Upload 11 files

LICENSE.md

@@ -0,0 +1,438 @@
+Attribution-NonCommercial-ShareAlike 4.0 International
+
+=======================================================================
+
+Creative Commons Corporation ("Creative Commons") is not a law firm and
+does not provide legal services or legal advice. Distribution of
+Creative Commons public licenses does not create a lawyer-client or
+other relationship. Creative Commons makes its licenses and related
+information available on an "as-is" basis. Creative Commons gives no
+warranties regarding its licenses, any material licensed under their
+terms and conditions, or any related information. Creative Commons
+disclaims all liability for damages resulting from their use to the
+fullest extent possible.
+
+Using Creative Commons Public Licenses
+
+Creative Commons public licenses provide a standard set of terms and
+conditions that creators and other rights holders may use to share
+original works of authorship and other material subject to copyright
+and certain other rights specified in the public license below. The
+following considerations are for informational purposes only, are not
+exhaustive, and do not form part of our licenses.
+
+     Considerations for licensors: Our public licenses are
+     intended for use by those authorized to give the public
+     permission to use material in ways otherwise restricted by
+     copyright and certain other rights. Our licenses are
+     irrevocable. Licensors should read and understand the terms
+     and conditions of the license they choose before applying it.
+     Licensors should also secure all rights necessary before
+     applying our licenses so that the public can reuse the
+     material as expected. Licensors should clearly mark any
+     material not subject to the license. This includes other CC-
+     licensed material, or material used under an exception or
+     limitation to copyright. More considerations for licensors:
+    wiki.creativecommons.org/Considerations_for_licensors
+
+     Considerations for the public: By using one of our public
+     licenses, a licensor grants the public permission to use the
+     licensed material under specified terms and conditions. If
+     the licensor's permission is not necessary for any reason--for
+     example, because of any applicable exception or limitation to
+     copyright--then that use is not regulated by the license. Our
+     licenses grant only permissions under copyright and certain
+     other rights that a licensor has authority to grant. Use of
+     the licensed material may still be restricted for other
+     reasons, including because others have copyright or other
+     rights in the material. A licensor may make special requests,
+     such as asking that all changes be marked or described.
+     Although not required by our licenses, you are encouraged to
+     respect those requests where reasonable. More considerations
+     for the public:
+    wiki.creativecommons.org/Considerations_for_licensees
+
+=======================================================================
+
+Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
+Public License
+
+By exercising the Licensed Rights (defined below), You accept and agree
+to be bound by the terms and conditions of this Creative Commons
+Attribution-NonCommercial-ShareAlike 4.0 International Public License
+("Public License"). To the extent this Public License may be
+interpreted as a contract, You are granted the Licensed Rights in
+consideration of Your acceptance of these terms and conditions, and the
+Licensor grants You such rights in consideration of benefits the
+Licensor receives from making the Licensed Material available under
+these terms and conditions.
+
+
+Section 1 -- Definitions.
+
+  a. Adapted Material means material subject to Copyright and Similar
+     Rights that is derived from or based upon the Licensed Material
+     and in which the Licensed Material is translated, altered,
+     arranged, transformed, or otherwise modified in a manner requiring
+     permission under the Copyright and Similar Rights held by the
+     Licensor. For purposes of this Public License, where the Licensed
+     Material is a musical work, performance, or sound recording,
+     Adapted Material is always produced where the Licensed Material is
+     synched in timed relation with a moving image.
+
+  b. Adapter's License means the license You apply to Your Copyright
+     and Similar Rights in Your contributions to Adapted Material in
+     accordance with the terms and conditions of this Public License.
+
+  c. BY-NC-SA Compatible License means a license listed at
+     creativecommons.org/compatiblelicenses, approved by Creative
+     Commons as essentially the equivalent of this Public License.
+
+  d. Copyright and Similar Rights means copyright and/or similar rights
+     closely related to copyright including, without limitation,
+     performance, broadcast, sound recording, and Sui Generis Database
+     Rights, without regard to how the rights are labeled or
+     categorized. For purposes of this Public License, the rights
+     specified in Section 2(b)(1)-(2) are not Copyright and Similar
+     Rights.
