based on the input. This approach narrows the performance gap between merged and fine-tuned models and improves adaptability to heterogeneous data. Extensive experiments on 12 datasets for both discriminative and generative tasks demonstrate the effectiveness of our method, showing an average improvement of 28.34% in absolute normalized score for discriminative tasks and even surpassing the fine-tuned upper bound on the generative tasks. (Our implementation is available in https://github.com/LZY-the-boys/Twin-Mergin.)

In this paper, a mathematical model is developed to describe the evolution of the concentration of compounds through a gas chromatography column. The model couples mass balances and kinetic equations for all components. Both single and multiple-component cases are considered with constant or variable velocity. Non-dimensionalisation indicates the small effect of diffusion. The system where diffusion is neglected is analysed using Laplace transforms. In the multiple-component case, it is demonstrated that the competition between the compounds is negligible and the equations may be decoupled. This reduces the problem to solving a single integral equation to determine the concentration profile for all components (since they are scaled versions of each other). For a given analyte, we then only two parameters need to be fitted to the data. To verify this approach, the full governing equations are also solved numerically using the finite difference method and a global adaptive quadrature method to integrate the Laplace transformation. Comparison with the Laplace solution verifies the high degree of accuracy of the simpler Laplace form. The Laplace solution is then verified against experimental data from BTEX chromatography. This novel method, which involves solving a single equation and fitting parameters in pairs for individual components, is highly efficient. It is significantly faster and simpler than the full numerical solution and avoids the computationally expensive methods that would normally be used to fit all curves at the same time.

We employ new tools from mechanistic interpretability in order to ask whether the internal structure of large language models (LLMs) shows correspondence to the linguistic structures which underlie the languages on which they are trained. In particular, we ask (1) when two languages employ the same morphosyntactic processes, do LLMs handle them using shared internal circuitry? and (2) when two languages require different morphosyntactic processes, do LLMs handle them using different internal circuitry? Using English and Chinese multilingual and monolingual models, we analyze the internal circuitry involved in two tasks. We find evidence that models employ the same circuit to handle the same syntactic process independently of the language in which it occurs, and that this is the case even for monolingual models trained completely independently. Moreover, we show that multilingual models employ language-specific components (attention heads and feed-forward networks) when needed to handle linguistic processes (e.g., morphological marking) that only exist in some languages. Together, our results provide new insights into how LLMs trade off between exploiting common structures and preserving linguistic differences when tasked with modeling multiple languages simultaneously.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

We release the Nemotron-4 340B model family, including Nemotron-4-340B-Base, Nemotron-4-340B-Instruct, and Nemotron-4-340B-Reward. Our models are open access under the NVIDIA Open Model License Agreement, a permissive model license that allows distribution, modification, and use of the models and its outputs. These models perform competitively to open access models on a wide range of evaluation benchmarks, and were sized to fit on a single DGX H100 with 8 GPUs when deployed in FP8 precision. We believe that the community can benefit from these models in various research studies and commercial applications, especially for generating synthetic data to train smaller language models. Notably, over 98% of data used in our model alignment process is synthetically generated, showcasing the effectiveness of these models in generating synthetic data. To further support open research and facilitate model development, we are also open-sourcing the synthetic data generation pipeline used in our model alignment process.

Combining different models is a widely used paradigm in machine learning applications. While the most common approach is to form an ensemble of models and average their individual predictions, this approach is often rendered infeasible by given resource constraints in terms of memory and computation, which grow linearly with the number of models. We present a layer-wise model fusion algorithm for neural networks that utilizes optimal transport to (soft-) align neurons across the models before averaging their associated parameters. We show that this can successfully yield "one-shot" knowledge transfer (i.e, without requiring any retraining) between neural networks trained on heterogeneous non-i.i.d. data. In both i.i.d. and non-i.i.d. settings , we illustrate that our approach significantly outperforms vanilla averaging, as well as how it can serve as an efficient replacement for the ensemble with moderate fine-tuning, for standard convolutional networks (like VGG11), residual networks (like ResNet18), and multi-layer perceptrons on CIFAR10, CIFAR100, and MNIST. Finally, our approach also provides a principled way to combine the parameters of neural networks with different widths, and we explore its application for model compression. The code is available at the following link, https://github.com/sidak/otfusion.

As Large Language Models (LLMs) excel across tasks and specialized domains, scaling LLMs based on existing models has garnered significant attention, which faces the challenge of decreasing performance when combining disparate models. Various techniques have been proposed for the aggregation of pre-trained LLMs, including model merging, Mixture-of-Experts, and stacking. Despite their merits, a comprehensive comparison and synergistic application of them to a diverse model zoo is yet to be adequately addressed. In light of this research gap, this paper introduces Model-GLUE, a holistic LLM scaling guideline. First, our work starts with a benchmarking of existing LLM scaling techniques, especially selective merging, and variants of mixture. Utilizing the insights from the benchmark results, we formulate an strategy for the selection and aggregation of a heterogeneous model zoo characterizing different architectures and initialization. Our methodology involves the clustering of mergeable models and optimal merging strategy selection, and the integration of clusters through a model mixture. Finally, evidenced by our experiments on a diverse Llama-2-based model zoo, Model-GLUE shows an average performance enhancement of 5.61%, achieved without additional training. Codes are available at: https://github.com/Model-GLUE/Model-GLUE.

Consistency models are a nascent family of generative models that can sample high quality data in one step without the need for adversarial training. Current consistency models achieve optimal sample quality by distilling from pre-trained diffusion models and employing learned metrics such as LPIPS. However, distillation limits the quality of consistency models to that of the pre-trained diffusion model, and LPIPS causes undesirable bias in evaluation. To tackle these challenges, we present improved techniques for consistency training, where consistency models learn directly from data without distillation. We delve into the theory behind consistency training and identify a previously overlooked flaw, which we address by eliminating Exponential Moving Average from the teacher consistency model. To replace learned metrics like LPIPS, we adopt Pseudo-Huber losses from robust statistics. Additionally, we introduce a lognormal noise schedule for the consistency training objective, and propose to double total discretization steps every set number of training iterations. Combined with better hyperparameter tuning, these modifications enable consistency models to achieve FID scores of 2.51 and 3.25 on CIFAR-10 and ImageNet 64times 64 respectively in a single sampling step. These scores mark a 3.5times and 4times improvement compared to prior consistency training approaches. Through two-step sampling, we further reduce FID scores to 2.24 and 2.77 on these two datasets, surpassing those obtained via distillation in both one-step and two-step settings, while narrowing the gap between consistency models and other state-of-the-art generative models.

In the artificial neuron, I replace the dot product with the weighted Lehmer mean, which may emulate different cases of a generalized mean. The single neuron instance is replaced by a multiplet of neurons which have the same averaging weights. A group of outputs feed forward, in lieu of the single scalar. The generalization parameter is typically set to a different value for each neuron in the multiplet. I further extend the concept to a multiplet taken from the Gini mean. Derivatives with respect to the weight parameters and with respect to the two generalization parameters are given. Some properties of the network are investigated, showing the capacity to emulate the classical exclusive-or problem organically in two layers and perform some multiplication and division. The network can instantiate truncated power series and variants, which can be used to approximate different functions, provided that parameters are constrained. Moreover, a mean case slope score is derived that can facilitate a learning-rate novelty based on homogeneity of the selected elements. The multiplet neuron equation provides a way to segment regularization timeframes and approaches.

The ability to quickly and accurately compute properties from atomic simulations is critical for advancing a large number of applications in chemistry and materials science including drug discovery, energy storage, and semiconductor manufacturing. To address this need, Meta FAIR presents a family of Universal Models for Atoms (UMA), designed to push the frontier of speed, accuracy, and generalization. UMA models are trained on half a billion unique 3D atomic structures (the largest training runs to date) by compiling data across multiple chemical domains, e.g. molecules, materials, and catalysts. We develop empirical scaling laws to help understand how to increase model capacity alongside dataset size to achieve the best accuracy. The UMA small and medium models utilize a novel architectural design we refer to as mixture of linear experts that enables increasing model capacity without sacrificing speed. For example, UMA-medium has 1.4B parameters but only ~50M active parameters per atomic structure. We evaluate UMA models on a diverse set of applications across multiple domains and find that, remarkably, a single model without any fine-tuning can perform similarly or better than specialized models. We are releasing the UMA code, weights, and associated data to accelerate computational workflows and enable the community to continue to build increasingly capable AI models.

Memorization in language models is typically treated as a homogenous phenomenon, neglecting the specifics of the memorized data. We instead model memorization as the effect of a set of complex factors that describe each sample and relate it to the model and corpus. To build intuition around these factors, we break memorization down into a taxonomy: recitation of highly duplicated sequences, reconstruction of inherently predictable sequences, and recollection of sequences that are neither. We demonstrate the usefulness of our taxonomy by using it to construct a predictive model for memorization. By analyzing dependencies and inspecting the weights of the predictive model, we find that different factors influence the likelihood of memorization differently depending on the taxonomic category.

