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Sep 9

A Comparative Study of Open-Source Large Language Models, GPT-4 and Claude 2: Multiple-Choice Test Taking in Nephrology

In recent years, there have been significant breakthroughs in the field of natural language processing, particularly with the development of large language models (LLMs). These LLMs have showcased remarkable capabilities on various benchmarks. In the healthcare field, the exact role LLMs and other future AI models will play remains unclear. There is a potential for these models in the future to be used as part of adaptive physician training, medical co-pilot applications, and digital patient interaction scenarios. The ability of AI models to participate in medical training and patient care will depend in part on their mastery of the knowledge content of specific medical fields. This study investigated the medical knowledge capability of LLMs, specifically in the context of internal medicine subspecialty multiple-choice test-taking ability. We compared the performance of several open-source LLMs (Koala 7B, Falcon 7B, Stable-Vicuna 13B, and Orca Mini 13B), to GPT-4 and Claude 2 on multiple-choice questions in the field of Nephrology. Nephrology was chosen as an example of a particularly conceptually complex subspecialty field within internal medicine. The study was conducted to evaluate the ability of LLM models to provide correct answers to nephSAP (Nephrology Self-Assessment Program) multiple-choice questions. The overall success of open-sourced LLMs in answering the 858 nephSAP multiple-choice questions correctly was 17.1% - 25.5%. In contrast, Claude 2 answered 54.4% of the questions correctly, whereas GPT-4 achieved a score of 73.3%. We show that current widely used open-sourced LLMs do poorly in their ability for zero-shot reasoning when compared to GPT-4 and Claude 2. The findings of this study potentially have significant implications for the future of subspecialty medical training and patient care.

DECO: Dense Estimation of 3D Human-Scene Contact In The Wild

Understanding how humans use physical contact to interact with the world is key to enabling human-centric artificial intelligence. While inferring 3D contact is crucial for modeling realistic and physically-plausible human-object interactions, existing methods either focus on 2D, consider body joints rather than the surface, use coarse 3D body regions, or do not generalize to in-the-wild images. In contrast, we focus on inferring dense, 3D contact between the full body surface and objects in arbitrary images. To achieve this, we first collect DAMON, a new dataset containing dense vertex-level contact annotations paired with RGB images containing complex human-object and human-scene contact. Second, we train DECO, a novel 3D contact detector that uses both body-part-driven and scene-context-driven attention to estimate vertex-level contact on the SMPL body. DECO builds on the insight that human observers recognize contact by reasoning about the contacting body parts, their proximity to scene objects, and the surrounding scene context. We perform extensive evaluations of our detector on DAMON as well as on the RICH and BEHAVE datasets. We significantly outperform existing SOTA methods across all benchmarks. We also show qualitatively that DECO generalizes well to diverse and challenging real-world human interactions in natural images. The code, data, and models are available at https://deco.is.tue.mpg.de.

IMPACT: A Generic Semantic Loss for Multimodal Medical Image Registration

Image registration is fundamental in medical imaging, enabling precise alignment of anatomical structures for diagnosis, treatment planning, image-guided treatment or longitudinal monitoring. This work introduces IMPACT (Image Metric with Pretrained model-Agnostic Comparison for Transmodality registration), a generic semantic similarity metric designed for seamless integration into diverse image registration frameworks (such as Elastix and Voxelmorph). It compares deep learning-based features extracted from medical images without requiring task-specific training, ensuring broad applicability across various modalities. By leveraging the features of the large-scale pretrained TotalSegmentator models and the ability to integrate Segment Anything Model (SAM) and other large-scale segmentation networks, this approach offers significant advantages. It provides robust, scalable, and efficient solutions for multimodal image registration. The IMPACT loss was evaluated on five challenging registration tasks involving thoracic CT/CBCT, and pelvic MR/CT datasets. Quantitative metrics, such as Target Registration Error and Dice Similarity Coefficient, demonstrated significant improvements in anatomical alignment compared to baseline methods. Qualitative analyses further confirmed the increased robustness of the proposed metric in the face of noise, artifacts, and modality variations. IMPACT's versatility and efficiency make it a valuable tool for advancing registration performance in clinical and research applications, addressing critical challenges in multimodal medical imaging.