+
+  e. Effective Technological Measures means those measures that, in the
+     absence of proper authority, may not be circumvented under laws
+     fulfilling obligations under Article 11 of the WIPO Copyright
+     Treaty adopted on December 20, 1996, and/or similar international
+     agreements.
+
+  f. Exceptions and Limitations means fair use, fair dealing, and/or
+     any other exception or limitation to Copyright and Similar Rights
+     that applies to Your use of the Licensed Material.
+
+  g. License Elements means the license attributes listed in the name
+     of a Creative Commons Public License. The License Elements of this
+     Public License are Attribution, NonCommercial, and ShareAlike.
+
+  h. Licensed Material means the artistic or literary work, database,
+     or other material to which the Licensor applied this Public
+     License.
+
+  i. Licensed Rights means the rights granted to You subject to the
+     terms and conditions of this Public License, which are limited to
+     all Copyright and Similar Rights that apply to Your use of the
+     Licensed Material and that the Licensor has authority to license.
+
+  j. Licensor means the individual(s) or entity(ies) granting rights
+     under this Public License.
+
+  k. NonCommercial means not primarily intended for or directed towards
+     commercial advantage or monetary compensation. For purposes of
+     this Public License, the exchange of the Licensed Material for
+     other material subject to Copyright and Similar Rights by digital
+     file-sharing or similar means is NonCommercial provided there is
+     no payment of monetary compensation in connection with the
+     exchange.
+
+  l. Share means to provide material to the public by any means or
+     process that requires permission under the Licensed Rights, such
+     as reproduction, public display, public performance, distribution,
+     dissemination, communication, or importation, and to make material
+     available to the public including in ways that members of the
+     public may access the material from a place and at a time
+     individually chosen by them.
+
+  m. Sui Generis Database Rights means rights other than copyright
+     resulting from Directive 96/9/EC of the European Parliament and of
+     the Council of 11 March 1996 on the legal protection of databases,
+     as amended and/or succeeded, as well as other essentially
+     equivalent rights anywhere in the world.
+
+  n. You means the individual or entity exercising the Licensed Rights
+     under this Public License. Your has a corresponding meaning.
+
+
+Section 2 -- Scope.
+
+  a. License grant.
+
+       1. Subject to the terms and conditions of this Public License,
+          the Licensor hereby grants You a worldwide, royalty-free,
+          non-sublicensable, non-exclusive, irrevocable license to
+          exercise the Licensed Rights in the Licensed Material to:
+
+            a. reproduce and Share the Licensed Material, in whole or
+               in part, for NonCommercial purposes only; and
+
+            b. produce, reproduce, and Share Adapted Material for
+               NonCommercial purposes only.
+
+       2. Exceptions and Limitations. For the avoidance of doubt, where
+          Exceptions and Limitations apply to Your use, this Public
+          License does not apply, and You do not need to comply with
+          its terms and conditions.
+
+       3. Term. The term of this Public License is specified in Section
+          6(a).
+
+       4. Media and formats; technical modifications allowed. The
+          Licensor authorizes You to exercise the Licensed Rights in
+          all media and formats whether now known or hereafter created,
+          and to make technical modifications necessary to do so. The
+          Licensor waives and/or agrees not to assert any right or
+          authority to forbid You from making technical modifications
+          necessary to exercise the Licensed Rights, including
+          technical modifications necessary to circumvent Effective
+          Technological Measures. For purposes of this Public License,
+          simply making modifications authorized by this Section 2(a)
+          (4) never produces Adapted Material.
+
+       5. Downstream recipients.
+
+            a. Offer from the Licensor -- Licensed Material. Every
+               recipient of the Licensed Material automatically
+               receives an offer from the Licensor to exercise the
+               Licensed Rights under the terms and conditions of this
+               Public License.
+
+            b. Additional offer from the Licensor -- Adapted Material.