In conversational AI research, there's a noticeable trend towards developing models with a larger number of parameters, exemplified by models like ChatGPT. While these expansive models tend to generate increasingly better chat responses, they demand significant computational resources and memory. This study explores a pertinent question: Can a combination of smaller models collaboratively achieve comparable or enhanced performance relative to a singular large model? We introduce an approach termed "blending", a straightforward yet effective method of integrating multiple chat AIs. Our empirical evidence suggests that when specific smaller models are synergistically blended, they can potentially outperform or match the capabilities of much larger counterparts. For instance, integrating just three models of moderate size (6B/13B paramaeters) can rival or even surpass the performance metrics of a substantially larger model like ChatGPT (175B+ paramaters). This hypothesis is rigorously tested using A/B testing methodologies with a large user base on the Chai research platform over a span of thirty days. The findings underscore the potential of the "blending" strategy as a viable approach for enhancing chat AI efficacy without a corresponding surge in computational demands.

The behavior of neural networks still remains opaque, and a recently widely noted phenomenon is that networks often achieve similar performance when initialized with different random parameters. This phenomenon has attracted significant attention in measuring the similarity between features learned by distinct networks. However, feature similarity could be vague in describing the same feature since equivalent features hardly exist. In this paper, we expand the concept of equivalent feature and provide the definition of what we call functionally equivalent features. These features produce equivalent output under certain transformations. Using this definition, we aim to derive a more intrinsic metric for the so-called feature complexity regarding the redundancy of features learned by a neural network at each layer. We offer a formal interpretation of our approach through the lens of category theory, a well-developed area in mathematics. To quantify the feature complexity, we further propose an efficient algorithm named Iterative Feature Merging. Our experimental results validate our ideas and theories from various perspectives. We empirically demonstrate that the functionally equivalence widely exists among different features learned by the same neural network and we could reduce the number of parameters of the network without affecting the performance.The IFM shows great potential as a data-agnostic model prune method. We have also drawn several interesting empirical findings regarding the defined feature complexity.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

Averaging the parameters of models that have the same architecture and initialization can provide a means of combining their respective capabilities. In this paper, we take the perspective that this "merging" operation can be seen as choosing parameters that approximately maximize the joint likelihood of the posteriors of the models' parameters. Computing a simple average of the models' parameters therefore corresponds to making an isotropic Gaussian approximation to their posteriors. We develop an alternative merging procedure based on the Laplace approximation where we approximate each model's posterior as a Gaussian distribution whose precision matrix corresponds to its Fisher information. We first show that our "Fisher merging" technique provides a performance boost in settings where simple parameter averaging is currently used -- specifically, robust fine-tuning and model ensembling. Then, we compare merging to standard gradient-based transfer learning and demonstrate that merging enables a fundamentally different method for transferring capabilities across models. Specifically, we show that Fisher merging is competitive with gradient-based transfer learning approaches (while being significantly cheaper) in intermediate-task training and domain-adaptive pre-training. We also show that our merging procedure makes it possible to combine models in previously unexplored ways. We release our code to facilitate future research into methods for merging models.

In the era of large-scale training, model merging has evolved into a tool for creating multitasking models efficiently. It enables the knowledge of models to be fused, without the need for heavy computation as required in traditional multitask learning. Existing merging methods often assume that entries at identical positions in weight matrices serve the same function, enabling straightforward entry-wise comparison and merging. However, this assumption overlooks the complexity of finetuned neural networks, where neurons may develop distinct feature compositions, making direct entry-wise merging problematic. We present Decom-Renorm-Merge (DRM), a simple yet effective approach that leverages Singular Value Decomposition to decompose and coordinate weight matrices into an aligned joint space, where entry-wise merging becomes possible. We showcase the effectiveness of DRM across various settings ranging from smaller encoder-based such as ViT and DeBERTa, encoder-decoder-based such as T5, and larger decoder-based such as Llama3.1-8B. Our experimental results show that DRM outperforms several state-of-the-art merging techniques across full finetuning and low-rank adaptation settings. Moreover, our analysis reveals renormalization as the crucial component for creating a robust and even joint space for merging, significantly contributing to the method's performance.

Time series foundation models have demonstrated impressive performance as zero-shot forecasters. However, achieving effectively unified training on time series remains an open challenge. Existing approaches introduce some level of model specialization to account for the highly heterogeneous nature of time series data. For instance, Moirai pursues unified training by employing multiple input/output projection layers, each tailored to handle time series at a specific frequency. Similarly, TimesFM maintains a frequency embedding dictionary for this purpose. We identify two major drawbacks to this human-imposed frequency-level model specialization: (1) Frequency is not a reliable indicator of the underlying patterns in time series. For example, time series with different frequencies can display similar patterns, while those with the same frequency may exhibit varied patterns. (2) Non-stationarity is an inherent property of real-world time series, leading to varied distributions even within a short context window of a single time series. Frequency-level specialization is too coarse-grained to capture this level of diversity. To address these limitations, this paper introduces Moirai-MoE, using a single input/output projection layer while delegating the modeling of diverse time series patterns to the sparse mixture of experts (MoE) within Transformers. With these designs, Moirai-MoE reduces reliance on human-defined heuristics and enables automatic token-level specialization. Extensive experiments on 39 datasets demonstrate the superiority of Moirai-MoE over existing foundation models in both in-distribution and zero-shot scenarios. Furthermore, this study conducts comprehensive model analyses to explore the inner workings of time series MoE foundation models and provides valuable insights for future research.

In many domains, autoregressive models can attain high likelihood on the task of predicting the next observation. However, this maximum-likelihood (MLE) objective does not necessarily match a downstream use-case of autoregressively generating high-quality sequences. The MLE objective weights sequences proportionally to their frequency under the data distribution, with no guidance for the model's behaviour out of distribution (OOD): leading to compounding error during autoregressive generation. In order to address this compounding error problem, we formulate sequence generation as an imitation learning (IL) problem. This allows us to minimize a variety of divergences between the distribution of sequences generated by an autoregressive model and sequences from a dataset, including divergences with weight on OOD generated sequences. The IL framework also allows us to incorporate backtracking by introducing a backspace action into the generation process. This further mitigates the compounding error problem by allowing the model to revert a sampled token if it takes the sequence OOD. Our resulting method, SequenceMatch, can be implemented without adversarial training or major architectural changes. We identify the SequenceMatch-chi^2 divergence as a more suitable training objective for autoregressive models which are used for generation. We show that empirically, SequenceMatch training leads to improvements over MLE on text generation with language models.

Learning compatible representations enables the interchangeable use of semantic features as models are updated over time. This is particularly relevant in search and retrieval systems where it is crucial to avoid reprocessing of the gallery images with the updated model. While recent research has shown promising empirical evidence, there is still a lack of comprehensive theoretical understanding about learning compatible representations. In this paper, we demonstrate that the stationary representations learned by the d-Simplex fixed classifier optimally approximate compatibility representation according to the two inequality constraints of its formal definition. This not only establishes a solid foundation for future works in this line of research but also presents implications that can be exploited in practical learning scenarios. An exemplary application is the now-standard practice of downloading and fine-tuning new pre-trained models. Specifically, we show the strengths and critical issues of stationary representations in the case in which a model undergoing sequential fine-tuning is asynchronously replaced by downloading a better-performing model pre-trained elsewhere. Such a representation enables seamless delivery of retrieval service (i.e., no reprocessing of gallery images) and offers improved performance without operational disruptions during model replacement. Code available at: https://github.com/miccunifi/iamcl2r.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

This paper describes our winning contribution to SemEval 2018 Task 4: Character Identification on Multiparty Dialogues. It is a simple, standard model with one key innovation, an entity library. Our results show that this innovation greatly facilitates the identification of infrequent characters. Because of the generic nature of our model, this finding is potentially relevant to any task that requires effective learning from sparse or unbalanced data.

Given appropriate representations of the semantic relations between carpenter and wood and between mason and stone (for example, vectors in a vector space model), a suitable algorithm should be able to recognize that these relations are highly similar (carpenter is to wood as mason is to stone; the relations are analogous). Likewise, with representations of dog, house, and kennel, an algorithm should be able to recognize that the semantic composition of dog and house, dog house, is highly similar to kennel (dog house and kennel are synonymous). It seems that these two tasks, recognizing relations and compositions, are closely connected. However, up to now, the best models for relations are significantly different from the best models for compositions. In this paper, we introduce a dual-space model that unifies these two tasks. This model matches the performance of the best previous models for relations and compositions. The dual-space model consists of a space for measuring domain similarity and a space for measuring function similarity. Carpenter and wood share the same domain, the domain of carpentry. Mason and stone share the same domain, the domain of masonry. Carpenter and mason share the same function, the function of artisans. Wood and stone share the same function, the function of materials. In the composition dog house, kennel has some domain overlap with both dog and house (the domains of pets and buildings). The function of kennel is similar to the function of house (the function of shelters). By combining domain and function similarities in various ways, we can model relations, compositions, and other aspects of semantics.