MSA-3D: Metallicity Gradients in Galaxies at $z\sim1$ with JWST/NIRSpec Slit-stepping Spectroscopy

The radial gradient of gas-phase metallicity is a powerful probe of the chemical and structural evolution of star-forming galaxies, closely tied to disk formation and gas kinematics in the early universe. We present spatially resolved chemical and dynamical properties for a sample of 25 galaxies at 0.5 lesssim z lesssim 1.7 from the \msasd survey. These innovative observations provide 3D spectroscopy of galaxies at a spatial resolution approaching JWST's diffraction limit and a high spectral resolution of Rsimeq2700. The metallicity gradients measured in our galaxy sample range from -0.03 to 0.02 dex~kpc^{-1}. Most galaxies exhibit negative or flat radial gradients, indicating lower metallicity in the outskirts or uniform metallicity throughout the entire galaxy. We confirm a tight relationship between stellar mass and metallicity gradient at zsim1 with small intrinsic scatter of 0.02 dex~kpc^{-1}. Our results indicate that metallicity gradients become increasingly negative as stellar mass increases, likely because the more massive galaxies tend to be more ``disky". This relationship is consistent with the predictions from cosmological hydrodynamic zoom-in simulations with strong stellar feedback. This work presents the effort to harness the multiplexing capability of JWST NIRSpec/MSA in slit-stepping mode to map the chemical and kinematic profiles of high-redshift galaxies in large samples and at high spatial and spectral resolution.

Elevated UV luminosity density at Cosmic Dawn explained by non-evolving, weakly-mass dependent star formation efficiency

Recent observations with the James Webb Space Telescope (JWST) have uncovered unexpectedly high cosmic star formation activity in the early Universe, mere hundreds of millions of years after the Big Bang. These observations are often understood to reflect an evolutionary shift in star formation efficiency (SFE) caused by changing galactic conditions during these early epochs. We present FIREbox-HR, a high-resolution, cosmological hydrodynamical simulation from the Feedback in Realistic Environments project, which offers insights into the SFE of galaxies during the first billion years of cosmic time. FIREbox-HR re-simulates the cosmic volume (L = 22.1 cMpc) of the original FIREbox run with eight times higher mass resolution (m_b ~ 7800 M_sun), but with identical physics, down to z ~ 6. FIREbox-HR predicts ultraviolet (UV) luminosity functions in good agreement with available observational data. The simulation also successfully reproduces the observed cosmic UV luminosity density at z ~ 6 - 14, demonstrating that relatively high star formation activity in the early Universe is a natural outcome of the baryonic processes encoded in the FIRE-2 model. According to FIREbox-HR, the SFE - halo mass relation for intermediate mass halos (M_halo ~ 10^9 - 10^11 M_sun) does not significantly evolve with redshift and is only weakly mass-dependent. These properties of the SFE - halo mass relation lead to a larger contribution from lower mass halos at higher z, driving the gradual evolution of the observed cosmic UV luminosity density. A theoretical model based on the SFE - halo mass relation inferred from FIREbox-HR allows us to explore implications for galaxy evolution. Future observations of UV faint galaxies at z > 12 will provide an opportunity to further test these predictions and deepen our understanding of star formation during Cosmic Dawn.

Beyond the Pixel: a Photometrically Calibrated HDR Dataset for Luminance and Color Prediction

Light plays an important role in human well-being. However, most computer vision tasks treat pixels without considering their relationship to physical luminance. To address this shortcoming, we introduce the Laval Photometric Indoor HDR Dataset, the first large-scale photometrically calibrated dataset of high dynamic range 360{\deg} panoramas. Our key contribution is the calibration of an existing, uncalibrated HDR Dataset. We do so by accurately capturing RAW bracketed exposures simultaneously with a professional photometric measurement device (chroma meter) for multiple scenes across a variety of lighting conditions. Using the resulting measurements, we establish the calibration coefficients to be applied to the HDR images. The resulting dataset is a rich representation of indoor scenes which displays a wide range of illuminance and color, and varied types of light sources. We exploit the dataset to introduce three novel tasks, where: per-pixel luminance, per-pixel color and planar illuminance can be predicted from a single input image. Finally, we also capture another smaller photometric dataset with a commercial 360{\deg} camera, to experiment on generalization across cameras. We are optimistic that the release of our datasets and associated code will spark interest in physically accurate light estimation within the community. Dataset and code are available at https://lvsn.github.io/beyondthepixel/.

Social-Implicit: Rethinking Trajectory Prediction Evaluation and The Effectiveness of Implicit Maximum Likelihood Estimation

Best-of-N (BoN) Average Displacement Error (ADE)/ Final Displacement Error (FDE) is the most used metric for evaluating trajectory prediction models. Yet, the BoN does not quantify the whole generated samples, resulting in an incomplete view of the model's prediction quality and performance. We propose a new metric, Average Mahalanobis Distance (AMD) to tackle this issue. AMD is a metric that quantifies how close the whole generated samples are to the ground truth. We also introduce the Average Maximum Eigenvalue (AMV) metric that quantifies the overall spread of the predictions. Our metrics are validated empirically by showing that the ADE/FDE is not sensitive to distribution shifts, giving a biased sense of accuracy, unlike the AMD/AMV metrics. We introduce the usage of Implicit Maximum Likelihood Estimation (IMLE) as a replacement for traditional generative models to train our model, Social-Implicit. IMLE training mechanism aligns with AMD/AMV objective of predicting trajectories that are close to the ground truth with a tight spread. Social-Implicit is a memory efficient deep model with only 5.8K parameters that runs in real time of about 580Hz and achieves competitive results. Interactive demo of the problem can be seen at https://www.abduallahmohamed.com/social-implicit-amdamv-adefde-demo . Code is available at https://github.com/abduallahmohamed/Social-Implicit .