+               Every recipient of Adapted Material from You
+               automatically receives an offer from the Licensor to
+               exercise the Licensed Rights in the Adapted Material
+               under the conditions of the Adapter's License You apply.
+
+            c. No downstream restrictions. You may not offer or impose
+               any additional or different terms or conditions on, or
+               apply any Effective Technological Measures to, the
+               Licensed Material if doing so restricts exercise of the
+               Licensed Rights by any recipient of the Licensed
+               Material.
+
+       6. No endorsement. Nothing in this Public License constitutes or
+          may be construed as permission to assert or imply that You
+          are, or that Your use of the Licensed Material is, connected
+          with, or sponsored, endorsed, or granted official status by,
+          the Licensor or others designated to receive attribution as
+          provided in Section 3(a)(1)(A)(i).
+
+  b. Other rights.
+
+       1. Moral rights, such as the right of integrity, are not
+          licensed under this Public License, nor are publicity,
+          privacy, and/or other similar personality rights; however, to
+          the extent possible, the Licensor waives and/or agrees not to
+          assert any such rights held by the Licensor to the limited
+          extent necessary to allow You to exercise the Licensed
+          Rights, but not otherwise.
+
+       2. Patent and trademark rights are not licensed under this
+          Public License.
+
+       3. To the extent possible, the Licensor waives any right to
+          collect royalties from You for the exercise of the Licensed
+          Rights, whether directly or through a collecting society
+          under any voluntary or waivable statutory or compulsory
+          licensing scheme. In all other cases the Licensor expressly
+          reserves any right to collect such royalties, including when
+          the Licensed Material is used other than for NonCommercial
+          purposes.
+
+
+Section 3 -- License Conditions.
+
+Your exercise of the Licensed Rights is expressly made subject to the
+following conditions.
+
+  a. Attribution.
+
+       1. If You Share the Licensed Material (including in modified
+          form), You must:
+
+            a. retain the following if it is supplied by the Licensor
+               with the Licensed Material:
+
+                 i. identification of the creator(s) of the Licensed
+                    Material and any others designated to receive
+                    attribution, in any reasonable manner requested by
+                    the Licensor (including by pseudonym if
+                    designated);
+
+                ii. a copyright notice;
+
+               iii. a notice that refers to this Public License;
+
+                iv. a notice that refers to the disclaimer of
+                    warranties;
+
+                 v. a URI or hyperlink to the Licensed Material to the
+                    extent reasonably practicable;
+
+            b. indicate if You modified the Licensed Material and
+               retain an indication of any previous modifications; and
+
+            c. indicate the Licensed Material is licensed under this
+               Public License, and include the text of, or the URI or
+               hyperlink to, this Public License.
+
+       2. You may satisfy the conditions in Section 3(a)(1) in any
+          reasonable manner based on the medium, means, and context in
+          which You Share the Licensed Material. For example, it may be
+          reasonable to satisfy the conditions by providing a URI or
+          hyperlink to a resource that includes the required
+          information.
+       3. If requested by the Licensor, You must remove any of the
+          information required by Section 3(a)(1)(A) to the extent
+          reasonably practicable.
+
+  b. ShareAlike.
+
+     In addition to the conditions in Section 3(a), if You Share
+     Adapted Material You produce, the following conditions also apply.
+
+       1. The Adapter's License You apply must be a Creative Commons
+          license with the same License Elements, this version or
+          later, or a BY-NC-SA Compatible License.
+
+       2. You must include the text of, or the URI or hyperlink to, the
+          Adapter's License You apply. You may satisfy this condition
+          in any reasonable manner based on the medium, means, and
+          context in which You Share Adapted Material.
+
+       3. You may not offer or impose any additional or different terms
+          or conditions on, or apply any Effective Technological
+          Measures to, Adapted Material that restrict exercise of the
+          rights granted under the Adapter's License You apply.
+
+
+Section 4 -- Sui Generis Database Rights.