While many languages possess processes of joining two or more words to create compound words, previous studies have been typically limited only to languages with excessively productive compound formation (e.g., German, Dutch) and there is no public dataset containing compound and non-compound words across a large number of languages. In this work, we systematically study decompounding, the task of splitting compound words into their constituents, at a wide scale. We first address the data gap by introducing a dataset of 255k compound and non-compound words across 56 diverse languages obtained from Wiktionary. We then use this dataset to evaluate an array of Large Language Models (LLMs) on the decompounding task. We find that LLMs perform poorly, especially on words which are tokenized unfavorably by subword tokenization. We thus introduce a novel methodology to train dedicated models for decompounding. The proposed two-stage procedure relies on a fully self-supervised objective in the first stage, while the second, supervised learning stage optionally fine-tunes the model on the annotated Wiktionary data. Our self-supervised models outperform the prior best unsupervised decompounding models by 13.9% accuracy on average. Our fine-tuned models outperform all prior (language-specific) decompounding tools. Furthermore, we use our models to leverage decompounding during the creation of a subword tokenizer, which we refer to as CompoundPiece. CompoundPiece tokenizes compound words more favorably on average, leading to improved performance on decompounding over an otherwise equivalent model using SentencePiece tokenization.

Diffusion models achieve superior generation quality but suffer from slow generation speed due to the iterative nature of denoising. In contrast, consistency models, a new generative family, achieve competitive performance with significantly faster sampling. These models are trained either through consistency distillation, which leverages pretrained diffusion models, or consistency training/tuning directly from raw data. In this work, we propose a novel framework for understanding consistency models by modeling the denoising process of the diffusion model as a Markov Decision Process (MDP) and framing consistency model training as the value estimation through Temporal Difference~(TD) Learning. More importantly, this framework allows us to analyze the limitations of current consistency training/tuning strategies. Built upon Easy Consistency Tuning (ECT), we propose Stable Consistency Tuning (SCT), which incorporates variance-reduced learning using the score identity. SCT leads to significant performance improvements on benchmarks such as CIFAR-10 and ImageNet-64. On ImageNet-64, SCT achieves 1-step FID 2.42 and 2-step FID 1.55, a new SoTA for consistency models.

Prompted models have demonstrated impressive few-shot learning abilities. Repeated interactions at test-time with a single model, or the composition of multiple models together, further expands capabilities. These compositions are probabilistic models, and may be expressed in the language of graphical models with random variables whose values are complex data types such as strings. Cases with control flow and dynamic structure require techniques from probabilistic programming, which allow implementing disparate model structures and inference strategies in a unified language. We formalize several existing techniques from this perspective, including scratchpads / chain of thought, verifiers, STaR, selection-inference, and tool use. We refer to the resulting programs as language model cascades.

Meta-learning usually refers to a learning algorithm that learns from other learning algorithms. The problem of uncertainty in the predictions of neural networks shows that the world is only partially predictable and a learned neural network cannot generalize to its ever-changing surrounding environments. Therefore, the question is how a predictive model can represent multiple predictions simultaneously. We aim to provide a fundamental understanding of learning to learn in the contents of Decentralized Neural Networks (Decentralized NNs) and we believe this is one of the most important questions and prerequisites to building an autonomous intelligence machine. To this end, we shall demonstrate several pieces of evidence for tackling the problems above with Meta Learning in Decentralized NNs. In particular, we will present three different approaches to building such a decentralized learning system: (1) learning from many replica neural networks, (2) building the hierarchy of neural networks for different functions, and (3) leveraging different modality experts to learn cross-modal representations.

Pretrained language models have shown superior performance on many natural language processing tasks, yet they still struggle at multi-step formal reasoning tasks like grade school math problems. One key challenge of finetuning them to solve such math reasoning problems is that many existing datasets only contain one reference solution for each problem, despite the fact that there are often alternative solutions resembling different reasoning paths to the final answer. This way, the finetuned models are biased towards the limited reference solutions, which limits their generalization to unseen examples. To mitigate this issue, we propose to let the model perform sampling during training and learn from both self-sampled fully-correct solutions, which yield the correct answer upon execution, and partially-correct solutions, whose intermediate state matches an intermediate state of a known correct solution. We show that our use of self-sampled correct and partially-correct solutions can benefit learning and help guide the sampling process, leading to more efficient exploration of the solution space. Additionally, we explore various training objectives to support learning from multiple solutions per example and find they greatly affect the performance. Experiments on two math reasoning datasets show the effectiveness of our method compared to learning from a single reference solution with MLE, where we improve PASS@100 from 35.5% to 44.5% for GSM8K, and 27.6% to 36.2% PASS@80 for MathQA. Such improvements are also consistent across different model sizes. Our code is available at https://github.com/microsoft/TraceCodegen.

In recent years, diffusion-based models have demonstrated exceptional performance in searching for simultaneously stable, unique, and novel (S.U.N.) crystalline materials. However, most of these models don't have the ability to change the number of atoms in the crystal during the generation process, which limits the variability of model sampling trajectories. In this paper, we demonstrate the severity of this restriction and introduce a simple yet powerful technique, mirage infusion, which enables diffusion models to change the state of the atoms that make up the crystal from existent to non-existent (mirage) and vice versa. We show that this technique improves model quality by up to times2.5 compared to the same model without this modification. The resulting model, Mirage Atom Diffusion (MiAD), is an equivariant joint diffusion model for de novo crystal generation that is capable of altering the number of atoms during the generation process. MiAD achieves an 8.2% S.U.N. rate on the MP-20 dataset, which substantially exceeds existing state-of-the-art approaches. The source code can be found at https://github.com/andrey-okhotin/miad.git{github.com/andrey-okhotin/miad}.

Diffusion models are trained by learning a sequence of models that reverse each step of noise corruption. Typically, the model parameters are fully shared across multiple timesteps to enhance training efficiency. However, since the denoising tasks differ at each timestep, the gradients computed at different timesteps may conflict, potentially degrading the overall performance of image generation. To solve this issue, this work proposes a Decouple-then-Merge (DeMe) framework, which begins with a pretrained model and finetunes separate models tailored to specific timesteps. We introduce several improved techniques during the finetuning stage to promote effective knowledge sharing while minimizing training interference across timesteps. Finally, after finetuning, these separate models can be merged into a single model in the parameter space, ensuring efficient and practical inference. Experimental results show significant generation quality improvements upon 6 benchmarks including Stable Diffusion on COCO30K, ImageNet1K, PartiPrompts, and DDPM on LSUN Church, LSUN Bedroom, and CIFAR10. Code is available at https://github.com/MqLeet/DeMe{GitHub}.

The training of modern large language models (LLMs) takes place in a regime where most training examples are seen only a few times by the model during the course of training. What does a model remember about such examples seen only a few times during training and how long does that memory persist in the face of continuous training with new examples? Here, we investigate these questions through simple recognition, recall, and retention experiments with LLMs. In recognition experiments, we ask if the model can distinguish the seen example from a novel example; in recall experiments, we ask if the model can correctly recall the seen example when cued by a part of it; and in retention experiments, we periodically probe the model's memory for the original examples as the model is trained continuously with new examples. We find that a single exposure is generally sufficient for a model to achieve near perfect accuracy even in very challenging recognition experiments. We estimate that the recognition performance of even small language models easily exceeds human recognition performance reported in similar experiments with humans (Shepard, 1967). Achieving near perfect recall takes more exposures, but most models can do it in just 3 exposures. The flip side of this remarkable capacity for fast learning is that precise memories are quickly overwritten: recall performance for the original examples drops steeply over the first 10 training updates with new examples, followed by a more gradual decline. Even after 100K updates, however, some of the original examples are still recalled near perfectly. A qualitatively similar retention pattern has been observed in human long-term memory retention studies before (Bahrick, 1984). Finally, recognition is much more robust to interference than recall and memory for natural language sentences is generally superior to memory for stimuli without structure.

Recent large language models have been trained on vast datasets, but also often on repeated data, either intentionally for the purpose of upweighting higher quality data, or unintentionally because data deduplication is not perfect and the model is exposed to repeated data at the sentence, paragraph, or document level. Some works have reported substantial negative performance effects of this repeated data. In this paper we attempt to study repeated data systematically and to understand its effects mechanistically. To do this, we train a family of models where most of the data is unique but a small fraction of it is repeated many times. We find a strong double descent phenomenon, in which repeated data can lead test loss to increase midway through training. A predictable range of repetition frequency leads to surprisingly severe degradation in performance. For instance, performance of an 800M parameter model can be degraded to that of a 2x smaller model (400M params) by repeating 0.1% of the data 100 times, despite the other 90% of the training tokens remaining unique. We suspect there is a range in the middle where the data can be memorized and doing so consumes a large fraction of the model's capacity, and this may be where the peak of degradation occurs. Finally, we connect these observations to recent mechanistic interpretability work - attempting to reverse engineer the detailed computations performed by the model - by showing that data repetition disproportionately damages copying and internal structures associated with generalization, such as induction heads, providing a possible mechanism for the shift from generalization to memorization. Taken together, these results provide a hypothesis for why repeating a relatively small fraction of data in large language models could lead to disproportionately large harms to performance.