Calibration and Uncertainty for multiRater Volume Assessment in multiorgan Segmentation (CURVAS) challenge results

Deep learning (DL) has become the dominant approach for medical image segmentation, yet ensuring the reliability and clinical applicability of these models requires addressing key challenges such as annotation variability, calibration, and uncertainty estimation. This is why we created the Calibration and Uncertainty for multiRater Volume Assessment in multiorgan Segmentation (CURVAS), which highlights the critical role of multiple annotators in establishing a more comprehensive ground truth, emphasizing that segmentation is inherently subjective and that leveraging inter-annotator variability is essential for robust model evaluation. Seven teams participated in the challenge, submitting a variety of DL models evaluated using metrics such as Dice Similarity Coefficient (DSC), Expected Calibration Error (ECE), and Continuous Ranked Probability Score (CRPS). By incorporating consensus and dissensus ground truth, we assess how DL models handle uncertainty and whether their confidence estimates align with true segmentation performance. Our findings reinforce the importance of well-calibrated models, as better calibration is strongly correlated with the quality of the results. Furthermore, we demonstrate that segmentation models trained on diverse datasets and enriched with pre-trained knowledge exhibit greater robustness, particularly in cases deviating from standard anatomical structures. Notably, the best-performing models achieved high DSC and well-calibrated uncertainty estimates. This work underscores the need for multi-annotator ground truth, thorough calibration assessments, and uncertainty-aware evaluations to develop trustworthy and clinically reliable DL-based medical image segmentation models.

Sloan Digital Sky Survey IV: Mapping the Milky Way, Nearby Galaxies, and the Distant Universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratio in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially-resolved spectroscopy for thousands of nearby galaxies (median redshift of z = 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between redshifts z = 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGN and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5-meter Sloan Foundation Telescope at Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5-meter du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in July 2016.

Paper2Agent: Reimagining Research Papers As Interactive and Reliable AI Agents

We introduce Paper2Agent, an automated framework that converts research papers into AI agents. Paper2Agent transforms research output from passive artifacts into active systems that can accelerate downstream use, adoption, and discovery. Conventional research papers require readers to invest substantial effort to understand and adapt a paper's code, data, and methods to their own work, creating barriers to dissemination and reuse. Paper2Agent addresses this challenge by automatically converting a paper into an AI agent that acts as a knowledgeable research assistant. It systematically analyzes the paper and the associated codebase using multiple agents to construct a Model Context Protocol (MCP) server, then iteratively generates and runs tests to refine and robustify the resulting MCP. These paper MCPs can then be flexibly connected to a chat agent (e.g. Claude Code) to carry out complex scientific queries through natural language while invoking tools and workflows from the original paper. We demonstrate Paper2Agent's effectiveness in creating reliable and capable paper agents through in-depth case studies. Paper2Agent created an agent that leverages AlphaGenome to interpret genomic variants and agents based on ScanPy and TISSUE to carry out single-cell and spatial transcriptomics analyses. We validate that these paper agents can reproduce the original paper's results and can correctly carry out novel user queries. By turning static papers into dynamic, interactive AI agents, Paper2Agent introduces a new paradigm for knowledge dissemination and a foundation for the collaborative ecosystem of AI co-scientists.

Dynamic Cheatsheet: Test-Time Learning with Adaptive Memory

Despite their impressive performance on complex tasks, current language models (LMs) typically operate in a vacuum: Each input query is processed separately, without retaining insights from previous attempts. Here, we present Dynamic Cheatsheet (DC), a lightweight framework that endows a black-box LM with a persistent, evolving memory. Rather than repeatedly re-discovering or re-committing the same solutions and mistakes, DC enables models to store and reuse accumulated strategies, code snippets, and general problem-solving insights at inference time. This test-time learning enhances performance substantially across a range of tasks without needing explicit ground-truth labels or human feedback. Leveraging DC, Claude 3.5 Sonnet's accuracy more than doubled on AIME math exams once it began retaining algebraic insights across questions. Similarly, GPT-4o's success rate on Game of 24 increased from 10% to 99% after the model discovered and reused a Python-based solution. In tasks prone to arithmetic mistakes, such as balancing equations, DC enabled GPT-4o and Claude to reach near-perfect accuracy by recalling previously validated code, whereas their baselines stagnated around 50%. Beyond arithmetic challenges, DC yields notable accuracy gains on knowledge-demanding tasks. Claude achieved a 9% improvement in GPQA-Diamond and an 8% boost on MMLU-Pro problems. Crucially, DC's memory is self-curated, focusing on concise, transferable snippets rather than entire transcript. Unlike finetuning or static retrieval methods, DC adapts LMs' problem-solving skills on the fly, without modifying their underlying parameters. Overall, our findings present DC as a promising approach for augmenting LMs with persistent memory, bridging the divide between isolated inference events and the cumulative, experience-driven learning characteristic of human cognition.