+
+Where the Licensed Rights include Sui Generis Database Rights that
+apply to Your use of the Licensed Material:
+
+  a. for the avoidance of doubt, Section 2(a)(1) grants You the right
+     to extract, reuse, reproduce, and Share all or a substantial
+     portion of the contents of the database for NonCommercial purposes
+     only;
+
+  b. if You include all or a substantial portion of the database
+     contents in a database in which You have Sui Generis Database
+     Rights, then the database in which You have Sui Generis Database
+     Rights (but not its individual contents) is Adapted Material,
+     including for purposes of Section 3(b); and
+
+  c. You must comply with the conditions in Section 3(a) if You Share
+     all or a substantial portion of the contents of the database.
+
+For the avoidance of doubt, this Section 4 supplements and does not
+replace Your obligations under this Public License where the Licensed
+Rights include other Copyright and Similar Rights.
+
+
+Section 5 -- Disclaimer of Warranties and Limitation of Liability.
+
+  a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE
+     EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS
+     AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF
+     ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS,
+     IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION,
+     WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
+     PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS,
+     ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT
+     KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT
+     ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU.
+
+  b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE
+     TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION,
+     NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT,
+     INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES,
+     COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR
+     USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN
+     ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR
+     DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR
+     IN PART, THIS LIMITATION MAY NOT APPLY TO YOU.
+
+  c. The disclaimer of warranties and limitation of liability provided
+     above shall be interpreted in a manner that, to the extent
+     possible, most closely approximates an absolute disclaimer and
+     waiver of all liability.
+
+
+Section 6 -- Term and Termination.
+
+  a. This Public License applies for the term of the Copyright and
+     Similar Rights licensed here. However, if You fail to comply with
+     this Public License, then Your rights under this Public License
+     terminate automatically.
+
+  b. Where Your right to use the Licensed Material has terminated under
+     Section 6(a), it reinstates:
+
+       1. automatically as of the date the violation is cured, provided
+          it is cured within 30 days of Your discovery of the
+          violation; or
+
+       2. upon express reinstatement by the Licensor.
+
+     For the avoidance of doubt, this Section 6(b) does not affect any
+     right the Licensor may have to seek remedies for Your violations
+     of this Public License.
+
+  c. For the avoidance of doubt, the Licensor may also offer the
+     Licensed Material under separate terms or conditions or stop
+     distributing the Licensed Material at any time; however, doing so
+     will not terminate this Public License.
+
+  d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
+     License.
+
+
+Section 7 -- Other Terms and Conditions.
+
+  a. The Licensor shall not be bound by any additional or different
+     terms or conditions communicated by You unless expressly agreed.
+
+  b. Any arrangements, understandings, or agreements regarding the
+     Licensed Material not stated herein are separate from and
+     independent of the terms and conditions of this Public License.
+
+
+Section 8 -- Interpretation.
+
+  a. For the avoidance of doubt, this Public License does not, and
+     shall not be interpreted to, reduce, limit, restrict, or impose
+     conditions on any use of the Licensed Material that could lawfully
+     be made without permission under this Public License.
+
+  b. To the extent possible, if any provision of this Public License is
+     deemed unenforceable, it shall be automatically reformed to the
+     minimum extent necessary to make it enforceable. If the provision
+     cannot be reformed, it shall be severed from this Public License
+     without affecting the enforceability of the remaining terms and
+     conditions.
+
+  c. No term or condition of this Public License will be waived and no
+     failure to comply consented to unless expressly agreed to by the
+     Licensor.
+
+  d. Nothing in this Public License constitutes or may be interpreted
+     as a limitation upon, or waiver of, any privileges and immunities
+     that apply to the Licensor or You, including from the legal
+     processes of any jurisdiction or authority.
+
+=======================================================================
+
+Creative Commons is not a party to its public
+licenses. Notwithstanding, Creative Commons may elect to apply one of
+its public licenses to material it publishes and in those instances
+will be considered the “Licensor.” The text of the Creative Commons
+public licenses is dedicated to the public domain under the CC0 Public
+Domain Dedication. Except for the limited purpose of indicating that
+material is shared under a Creative Commons public license or as
+otherwise permitted by the Creative Commons policies published at
+creativecommons.org/policies, Creative Commons does not authorize the
+use of the trademark "Creative Commons" or any other trademark or logo
+of Creative Commons without its prior written consent including,
+without limitation, in connection with any unauthorized modifications
+to any of its public licenses or any other arrangements,
+understandings, or agreements concerning use of licensed material. For
+the avoidance of doubt, this paragraph does not form part of the
+public licenses.