Large language models (LLMs) have demonstrated remarkable abilities in representation learning for program synthesis and understanding tasks. The quality of the learned representations appears to be dictated by the neural scaling laws as a function of the number of model parameters and observations, while imposing upper bounds on the model performance by the amount of available data and compute, which is costly. In this study, we attempt to render the training of LLMs for program synthesis more efficient by unifying four key components: (1) model architectures, (2) learning methods, (3) infill sampling, and, (4) data distributions. Specifically, for the model architecture, we attempt to unify encoder and decoder-based models into a single prefix-LM. For learning methods, (i) causal language modeling, (ii) span corruption, (iii) infilling are unified into a simple learning algorithm. For infill sampling, we explore the claim of a "free lunch" hypothesis. For data distributions, the effect of a mixture distribution of programming and natural languages on model performance is explored. We conduct a comprehensive series of empirical experiments on 1B LLMs, for which failures and successes of this exploration are distilled into four lessons. We will provide a final recipe for training and release CodeGen2 models in size 1B, 3.7B, 7B, and, 16B parameters, along with the training framework as open-source: https://github.com/salesforce/CodeGen2.

The equivalence of realizable and agnostic learnability is a fundamental phenomenon in learning theory. With variants ranging from classical settings like PAC learning and regression to recent trends such as adversarially robust learning, it's surprising that we still lack a unified theory; traditional proofs of the equivalence tend to be disparate, and rely on strong model-specific assumptions like uniform convergence and sample compression. In this work, we give the first model-independent framework explaining the equivalence of realizable and agnostic learnability: a three-line blackbox reduction that simplifies, unifies, and extends our understanding across a wide variety of settings. This includes models with no known characterization of learnability such as learning with arbitrary distributional assumptions and more general loss functions, as well as a host of other popular settings such as robust learning, partial learning, fair learning, and the statistical query model. More generally, we argue that the equivalence of realizable and agnostic learning is actually a special case of a broader phenomenon we call property generalization: any desirable property of a learning algorithm (e.g. noise tolerance, privacy, stability) that can be satisfied over finite hypothesis classes extends (possibly in some variation) to any learnable hypothesis class.

Model merging integrates the weights of multiple task-specific models into a single multi-task model. Despite recent interest in the problem, a significant performance gap between the combined and single-task models remains. In this paper, we investigate the key characteristics of task matrices -- weight update matrices applied to a pre-trained model -- that enable effective merging. We show that alignment between singular components of task-specific and merged matrices strongly correlates with performance improvement over the pre-trained model. Based on this, we propose an isotropic merging framework that flattens the singular value spectrum of task matrices, enhances alignment, and reduces the performance gap. Additionally, we incorporate both common and task-specific subspaces to further improve alignment and performance. Our proposed approach achieves state-of-the-art performance across multiple scenarios, including various sets of tasks and model scales. This work advances the understanding of model merging dynamics, offering an effective methodology to merge models without requiring additional training. Code is available at https://github.com/danielm1405/iso-merging .

Recent studies have shown that, relative position encoding performs well in selective state space model scanning algorithms, and the architecture that balances SSM and Attention enhances the efficiency and effectiveness of the algorithm, while the sparse activation of the mixture of experts reduces the training cost. I studied the effectiveness of using different position encodings in structured state space dual algorithms, and the more effective SSD-Attn internal and external function mixing method, and designed a more efficient cross domain mixture of experts. I found that the same matrix is very wonderful in different algorithms, which allows us to establish a new hybrid sparse architecture: Cheems. Compared with other hybrid architectures, it is more efficient and more effective in language modeling tasks.

We study the probabilistic modeling performed by Autoregressive Large Language Models (LLMs) through the angle of time directionality, addressing a question first raised in (Shannon, 1951). For large enough models, we empirically find a time asymmetry in their ability to learn natural language: a difference in the average log-perplexity when trying to predict the next token versus when trying to predict the previous one. This difference is at the same time subtle and very consistent across various modalities (language, model size, training time, ...). Theoretically, this is surprising: from an information-theoretic point of view, there should be no such difference. We provide a theoretical framework to explain how such an asymmetry can appear from sparsity and computational complexity considerations, and outline a number of perspectives opened by our results.

Large Language Models (LLMs) have made the ambitious quest for generalist agents significantly far from being a fantasy. A key hurdle for building such general models is the diversity and heterogeneity of tasks and modalities. A promising solution is unification, allowing the support of a myriad of tasks and modalities within one unified framework. While few large models (e.g., Flamingo (Alayrac et al., 2022), trained on massive datasets, can support more than two modalities, current small to mid-scale unified models are still limited to 2 modalities, usually image-text or video-text. The question that we ask is: is it possible to build efficiently a unified model that can support all modalities? To answer this, we propose UnIVAL, a step further towards this ambitious goal. Without relying on fancy datasets sizes or models with billions of parameters, the ~ 0.25B parameter UnIVAL model goes beyond two modalities and unifies text, images, video, and audio into a single model. Our model is efficiently pretrained on many tasks, based on task balancing and multimodal curriculum learning. UnIVAL shows competitive performance to existing state-of-the-art approaches, across image and video-text tasks. The feature representations learned from image and video-text modalities, allows the model to achieve competitive performance when finetuned on audio-text tasks, despite not being pretrained on audio. Thanks to the unified model, we propose a novel study on multimodal model merging via weight interpolation of models trained on different multimodal tasks, showing their benefits in particular for out-of-distribution generalization. Finally, we motivate unification by showing the synergy between tasks. The model weights and code are released here: https://github.com/mshukor/UnIVAL.

We present a novel approach for the prediction of anticancer compound sensitivity by means of multi-modal attention-based neural networks (PaccMann). In our approach, we integrate three key pillars of drug sensitivity, namely, the molecular structure of compounds, transcriptomic profiles of cancer cells as well as prior knowledge about interactions among proteins within cells. Our models ingest a drug-cell pair consisting of SMILES encoding of a compound and the gene expression profile of a cancer cell and predicts an IC50 sensitivity value. Gene expression profiles are encoded using an attention-based encoding mechanism that assigns high weights to the most informative genes. We present and study three encoders for SMILES string of compounds: 1) bidirectional recurrent 2) convolutional 3) attention-based encoders. We compare our devised models against a baseline model that ingests engineered fingerprints to represent the molecular structure. We demonstrate that using our attention-based encoders, we can surpass the baseline model. The use of attention-based encoders enhance interpretability and enable us to identify genes, bonds and atoms that were used by the network to make a prediction.

Transfer learning - i.e., further fine-tuning a pre-trained model on a downstream task - can confer significant advantages, including improved downstream performance, faster convergence, and better sample efficiency. These advantages have led to a proliferation of task-specific fine-tuned models, which typically can only perform a single task and do not benefit from one another. Recently, model merging techniques have emerged as a solution to combine multiple task-specific models into a single multitask model without performing additional training. However, existing merging methods often ignore the interference between parameters of different models, resulting in large performance drops when merging multiple models. In this paper, we demonstrate that prior merging techniques inadvertently lose valuable information due to two major sources of interference: (a) interference due to redundant parameter values and (b) disagreement on the sign of a given parameter's values across models. To address this, we propose our method, TrIm, Elect Sign & Merge (TIES-Merging), which introduces three novel steps when merging models: (1) resetting parameters that only changed a small amount during fine-tuning, (2) resolving sign conflicts, and (3) merging only the parameters that are in alignment with the final agreed-upon sign. We find that TIES-Merging outperforms several existing methods in diverse settings covering a range of modalities, domains, number of tasks, model sizes, architectures, and fine-tuning settings. We further analyze the impact of different types of interference on model parameters, highlight the importance of resolving sign interference. Our code is available at https://github.com/prateeky2806/ties-merging

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

When using Large Language Models (LLMs) to support Knowledge Graph Engineering (KGE), one of the first indications when searching for an appropriate model is its size. According to the scaling laws, larger models typically show higher capabilities. However, in practice, resource costs are also an important factor and thus it makes sense to consider the ratio between model performance and costs. The LLM-KG-Bench framework enables the comparison of LLMs in the context of KGE tasks and assesses their capabilities of understanding and producing KGs and KG queries. Based on a dataset created in an LLM-KG-Bench run covering 26 open state-of-the-art LLMs, we explore the model size scaling laws specific to KGE tasks. In our analyses, we assess how benchmark scores evolve between different model size categories. Additionally, we inspect how the general score development of single models and families of models correlates to their size. Our analyses revealed that, with a few exceptions, the model size scaling laws generally also apply to the selected KGE tasks. However, in some cases, plateau or ceiling effects occurred, i.e., the task performance did not change much between a model and the next larger model. In these cases, smaller models could be considered to achieve high cost-effectiveness. Regarding models of the same family, sometimes larger models performed worse than smaller models of the same family. These effects occurred only locally. Hence it is advisable to additionally test the next smallest and largest model of the same family.

Foundation models are redefining how AI systems are built. Practitioners now follow a standard procedure to build their machine learning solutions: from a pre-trained foundation model, they fine-tune the weights on the target task of interest. So, the Internet is swarmed by a handful of foundation models fine-tuned on many diverse tasks: these individual fine-tunings exist in isolation without benefiting from each other. In our opinion, this is a missed opportunity, as these specialized models contain rich and diverse features. In this paper, we thus propose model ratatouille, a new strategy to recycle the multiple fine-tunings of the same foundation model on diverse auxiliary tasks. Specifically, we repurpose these auxiliary weights as initializations for multiple parallel fine-tunings on the target task; then, we average all fine-tuned weights to obtain the final model. This recycling strategy aims at maximizing the diversity in weights by leveraging the diversity in auxiliary tasks. Empirically, it improves the state of the art on the reference DomainBed benchmark for out-of-distribution generalization. Looking forward, this work contributes to the emerging paradigm of updatable machine learning where, akin to open-source software development, the community collaborates to reliably update machine learning models.