AstroMLab 1: Who Wins Astronomy Jeopardy!?

We present a comprehensive evaluation of proprietary and open-weights large language models using the first astronomy-specific benchmarking dataset. This dataset comprises 4,425 multiple-choice questions curated from the Annual Review of Astronomy and Astrophysics, covering a broad range of astrophysical topics. Our analysis examines model performance across various astronomical subfields and assesses response calibration, crucial for potential deployment in research environments. Claude-3.5-Sonnet outperforms competitors by up to 4.6 percentage points, achieving 85.0% accuracy. For proprietary models, we observed a universal reduction in cost every 3-to-12 months to achieve similar score in this particular astronomy benchmark. Open-source models have rapidly improved, with LLaMA-3-70b (80.6%) and Qwen-2-72b (77.7%) now competing with some of the best proprietary models. We identify performance variations across topics, with non-English-focused models generally struggling more in exoplanet-related fields, stellar astrophysics, and instrumentation related questions. These challenges likely stem from less abundant training data, limited historical context, and rapid recent developments in these areas. This pattern is observed across both open-weights and proprietary models, with regional dependencies evident, highlighting the impact of training data diversity on model performance in specialized scientific domains. Top-performing models demonstrate well-calibrated confidence, with correlations above 0.9 between confidence and correctness, though they tend to be slightly underconfident. The development for fast, low-cost inference of open-weights models presents new opportunities for affordable deployment in astronomy. The rapid progress observed suggests that LLM-driven research in astronomy may become feasible in the near future.

HoneyBee: Progressive Instruction Finetuning of Large Language Models for Materials Science

We propose an instruction-based process for trustworthy data curation in materials science (MatSci-Instruct), which we then apply to finetune a LLaMa-based language model targeted for materials science (HoneyBee). MatSci-Instruct helps alleviate the scarcity of relevant, high-quality materials science textual data available in the open literature, and HoneyBee is the first billion-parameter language model specialized to materials science. In MatSci-Instruct we improve the trustworthiness of generated data by prompting multiple commercially available large language models for generation with an Instructor module (e.g. Chat-GPT) and verification from an independent Verifier module (e.g. Claude). Using MatSci-Instruct, we construct a dataset of multiple tasks and measure the quality of our dataset along multiple dimensions, including accuracy against known facts, relevance to materials science, as well as completeness and reasonableness of the data. Moreover, we iteratively generate more targeted instructions and instruction-data in a finetuning-evaluation-feedback loop leading to progressively better performance for our finetuned HoneyBee models. Our evaluation on the MatSci-NLP benchmark shows HoneyBee's outperformance of existing language models on materials science tasks and iterative improvement in successive stages of instruction-data refinement. We study the quality of HoneyBee's language modeling through automatic evaluation and analyze case studies to further understand the model's capabilities and limitations. Our code and relevant datasets are publicly available at https://github.com/BangLab-UdeM-Mila/NLP4MatSci-HoneyBee.

ArxivBench: Can LLMs Assist Researchers in Conducting Research?

Large language models (LLMs) have demonstrated remarkable effectiveness in completing various tasks such as reasoning, translation, and question answering. However the issue of factual incorrect content in LLM-generated responses remains a persistent challenge. In this study, we evaluate both proprietary and open-source LLMs on their ability to respond with relevant research papers and accurate links to articles hosted on the arXiv platform, based on high level prompts. To facilitate this evaluation, we introduce arXivBench, a benchmark specifically designed to assess LLM performance across eight major subject categories on arXiv and five subfields within computer science, one of the most popular categories among them. Our findings reveal a concerning accuracy of LLM-generated responses depending on the subject, with some subjects experiencing significantly lower accuracy than others. Notably, Claude-3.5-Sonnet exhibits a substantial advantage in generating both relevant and accurate responses. And interestingly, most LLMs achieve a much higher accuracy in the Artificial Intelligence sub-field than other sub-fields. This benchmark provides a standardized tool for evaluating the reliability of LLM-generated scientific responses, promoting more dependable use of LLMs in academic and research environments. Our code is open-sourced at https://github.com/arxivBenchLLM/arXivBench and our dataset is available on huggingface at https://huggingface.co/datasets/arXivBenchLLM/arXivBench.