+
+Creative Commons may be contacted at creativecommons.org.
+

MODEL_ACCEPTABLE_USE_POLICY.md

@@ -0,0 +1,53 @@
+
+# Arc Research Institute State Model Acceptable Use Policy
+
+**_Last updated June 23, 2025_**
+
+Arc Research Institute (the “**Institute**,” “**we**” or “**us**”) makes its State Model available and free to use for non-commercial purposes, subject to the terms of the [Arc Research Institute State Model Non-Commercial License](MODEL_LICENSE.md) (the “**License**”) and this Acceptable Use Policy (“**Policy**”). The purpose of this Policy is to ensure the State Model is used safely, ethically, and in accordance with all applicable laws and regulations. Any defined terms used but not defined in this Policy have the meaning given in the License. 
+
+## Purpose and Permitted Use
+
+The intent of the State Model is to support and enable research that advances knowledge and serves the public interest. This model is made available for use only by non-commercial entities such as government institutions, non-profit organizations, research institutes, and educational institutions.
+
+Although the State Model may only be used for non-commercial purposes, you are free to use any outputs you create for any purpose. 
+
+## Prohibited Uses
+
+Unless otherwise expressly permitted pursuant to the License, you may not use the State Model, or any outputs or derivatives thereof, for any of the following purposes:
+
+**1)  For-Profit Use:**
+-  Use by or for any for-profit entity, including but not limited to corporations, partnerships, or other commercial organizations.
+-  Use for any for-profit purpose, including but not limited to commercial research, sponsored research, product or service development, marketing, advertising, or any activity intended to generate revenue or commercial advantage.
+-  For clarity, Outputs (as defined in the License) are not subject to this Section 1.
+
+**2)  Unlawful, Harmful, or Unethical Activities:**
+-  Any activity that violates applicable local, national, or international laws, rules, or regulations.
+-  Any activity that causes or is intended to cause harm, including but not limited to the generation of offensive, abusive, or unlawful content.
+-  Any use that infringes upon the rights of others, including invasion of privacy or jeopardizing the safety of others.
+
+**3)  Misinforming or Misleading:**
+-  Generation, dissemination, or promotion of false, incomplete, or otherwise misleading information.
+-  Any use intended to deceive, misinform, or otherwise mislead individuals or organizations, including but not limited fabrication of data, fabrication or manipulation of outputs, impersonation, or to otherwise misrepresent facts or scientific findings.
+
+**4)  Security and Privacy Violations:**
+-  Introducing malware, viruses, or other malicious code.
+-  Circumventing or attempting to circumvent any security or access controls.
+-  Collecting, storing, or sharing sensitive, health, or personal data without proper authorization or consent.
+
+**5)  Claiming Endorsement:**
+-  Making any statements or claims or engaging in any other behavior or communication that indicates or suggests that the Institute endorses your use of the State Model, including any Derivative Works or Outputs (each as defined in the License). 
+
+## Attribution
+
+If You redistribute the State Model, or any outputs or derivatives thereof, you must also include a prominent and readable citation to the State Model research paper: Adduri, A. et al. (2025) State: Learning Perturbation Effects across Heterogenous Cellular Contexts at Scale.
+
+## Disclaimer
+
+The State Model is provided AS IS and is intended for informational, theoretical, and research purposes only and is not intended for use in the diagnosis of disease or other conditions, or in the cure, mitigation, treatment, or prevention of disease. It should not be used or substituted for professional, medical advice.
+
+## Third Party Integrations
+
+The Institute is not responsible for the content, security, or privacy practices of any third-party technology, data, materials, or services that you may use in connection with the State Model. Use of such integrations is at your own risk and subject to the terms and policies of the respective third parties. The Institute disclaims any liability for damages or losses resulting from third-party integrations.