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.

Many mathematical models have been leveraged to design embeddings for representing Knowledge Graph (KG) entities and relations for link prediction and many downstream tasks. These mathematically-inspired models are not only highly scalable for inference in large KGs, but also have many explainable advantages in modeling different relation patterns that can be validated through both formal proofs and empirical results. In this paper, we make a comprehensive overview of the current state of research in KG completion. In particular, we focus on two main branches of KG embedding (KGE) design: 1) distance-based methods and 2) semantic matching-based methods. We discover the connections between recently proposed models and present an underlying trend that might help researchers invent novel and more effective models. Next, we delve into CompoundE and CompoundE3D, which draw inspiration from 2D and 3D affine operations, respectively. They encompass a broad spectrum of techniques including distance-based and semantic-based methods. We will also discuss an emerging approach for KG completion which leverages pre-trained language models (PLMs) and textual descriptions of entities and relations and offer insights into the integration of KGE embedding methods with PLMs for KG completion.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

Applications of machine learning techniques for materials modeling typically involve functions known to be equivariant or invariant to specific symmetries. While graph neural networks (GNNs) have proven successful in such tasks, they enforce symmetries via the model architecture, which often reduces their expressivity, scalability and comprehensibility. In this paper, we introduce (1) a flexible framework relying on stochastic frame-averaging (SFA) to make any model E(3)-equivariant or invariant through data transformations. (2) FAENet: a simple, fast and expressive GNN, optimized for SFA, that processes geometric information without any symmetrypreserving design constraints. We prove the validity of our method theoretically and empirically demonstrate its superior accuracy and computational scalability in materials modeling on the OC20 dataset (S2EF, IS2RE) as well as common molecular modeling tasks (QM9, QM7-X). A package implementation is available at https://faenet.readthedocs.io.

State-of-the-art machine learning methods exhibit limited compositional generalization. At the same time, there is a lack of realistic benchmarks that comprehensively measure this ability, which makes it challenging to find and evaluate improvements. We introduce a novel method to systematically construct such benchmarks by maximizing compound divergence while guaranteeing a small atom divergence between train and test sets, and we quantitatively compare this method to other approaches for creating compositional generalization benchmarks. We present a large and realistic natural language question answering dataset that is constructed according to this method, and we use it to analyze the compositional generalization ability of three machine learning architectures. We find that they fail to generalize compositionally and that there is a surprisingly strong negative correlation between compound divergence and accuracy. We also demonstrate how our method can be used to create new compositionality benchmarks on top of the existing SCAN dataset, which confirms these findings.

Finding new drugs is getting harder and harder. One of the hopes of drug discovery is to use machine learning models to predict molecular properties. That is why models for molecular property prediction are being developed and tested on benchmarks such as MoleculeNet. However, existing benchmarks are unrealistic and are too different from applying the models in practice. We have created a new practical Lo-Hi benchmark consisting of two tasks: Lead Optimization (Lo) and Hit Identification (Hi), corresponding to the real drug discovery process. For the Hi task, we designed a novel molecular splitting algorithm that solves the Balanced Vertex Minimum k-Cut problem. We tested state-of-the-art and classic ML models, revealing which works better under practical settings. We analyzed modern benchmarks and showed that they are unrealistic and overoptimistic. Review: https://openreview.net/forum?id=H2Yb28qGLV Lo-Hi benchmark: https://github.com/SteshinSS/lohi_neurips2023 Lo-Hi splitter library: https://github.com/SteshinSS/lohi_splitter

Merging various task-specific Transformer-based models trained on different tasks into a single unified model can execute all the tasks concurrently. Previous methods, exemplified by task arithmetic, have been proven to be both effective and scalable. Existing methods have primarily focused on seeking a static optimal solution within the original model parameter space. A notable challenge is mitigating the interference between parameters of different models, which can substantially deteriorate performance. In this paper, we propose to merge most of the parameters while upscaling the MLP of the Transformer layers to a weight-ensembling mixture of experts (MoE) module, which can dynamically integrate shared and task-specific knowledge based on the input, thereby providing a more flexible solution that can adapt to the specific needs of each instance. Our key insight is that by identifying and separating shared knowledge and task-specific knowledge, and then dynamically integrating them, we can mitigate the parameter interference problem to a great extent. We conduct the conventional multi-task model merging experiments and evaluate the generalization and robustness of our method. The results demonstrate the effectiveness of our method and provide a comprehensive understanding of our method. The code is available at https://anonymous.4open.science/r/weight-ensembling_MoE-67C9/

Generative machine learning (ML) models hold great promise for accelerating materials discovery through the inverse design of inorganic crystals, enabling an unprecedented exploration of chemical space. Yet, the lack of standardized evaluation frameworks makes it challenging to evaluate, compare, and further develop these ML models meaningfully. In this work, we introduce LeMat-GenBench, a unified benchmark for generative models of crystalline materials, supported by a set of evaluation metrics designed to better inform model development and downstream applications. We release both an open-source evaluation suite and a public leaderboard on Hugging Face, and benchmark 12 recent generative models. Results reveal that an increase in stability leads to a decrease in novelty and diversity on average, with no model excelling across all dimensions. Altogether, LeMat-GenBench establishes a reproducible and extensible foundation for fair model comparison and aims to guide the development of more reliable, discovery-oriented generative models for crystalline materials.

Large language models (LLMs) have achieved impressive success on many benchmarks for mathematical reasoning. However, there is growing concern that some of this performance actually reflects dataset contamination, where data closely resembling benchmark questions leaks into the training data, instead of true reasoning ability. To investigate this claim rigorously, we commission Grade School Math 1000 (GSM1k). GSM1k is designed to mirror the style and complexity of the established GSM8k benchmark, the gold standard for measuring elementary mathematical reasoning. We ensure that the two benchmarks are comparable across important metrics such as human solve rates, number of steps in solution, answer magnitude, and more. When evaluating leading open- and closed-source LLMs on GSM1k, we observe accuracy drops of up to 13%, with several families of models (e.g., Phi and Mistral) showing evidence of systematic overfitting across almost all model sizes. At the same time, many models, especially those on the frontier, (e.g., Gemini/GPT/Claude) show minimal signs of overfitting. Further analysis suggests a positive relationship (Spearman's r^2=0.32) between a model's probability of generating an example from GSM8k and its performance gap between GSM8k and GSM1k, suggesting that many models may have partially memorized GSM8k.

Model merging has become one of the key technologies for enhancing the capabilities and efficiency of Large Language Models (LLMs). However, our understanding of the expected performance gains and principles when merging any two models remains limited. In this work, we introduce model kinship, the degree of similarity or relatedness between LLMs, analogous to biological evolution. With comprehensive empirical analysis, we find that there is a certain relationship between model kinship and the performance gains after model merging, which can help guide our selection of candidate models. Inspired by this, we propose a new model merging strategy: Top-k Greedy Merging with Model Kinship, which can yield better performance on benchmark datasets. Specifically, we discover that using model kinship as a criterion can assist us in continuously performing model merging, alleviating the degradation (local optima) in model evolution, whereas model kinship can serve as a guide to escape these traps. Code is available at https://github.com/zjunlp/ModelKinship.

Automated model selection is often proposed to users to choose which machine learning model (or method) to apply to a given regression task. In this paper, we show that combining different regression models can yield better results than selecting a single ('best') regression model, and outline an efficient method that obtains optimally weighted convex linear combination from a heterogeneous set of regression models. More specifically, in this paper, a heuristic weight optimization, used in a preceding conference paper, is replaced by an exact optimization algorithm using convex quadratic programming. We prove convexity of the quadratic programming formulation for the straightforward formulation and for a formulation with weighted data points. The novel weight optimization is not only (more) exact but also more efficient. The methods we develop in this paper are implemented and made available via github-open source. They can be executed on commonly available hardware and offer a transparent and easy to interpret interface. The results indicate that the approach outperforms model selection methods on a range of data sets, including data sets with mixed variable type from drug discovery applications.

Model merging provides a scalable alternative to multi-task training by combining specialized finetuned models through parameter arithmetic, enabling efficient deployment without the need for joint training or access to all task data. While recent methods have shown promise, existing evaluations are limited in both model scale and task diversity, leaving open questions about their applicability to large, domain-specialized LLMs. To tackle the challenges, we introduce MergeBench, a comprehensive evaluation suite designed to assess model merging at scale. MergeBench builds on state-of-the-art open-source language models, including Llama and Gemma families at 2B to 9B scales, and covers five key domains: instruction following, mathematics, multilingual understanding, coding and safety. We standardize finetuning and evaluation protocols, and assess eight representative merging methods across multi-task performance, forgetting and runtime efficiency. Based on extensive experiments, we provide practical guidelines for algorithm selection and share insights showing that model merging tends to perform better on stronger base models, with techniques such as merging coefficient tuning and sparsification improving knowledge retention. However, several challenges remain, including the computational cost on large models, the gap for in-domain performance compared to multi-task models, and the underexplored role of model merging in standard LLM training pipelines. We hope MergeBench provides a foundation for future research to advance the understanding and practical application of model merging. Our project page is at https://yifei-he.github.io/mergebench/{https://yifei-he.github.io/mergebench/}.

Large deep learning models have achieved remarkable success in many scenarios. However, training large models is usually challenging, e.g., due to the high computational cost, the unstable and painfully slow optimization procedure, and the vulnerability to overfitting. To alleviate these problems, this work studies a divide-and-conquer strategy, i.e., dividing a large model into smaller modules, training them independently, and reassembling the trained modules to obtain the target model. This approach is promising since it avoids directly training large models from scratch. Nevertheless, implementing this idea is non-trivial, as it is difficult to ensure the compatibility of the independently trained modules. In this paper, we present an elegant solution to address this issue, i.e., we introduce a global, shared meta model to implicitly link all the modules together. This enables us to train highly compatible modules that collaborate effectively when they are assembled together. We further propose a module incubation mechanism that enables the meta model to be designed as an extremely shallow network. As a result, the additional overhead introduced by the meta model is minimalized. Though conceptually simple, our method significantly outperforms end-to-end (E2E) training in terms of both final accuracy and training efficiency. For example, on top of ViT-Huge, it improves the accuracy by 2.7% compared to the E2E baseline on ImageNet-1K, while saving the training cost by 43% in the meantime. Code is available at https://github.com/LeapLabTHU/Model-Assembling.

Diffusion models and Flow Matching generate high-quality samples but are slow at inference, and distilling them into few-step models often leads to instability and extensive tuning. To resolve these trade-offs, we propose Inductive Moment Matching (IMM), a new class of generative models for one- or few-step sampling with a single-stage training procedure. Unlike distillation, IMM does not require pre-training initialization and optimization of two networks; and unlike Consistency Models, IMM guarantees distribution-level convergence and remains stable under various hyperparameters and standard model architectures. IMM surpasses diffusion models on ImageNet-256x256 with 1.99 FID using only 8 inference steps and achieves state-of-the-art 2-step FID of 1.98 on CIFAR-10 for a model trained from scratch.

De novo drug design requires simultaneously generating novel molecules outside of training data and predicting their target properties, making it a hard task for generative models. To address this, we propose Joint Transformer that combines a Transformer decoder, Transformer encoder, and a predictor in a joint generative model with shared weights. We formulate a probabilistic black-box optimization algorithm that employs Joint Transformer to generate novel molecules with improved target properties and outperforms other SMILES-based optimization methods in de novo drug design.

Med42-v2 introduces a suite of clinical large language models (LLMs) designed to address the limitations of generic models in healthcare settings. These models are built on Llama3 architecture and fine-tuned using specialized clinical data. They underwent multi-stage preference alignment to effectively respond to natural prompts. While generic models are often preference-aligned to avoid answering clinical queries as a precaution, Med42-v2 is specifically trained to overcome this limitation, enabling its use in clinical settings. Med42-v2 models demonstrate superior performance compared to the original Llama3 models in both 8B and 70B parameter configurations and GPT-4 across various medical benchmarks. These LLMs are developed to understand clinical queries, perform reasoning tasks, and provide valuable assistance in clinical environments. The models are now publicly available at https://huggingface.co/m42-health{https://huggingface.co/m42-health}.

The success of deep learning is due in large part to our ability to solve certain massive non-convex optimization problems with relative ease. Though non-convex optimization is NP-hard, simple algorithms -- often variants of stochastic gradient descent -- exhibit surprising effectiveness in fitting large neural networks in practice. We argue that neural network loss landscapes often contain (nearly) a single basin after accounting for all possible permutation symmetries of hidden units a la Entezari et al. 2021. We introduce three algorithms to permute the units of one model to bring them into alignment with a reference model in order to merge the two models in weight space. This transformation produces a functionally equivalent set of weights that lie in an approximately convex basin near the reference model. Experimentally, we demonstrate the single basin phenomenon across a variety of model architectures and datasets, including the first (to our knowledge) demonstration of zero-barrier linear mode connectivity between independently trained ResNet models on CIFAR-10. Additionally, we identify intriguing phenomena relating model width and training time to mode connectivity. Finally, we discuss shortcomings of the linear mode connectivity hypothesis, including a counterexample to the single basin theory.

This paper investigates the extent to which pretrained German BERT encodes knowledge of noun compound semantics. We comprehensively vary combinations of target tokens, layers, and cased vs. uncased models, and evaluate them by predicting the compositionality of 868 gold standard compounds. Looking at representational patterns within the transformer architecture, we observe trends comparable to equivalent prior work on English, with compositionality information most easily recoverable in the early layers. However, our strongest results clearly lag behind those reported for English, suggesting an inherently more difficult task in German. This may be due to the higher productivity of compounding in German than in English and the associated increase in constituent-level ambiguity, including in our target compound set.

Protein design with desirable properties has been a significant challenge for many decades. Generative artificial intelligence is a promising approach and has achieved great success in various protein generation tasks. Notably, diffusion models stand out for their robust mathematical foundations and impressive generative capabilities, offering unique advantages in certain applications such as protein design. In this review, we first give the definition and characteristics of diffusion models and then focus on two strategies: Denoising Diffusion Probabilistic Models and Score-based Generative Models, where DDPM is the discrete form of SGM. Furthermore, we discuss their applications in protein design, peptide generation, drug discovery, and protein-ligand interaction. Finally, we outline the future perspectives of diffusion models to advance autonomous protein design and engineering. The E(3) group consists of all rotations, reflections, and translations in three-dimensions. The equivariance on the E(3) group can keep the physical stability of the frame of each amino acid as much as possible, and we reflect on how to keep the diffusion model E(3) equivariant for protein generation.

Most currently deployed large language models (LLMs) undergo continuous training or additional finetuning. By contrast, most research into LLMs' internal mechanisms focuses on models at one snapshot in time (the end of pre-training), raising the question of whether their results generalize to real-world settings. Existing studies of mechanisms over time focus on encoder-only or toy models, which differ significantly from most deployed models. In this study, we track how model mechanisms, operationalized as circuits, emerge and evolve across 300 billion tokens of training in decoder-only LLMs, in models ranging from 70 million to 2.8 billion parameters. We find that task abilities and the functional components that support them emerge consistently at similar token counts across scale. Moreover, although such components may be implemented by different attention heads over time, the overarching algorithm that they implement remains. Surprisingly, both these algorithms and the types of components involved therein can replicate across model scale. These results suggest that circuit analyses conducted on small models at the end of pre-training can provide insights that still apply after additional pre-training and over model scale.

Deep networks are gradually penetrating almost every domain in our lives due to their amazing success. However, with substantive performance accuracy improvements comes the price of irreproducibility. Two identical models, trained on the exact same training dataset may exhibit large differences in predictions on individual examples even when average accuracy is similar, especially when trained on highly distributed parallel systems. The popular Rectified Linear Unit (ReLU) activation has been key to recent success of deep networks. We demonstrate, however, that ReLU is also a catalyzer to irreproducibility in deep networks. We show that not only can activations smoother than ReLU provide better accuracy, but they can also provide better accuracy-reproducibility tradeoffs. We propose a new family of activations; Smooth ReLU (SmeLU), designed to give such better tradeoffs, while also keeping the mathematical expression simple, and thus implementation cheap. SmeLU is monotonic, mimics ReLU, while providing continuous gradients, yielding better reproducibility. We generalize SmeLU to give even more flexibility and then demonstrate that SmeLU and its generalized form are special cases of a more general methodology of REctified Smooth Continuous Unit (RESCU) activations. Empirical results demonstrate the superior accuracy-reproducibility tradeoffs with smooth activations, SmeLU in particular.

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

Effective generalization in language models depends critically on the diversity of their training data. Yet existing diversity metrics often fall short of this goal, relying on surface-level heuristics that are decoupled from model behavior. This motivates us to ask: What kind of diversity in training data actually drives generalization in language models -- and how can we measure and amplify it? Through large-scale empirical analyses spanning over 300 training runs, carefully controlled for data scale and quality, we show that data diversity can be a strong predictor of generalization in LLM reasoning -- as measured by average model performance on unseen out-of-distribution benchmarks. We introduce G-Vendi, a metric that quantifies diversity via the entropy of model-induced gradients. Despite using a small off-the-shelf proxy model for gradients, G-Vendi consistently outperforms alternative measures, achieving strong correlation (Spearman's rho approx 0.9) with out-of-distribution (OOD) performance on both natural language inference (NLI) and math reasoning tasks. Building on this insight, we present Prismatic Synthesis, a framework for generating diverse synthetic data by targeting underrepresented regions in gradient space. Experimental results show that Prismatic Synthesis consistently improves model performance as we scale synthetic data -- not just on in-distribution test but across unseen, out-of-distribution benchmarks -- significantly outperforming state-of-the-art models that rely on 20 times larger data generator than ours. For example, PrismMath-7B, our model distilled from a 32B LLM, outperforms R1-Distill-Qwen-7B -- the same base model trained on proprietary data generated by 671B R1 -- on 6 out of 7 challenging benchmarks.