+
+## Legal and Regulatory Compliance
+

MODEL_LICENSE.md

@@ -0,0 +1,74 @@
+# Arc Research Institute State Model Non-Commercial License
+
+**_Last Updated: June 23, 2025_**
+
+Arc Research Institute (“**Licensor**”) is releasing certain materials collectively defined below as the “**State Model**”.  This license (the “**License**”) is between Licensor and any individual or legal entity exercising permissions granted under this License (“**You**”).
+
+By downloading, copying, executing, or otherwise exercising any permission granted by this License or using the State Model, You acknowledge that You accept and agree to be bound by the terms and conditions of this License.  If use of the State Model is within the scope of Your employment, You hereby represent that you are fully authorized to enter into this Agreement on behalf of any such employer.
+
+Licensor may make changes to this License. The “_Last Updated_” date above indicates when this License was last changed.  The amended License will be effective immediately, and Your continued use of the State Model after such update will confirm Your acceptance of the changes.  If You do not agree to the amended License, You must immediately stop using the State Model.
+
+## 1. Definitions
+
+1.1  “**Commercial Entity**” means any natural person, legal entity, organization, or institution that is for-profit, or otherwise not a Non-Commercial Entity.
+
+1.2  “**Derivative Work**” means any modification of, work based upon, or derived from, the State Model or any portion thereof, including adaptations, fine-tunings, adjusted model weights, distilled or pruned versions, additional training, or any other alteration, transformation, or integration, including use as a prior, of the State Model or any part of it.
+
+1.3  “**Non-Commercial Entity**” means a (a) government body or (b) a natural person, academic institution, research institute, or other entity registered with relevant tax authorities as a not-for-profit organization that, in each (a) and (b) above, does not own or control or is not owned or controlled by and is not acting with or on behalf of a Commercial Entity.
+
+1.4  “**Non-Commercial Purpose**” means a purpose that is not undertaken for direct or indirect monetary compensation, financial consideration, or any other commercial undertaking or advantage.  For the purposes of this License, research, development, or educational activities engaged in or sponsored by a Commercial Entity (whether or not performed by a Non-Commercial Entity or otherwise undertaken for a purpose not associated with monetary compensation, financial consideration or other commercial undertaking or advantage) are not Non-Commercial Purposes.
+
+1.5  “**Output**” means any results, data, or other material generated by execution of the unmodified State Model or a Derivative Work.
+
+1.6  “**State Model**” includes, individually and collectively, the pretrained model (_i.e._, the model code combined with the trained model weights), model weights, documentation, and any other files released by Licensor under this License (provided that source code and object code are licensed under a separate license made available by Licensor).
+
+## 2.	Grant of Rights
+
+2.1  **License**  Subject to the terms and conditions of this License, Licensor hereby grants You a personal, worldwide, royalty-free, non-exclusive, irrevocable (except as provided in Section 8), non-sublicensable license: (a) to use, copy, modify, and display the State Model; (b) to create Derivative Works and Outputs; (c) to reproduce, distribute, and make publicly available (i) the State Model and any Derivative Work, each subject to Section 3 (Redistribution Conditions), and (ii) any Output; and (d) under the Licensor’s patent rights covering the State Model, to make, use, import, and otherwise exploit the State Model and any Derivative Works, each (a) through (c)(i) and (d), solely for Non-Commercial Purposes.
+
+2.2  **Patent Infringement**  If You initiate patent litigation (including a cross-claim or counterclaim in a lawsuit) alleging that the State Model or a Derivative Work infringes a patent, this  License to You is terminated as of the date such litigation is filed.
+
+2.3  **Reservation of Rights**.  All rights other than those expressly granted to You herein are reserved by Licensor. 