Developing accurate models for chemical reactors is often challenging due to the complexity of reaction kinetics and process dynamics. Traditional approaches require retraining models for each new system, limiting generalizability and efficiency. In this work, we take a step toward foundation models for chemical reactor modeling by introducing a neural network framework that generalizes across diverse reactor types and rapidly adapts to new chemical processes. Our approach leverages meta-learning to pretrain the model on a broad set of reactor dynamics, enabling efficient adaptation to unseen reactions with minimal data. To further enhance generalizability, we incorporate physics-informed fine-tuning, ensuring physically consistent adaptation to new reactor conditions. Our framework is evaluated across three integer-order fundamental reactor types - continuous stirred tank reactors, batch reactors, and plug flow reactors - demonstrating superior few-shot adaptation compared to conventional data-driven, physics-informed, and transfer learning approaches. By combining meta-learning with physics-informed adaptation, this work lays the foundation for a generalizable modeling framework, advancing the development of foundation models for chemical engineering applications. Source code is available at https://github.com/killingbear999/chemical-reactor-foundation-model.

A compartmental deterministic model that allows (1) immunity from two stages of infection and carriage, and (2) disease induced death, is used in studying the dynamics of meningitis epidemic process in a closed population. It allows for difference in the transmission rate of infection to a susceptible by a carrier and an infective. It is generalized to allow a proportion ({\phi}) of those susceptibles infected to progress directly to infectives in stage I. Both models are used in this study. The threshold conditions for the spread of carrier and infectives in stage I are derived for the two models. Sensitivity analysis is performed on the reproductive number derived from the next generation matrix. The case-carrier ratio profile for various parameters and threshold values are shown. So also are the graphs of the total number ever infected as influenced by {\epsilon} and {\phi}. The infection transmission rate (eta), the odds in favor of a carrier, over an infective, in transmitting an infection to a susceptible ({\epsilon}) and the carrier conversion rate ({\phi}) to an infective in stage I, are identified as key parameters that should be subject of attention for any control intervention strategy. The case-carrier ratio profiles provide evidence of a critical case-carrier ratio attained before the number of reported cases grows to an epidemic level. They also provide visual evidence of epidemiological context, in this case, epidemic incidence (in later part of dry season) and endemic incidence (during rainy season). Results from total proportion ever infected suggest that the model, in which {\phi}=0 obtained, can adequately represent, in essence, the generalized model for this study.

In continual learning, catastrophic forgetting is affected by multiple aspects of the tasks. Previous works have analyzed separately how forgetting is affected by either task similarity or overparameterization. In contrast, our paper examines how task similarity and overparameterization jointly affect forgetting in an analyzable model. Specifically, we focus on two-task continual linear regression, where the second task is a random orthogonal transformation of an arbitrary first task (an abstraction of random permutation tasks). We derive an exact analytical expression for the expected forgetting - and uncover a nuanced pattern. In highly overparameterized models, intermediate task similarity causes the most forgetting. However, near the interpolation threshold, forgetting decreases monotonically with the expected task similarity. We validate our findings with linear regression on synthetic data, and with neural networks on established permutation task benchmarks.

We study neural network loss landscapes through the lens of mode connectivity, the observation that minimizers of neural networks retrieved via training on a dataset are connected via simple paths of low loss. Specifically, we ask the following question: are minimizers that rely on different mechanisms for making their predictions connected via simple paths of low loss? We provide a definition of mechanistic similarity as shared invariances to input transformations and demonstrate that lack of linear connectivity between two models implies they use dissimilar mechanisms for making their predictions. Relevant to practice, this result helps us demonstrate that naive fine-tuning on a downstream dataset can fail to alter a model's mechanisms, e.g., fine-tuning can fail to eliminate a model's reliance on spurious attributes. Our analysis also motivates a method for targeted alteration of a model's mechanisms, named connectivity-based fine-tuning (CBFT), which we analyze using several synthetic datasets for the task of reducing a model's reliance on spurious attributes.

In recent years, a plethora of open-source foundation models have emerged, achieving remarkable progress in some widely attended fields, with performance being quite close to that of closed-source models. However, in high-value but more challenging scientific professional fields, either the fields still rely on expert models, or the progress of general foundation models lags significantly compared to those in popular areas, far from sufficient for transforming scientific research and leaving substantial gap between open-source models and closed-source models in these scientific domains. To mitigate this gap and explore a step further toward Artificial General Intelligence (AGI), we introduce Intern-S1, a specialized generalist equipped with general understanding and reasoning capabilities with expertise to analyze multiple science modal data. Intern-S1 is a multimodal Mixture-of-Experts (MoE) model with 28 billion activated parameters and 241 billion total parameters, continually pre-trained on 5T tokens, including over 2.5T tokens from scientific domains. In the post-training stage, Intern-S1 undergoes offline and then online reinforcement learning (RL) in InternBootCamp, where we propose Mixture-of-Rewards (MoR) to synergize the RL training on more than 1000 tasks simultaneously. Through integrated innovations in algorithms, data, and training systems, Intern-S1 achieved top-tier performance in online RL training.On comprehensive evaluation benchmarks, Intern-S1 demonstrates competitive performance on general reasoning tasks among open-source models and significantly outperforms open-source models in scientific domains, surpassing closed-source state-of-the-art models in professional tasks, such as molecular synthesis planning, reaction condition prediction, predicting thermodynamic stabilities for crystals. Our models are available at https://huggingface.co/internlm/Intern-S1.

Today's generative models are capable of synthesizing high-fidelity images, but each model specializes on a specific target domain. This raises the need for model merging: combining two or more pretrained generative models into a single unified one. In this work we tackle the problem of model merging, given two constraints that often come up in the real world: (1) no access to the original training data, and (2) without increasing the size of the neural network. To the best of our knowledge, model merging under these constraints has not been studied thus far. We propose a novel, two-stage solution. In the first stage, we transform the weights of all the models to the same parameter space by a technique we term model rooting. In the second stage, we merge the rooted models by averaging their weights and fine-tuning them for each specific domain, using only data generated by the original trained models. We demonstrate that our approach is superior to baseline methods and to existing transfer learning techniques, and investigate several applications.

Data-driven techniques have a large potential to transform and accelerate the chemical sciences. However, chemical sciences also pose the unique challenge of very diverse, small, fuzzy datasets that are difficult to leverage in conventional machine learning approaches completely. A new class of models, general-purpose models (GPMs) such as large language models, have shown the ability to solve tasks they have not been directly trained on, and to flexibly operate with low amounts of data in different formats. In this review, we discuss fundamental building principles of GPMs and review recent applications of those models in the chemical sciences across the entire scientific process. While many of these applications are still in the prototype phase, we expect that the increasing interest in GPMs will make many of them mature in the coming years.

This paper argues that continual learning methods can benefit by splitting the capacity of the learner across multiple models. We use statistical learning theory and experimental analysis to show how multiple tasks can interact with each other in a non-trivial fashion when a single model is trained on them. The generalization error on a particular task can improve when it is trained with synergistic tasks, but can also deteriorate when trained with competing tasks. This theory motivates our method named Model Zoo which, inspired from the boosting literature, grows an ensemble of small models, each of which is trained during one episode of continual learning. We demonstrate that Model Zoo obtains large gains in accuracy on a variety of continual learning benchmark problems. Code is available at https://github.com/grasp-lyrl/modelzoo_continual.

Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our efforts to develop such a tool for exploring the organic chemical space in search of potentially electro-active compounds, we present "LLamol", a single novel generative transformer model based on the LLama 2 architecture, which was trained on a 13M superset of organic compounds drawn from diverse public sources. To allow for a maximum flexibility in usage and robustness in view of potentially incomplete data, we introduce "Stochastic Context Learning" as a new training procedure. We demonstrate that the resulting model adeptly handles single- and multi-conditional organic molecule generation with up to four conditions, yet more are possible. The model generates valid molecular structures in SMILES notation while flexibly incorporating three numerical and/or one token sequence into the generative process, just as requested. The generated compounds are very satisfactory in all scenarios tested. In detail, we showcase the model's capability to utilize token sequences for conditioning, either individually or in combination with numerical properties, making LLamol a potent tool for de novo molecule design, easily expandable with new properties.

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem. This introduces a new paradigm of multitask language models which seamlessly bridge sequence regression and conditional sequence generation. We thoroughly demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction tasks of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a highly competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by a novel, alternating training scheme that enables the model to decorate seed sequences by desired properties, e.g., to optimize reaction yield. In sum, the RT is the first report of a multitask model that concurrently excels at predictive and generative tasks in biochemistry. This finds particular application in property-driven, local exploration of the chemical or protein space and could pave the road toward foundation models in material design. The code to reproduce all experiments of the paper is available at: https://github.com/IBM/regression-transformer

We introduce phi-3-mini, a 3.8 billion parameter language model trained on 3.3 trillion tokens, whose overall performance, as measured by both academic benchmarks and internal testing, rivals that of models such as Mixtral 8x7B and GPT-3.5 (e.g., phi-3-mini achieves 69% on MMLU and 8.38 on MT-bench), despite being small enough to be deployed on a phone. The innovation lies entirely in our dataset for training, a scaled-up version of the one used for phi-2, composed of heavily filtered web data and synthetic data. The model is also further aligned for robustness, safety, and chat format. We also provide some initial parameter-scaling results with a 7B and 14B models trained for 4.8T tokens, called phi-3-small and phi-3-medium, both significantly more capable than phi-3-mini (e.g., respectively 75% and 78% on MMLU, and 8.7 and 8.9 on MT-bench).