+
+## 3. Redistribution Conditions
+
+If You redistribute the State Model or any Derivative Work, You must (a) include a complete, unaltered copy of this License; (b) keep intact all original copyright, license, and disclaimer notices; and (c) provide prominent notice stating that the redistributed State Model is governed by this License.  If You redistribute the State Model, any Derivative Work or any Output, You must also include a prominent and readable citation to the State Model research paper: Adduri, A. et al. (2025) State: Learning Perturbation Effects across Heterogenous Cellular Contexts at Scale.  You may choose to license a Derivative Work or Output under different terms and conditions, provided that the limitations and restrictions herein (including, in the case of a Derivative Work, the Non-Commercial Purpose) remain in substance and effect.
+
+## 4. Restrictions
+
+4.1  You may not use or distribute the State Model, any or Derivative Work for any purpose other than Non-Commercial Purposes, unless You first obtain a separate, express, written license from Licensor granting such rights.  If you wish to inquire about such separate license, you may contact <[email protected]>.
+
+4.2  You may not remove, obfuscate, or alter any copyright, trademark, citation or other proprietary notice included in the State Model.
+
+4.3  You must comply with all applicable laws and regulations, including export-control and sanctions regimes, in connection with Your use of the State Model and any Derivative Work or Output.
+
+4.4  If You elect to collect or process personal data, health data or any other regulated data using the State Model or any Derivative Work, You are solely responsible for compliance with all data-protection, privacy, and related laws.
+
+## 5.	 Feedback
+
+If You provide Licensor with ideas, suggestions, or improvements regarding the State Model (“**Feedback**”), Licensor may incorporate such Feedback without obligation or restriction, and You hereby irrevocably assign to Licensor all right, title, and interest in and to such Feedback and all intellectual property rights therein and thereto.  To the extent any rights in and to such Feedback cannot be assigned by You, You hereby grants to Licensor a nonexclusive, worldwide, perpetual, irrevocable, transferable, sublicensable, royalty-free, fully paid-up license to use, practice, and otherwise exercise the Feedback without restriction.
+
+## 6. Trademarks 
+
+This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the State Model and reproducing the content of the license as required herein.
+
+## 7. Disclaimer of Warranty; Limitation of Liability
+
+THE STATE MODEL, ANY DERIVATIVE WORK, AND ANY OUTPUT ARE PROVIDED “AS IS” AND “WITH ALL FAULTS,” WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, OR THAT OPERATION OF THE STATE MODEL WILL BE UNINTERRUPTED OR ERROR-FREE.  TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, LICENSOR SHALL NOT BE LIABLE UNDER ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, TORT (INCLUDING NEGLIGENCE), STRICT LIABILITY, OR OTHERWISE, FOR ANY INDIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL, OR EXEMPLARY DAMAGES ARISING OUT OF OR RELATED TO THIS LICENSE OR THE USE OF THE STATE MODEL, DERIVATIVE WORKS, OR OUTPUTS, EVEN IF LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.  LICENSOR’S TOTAL AGGREGATE LIABILITY UNDER THIS LICENSE SHALL NOT EXCEED TWENTY U.S. DOLLARS (USD $20).
+
+## 8.	 Termination
+
+8.1  This License and the rights granted herein terminate automatically without notice if You breach Sections 2, 3, or 4.  Upon termination, You shall cease all use, reproduction, and distribution of the State Model, any Derivative Work, and any Output, and Sections 2.3, 4.4, 5, 7, 8.2, and 9 shall remain in effect.
+
+8.2  Termination shall not affect any third-party’s legitimate possession, under this License, of copies of the State Model, Derivative Works, or Outputs obtained from You prior to termination, provided such third party is itself in full compliance with this License.
+
+## 9.	 Miscellaneous
+
+9.1  **Governing Law**.  This License shall be governed by and construed in accordance with the laws of the state of California, excluding its or any other jurisdiction’s conflict-of-laws principles. Venue for any disputes related to this License shall be in the federal courts in Santa Clara County, California and You and Licensor hereby agree to the exclusive jurisdiction of such courts.
+
+9.2  **Severability**.  If any provision of this License is held to be unenforceable, such provision shall be reformed only to the extent necessary to make it enforceable, and the remaining provisions shall remain in full force and effect.