Recent progress in image generation has sparked research into controlling these models through condition signals, with various methods addressing specific challenges in conditional generation. Instead of proposing another specialized technique, we introduce a simple, unified framework to handle diverse conditional generation tasks involving a specific image-condition correlation. By learning a joint distribution over a correlated image pair (e.g. image and depth) with a diffusion model, our approach enables versatile capabilities via different inference-time sampling schemes, including controllable image generation (e.g. depth to image), estimation (e.g. image to depth), signal guidance, joint generation (image & depth), and coarse control. Previous attempts at unification often introduce significant complexity through multi-stage training, architectural modification, or increased parameter counts. In contrast, our simple formulation requires a single, computationally efficient training stage, maintains the standard model input, and adds minimal learned parameters (15% of the base model). Moreover, our model supports additional capabilities like non-spatially aligned and coarse conditioning. Extensive results show that our single model can produce comparable results with specialized methods and better results than prior unified methods. We also demonstrate that multiple models can be effectively combined for multi-signal conditional generation.

This work aims to implement Long Short-Term Memory mixture density networks (LSTM-MDNs) for Value-at-Risk forecasting and compare their performance with established models (historical simulation, CMM, and GARCH) using a defined backtesting procedure. The focus was on the neural network's ability to capture volatility clustering and its real-world applicability. Three architectures were tested: a 2-component mixture density network, a regularized 2-component model (Arimond et al., 2020), and a 3-component mixture model, the latter being tested for the first time in Value-at-Risk forecasting. Backtesting was performed on three stock indices (FTSE 100, S&P 500, EURO STOXX 50) over two distinct two-year periods (2017-2018 as a calm period, 2021-2022 as turbulent). Model performance was assessed through unconditional coverage and independence assumption tests. The neural network's ability to handle volatility clustering was validated via correlation analysis and graphical evaluation. Results show limited success for the neural network approach. LSTM-MDNs performed poorly for 2017/2018 but outperformed benchmark models in 2021/2022. The LSTM mechanism allowed the neural network to capture volatility clustering similarly to GARCH models. However, several issues were identified: the need for proper model initialization and reliance on large datasets for effective learning. The findings suggest that while LSTM-MDNs provide adequate risk forecasts, further research and adjustments are necessary for stable performance.

Data arrives at our senses as a continuous stream, smoothly transforming from one instant to the next. These smooth transformations can be viewed as continuous symmetries of the environment that we inhabit, defining equivalence relations between stimuli over time. In machine learning, neural network architectures that respect symmetries of their data are called equivariant and have provable benefits in terms of generalization ability and sample efficiency. To date, however, equivariance has been considered only for static transformations and feed-forward networks, limiting its applicability to sequence models, such as recurrent neural networks (RNNs), and corresponding time-parameterized sequence transformations. In this work, we extend equivariant network theory to this regime of `flows' -- one-parameter Lie subgroups capturing natural transformations over time, such as visual motion. We begin by showing that standard RNNs are generally not flow equivariant: their hidden states fail to transform in a geometrically structured manner for moving stimuli. We then show how flow equivariance can be introduced, and demonstrate that these models significantly outperform their non-equivariant counterparts in terms of training speed, length generalization, and velocity generalization, on both next step prediction and sequence classification. We present this work as a first step towards building sequence models that respect the time-parameterized symmetries which govern the world around us.

We present a model that can perform multiple vision tasks and can be adapted to other downstream tasks efficiently. Despite considerable progress in multi-task learning, most efforts focus on learning from multi-label data: a single image set with multiple task labels. Such multi-label data sets are rare, small, and expensive. We say heterogeneous to refer to image sets with different task labels, or to combinations of single-task datasets. Few have explored training on such heterogeneous datasets. General-purpose vision models are still dominated by single-task pretraining, and it remains unclear how to scale up multi-task models by leveraging mainstream vision datasets designed for different purposes. The challenges lie in managing large intrinsic differences among vision tasks, including data distribution, architectures, task-specific modules, dataset scales, and sampling strategies. To address these challenges, we propose to modify and scale up mixture-of-experts (MoE) vision transformers, so that they can simultaneously learn classification, detection, and segmentation on diverse mainstream vision datasets including ImageNet, COCO, and ADE20K. Our approach achieves comparable results to single-task state-of-the-art models and demonstrates strong generalization on downstream tasks. Due to its emergent modularity, this general-purpose model decomposes into high-performing components, efficiently adapting to downstream tasks. We can fine-tune it with fewer training parameters, fewer model parameters, and less computation. Additionally, its modularity allows for easy expansion in continual-learning-without-forgetting scenarios. Finally, these functions can be controlled and combined to meet various demands of downstream tasks.

Regression Mean (RegMean), an approach that formulates model merging as a linear regression problem, aims to find the optimal weights for each linear layer in the merge model by minimizing the discrepancy in predictions between the merge and candidate models. RegMean provides a precise closed-form solution for the merging problem; therefore, it offers explainability and computational efficiency. However, RegMean merges each linear layer independently, overlooking how the features and information in the earlier layers propagate through the layers and influence the final prediction in the merge model. In this paper, we introduce RegMean++, a simple yet effective alternative to RegMean, that explicitly incorporates both intra- and cross-layer dependencies between merge models' layers into RegMean's objective. By accounting for these dependencies, RegMean++ better captures the behaviors of the merge model. Extensive experiments demonstrate that RegMean++ consistently outperforms RegMean across diverse settings, including in-domain (ID) and out-of-domain (OOD) generalization, sequential merging, large-scale tasks, and robustness under several types of distribution shifts. Furthermore, RegMean++ achieves competitive or state-of-the-art performance compared to various recent advanced model merging methods. Our code is available at https://github.com/nthehai01/RegMean-plusplus.

Deep generative models have recently achieved superior performance in 3D molecule generation. Most of them first generate atoms and then add chemical bonds based on the generated atoms in a post-processing manner. However, there might be no corresponding bond solution for the temporally generated atoms as their locations are generated without considering potential bonds. We define this problem as the atom-bond inconsistency problem and claim it is the main reason for current approaches to generating unrealistic 3D molecules. To overcome this problem, we propose a new diffusion model called MolDiff which can generate atoms and bonds simultaneously while still maintaining their consistency by explicitly modeling the dependence between their relationships. We evaluated the generation ability of our proposed model and the quality of the generated molecules using criteria related to both geometry and chemical properties. The empirical studies showed that our model outperforms previous approaches, achieving a three-fold improvement in success rate and generating molecules with significantly better quality.

Pretraining data of large language models composes multiple domains (e.g., web texts, academic papers, codes), whose mixture proportions crucially impact the competence of outcome models. While existing endeavors rely on heuristics or qualitative strategies to tune the proportions, we discover the quantitative predictability of model performance regarding the mixture proportions in function forms, which we refer to as the data mixing laws. Fitting such functions on sample mixtures unveils model performance on unseen mixtures before actual runs, thus guiding the selection of an ideal data mixture. Furthermore, we propose nested use of the scaling laws of training steps, model sizes, and our data mixing law to enable predicting the performance of large models trained on massive data under various mixtures with only small-scale training. Moreover, experimental results verify that our method effectively optimizes the training mixture of a 1B model trained for 100B tokens in RedPajama, reaching a performance comparable to the one trained for 48% more steps on the default mixture. Extending the application of data mixing laws to continual training accurately predicts the critical mixture proportion that avoids catastrophic forgetting and outlooks the potential for dynamic data schedules

The study demonstrates the capabilities of a vector-based approach for calculating stoichiometric coefficients in chemical equations, using black powder as an illustrative example. A method is proposed for selecting and constraining intermediate interactions between reactants, as well as for identifying final products. It is shown that even a small number of components can lead to a large number of final and intermediate products. Through concrete calculations, a correlation is established between the number of possible chemical equations and the number of reactants. A methodology is proposed for computing all possible chemical equations within a reaction system for arbitrary component ratios, enabling the derivation of all feasible chemical reactions. Additionally, a method is developed for calculating the chemical composition for a fixed set of reactants, allowing for the evaluation of the set of products resulting from all possible chemical interactions given a specified initial composition.

Model merging refers to the process of integrating multiple distinct models into a unified model that preserves and combines the strengths and capabilities of the individual models. Most existing approaches rely on task vectors to combine models, typically under the assumption that model parameters are accessible. However, for extremely large language models (LLMs) such as GPT-4, which are often provided solely as black-box services through API interfaces (Language-Model-as-a-Service), model weights are not available to end users. This presents a significant challenge, which we refer to as black-box model merging (BMM) with massive LLMs. To address this challenge, we propose a derivative-free optimization framework based on the evolutionary algorithm (Evo-Merging) that enables effective model merging using only inference-time API queries. Our method consists of two key components: (1) sparsity-based denoising, designed to identify and filter out irrelevant or redundant information across models, and (2) sign-aware scaling, which dynamically computes optimal combination weights for the relevant models based on their performance. We also provide a formal justification, along with a theoretical analysis, for our asymmetric sparsification. Extensive experimental evaluations demonstrate that our approach achieves state-of-the-art results on a range of tasks, significantly outperforming existing strong baselines.