+
+9.3  **No Waiver**.  Failure by Licensor to enforce any provision of this License shall not constitute a waiver of future enforcement of that or any other provision.
+
+9.4  **Entire Agreement**.  This License constitutes the entire agreement between the parties with respect to the State Model and supersedes all prior or contemporaneous understandings, whether written or oral, regarding such subject matter. References herein to “including” will be interpreted to mean “including but not limited to” and any examples provided are illustrative and not intended to be the sole examples of a particular concept.
+

batch_onehot_map.pkl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:aa859ba5c7330e2d83d97703d83d4d54237e1ca0a2b6074c56bba9504504e121
+size 29727

cell_type_onehot_map.pkl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:482a4edbcf131a3897f33f806b15a662cbc38bd3bc5e3af4d97e6b6a7904a428
+size 11159

config.yaml

@@ -0,0 +1,90 @@
+data:
+  name: PerturbationDataModule
+  kwargs:
+    toml_config_path: /large_storage/ctc/ML/state_sets/parse/donor.toml
+    embed_key: X_hvg
+    output_space: gene
+    pert_rep: onehot
+    basal_rep: sample
+    num_workers: 24
+    pin_memory: true
+    n_basal_samples: 1
+    basal_mapping_strategy: random
+    should_yield_control_cells: true
+    batch_col: cell_type
+    pert_col: cytokine
+    cell_type_key: donor
+    control_pert: PBS
+    map_controls: true
+    perturbation_features_file: null
+    store_raw_basal: false
+    int_counts: false
+  output_dir: null
+  debug: true
+model:
+  name: PertSets
+  checkpoint: null
+  device: cuda
+  kwargs:
+    cell_set_len: 512
+    blur: 0.05
+    hidden_dim: 1440
+    loss: energy
+    confidence_head: false
+    n_encoder_layers: 4
+    n_decoder_layers: 4
+    predict_residual: true
+    softplus: true
+    freeze_pert: false
+    transformer_decoder: false
+    finetune_vci_decoder: false
+    residual_decoder: false
+    batch_encoder: true
+    nb_decoder: false
+    mask_attn: false
+    use_effect_gating_token: false
+    distributional_loss: energy
+    init_from: /large_storage/ctc/userspace/aadduri/preprint_parse/parse_donor_tahoe_best_cs512_2000_hvg/parse_donor_tahoe_best_2000/checkpoints/step=100000.ckpt
+    transformer_backbone_key: llama
+    transformer_backbone_kwargs:
+      max_position_embeddings: 512
+      hidden_size: 1440
+      intermediate_size: 4416
+      num_hidden_layers: 4
+      num_attention_heads: 12
+      num_key_value_heads: 12
+      head_dim: 120
+      use_cache: false
+      attention_dropout: 0.0
+      hidden_dropout: 0.0
+      layer_norm_eps: 1.0e-06
+      pad_token_id: 0
+      bos_token_id: 1
+      eos_token_id: 2
+      tie_word_embeddings: false
+      rotary_dim: 0
+      use_rotary_embeddings: false
+training:
+  wandb_track: false
+  weight_decay: 0.0005
+  batch_size: 32
+  lr: 0.0001
+  max_steps: 10
+  train_seed: 42
+  val_freq: 100
+  ckpt_every_n_steps: 1
+  gradient_clip_val: 10
+  loss_fn: mse
+wandb:
+  entity: arcinstitute
+  project: vci1
+  local_wandb_dir: /large_storage/ctc/userspace/aadduri/wandb_dir/vci1
+  tags:
+  - parse_fig2_final_donor
+name: cs512
+output_dir: /large_storage/ctc/userspace/aadduri/preprint/parse_fig2_release
+use_wandb: true
+overwrite: false
+return_adatas: false
+pred_adata_path: null
+true_adata_path: null

final.ckpt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0ba94d612de1e5d78cc21396563d656bec06461066f7a6e1f727b68da6247241
+size 1812212909

pert_onehot_map.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d346acd0d271e5a7a4fbc9d9416dcaabc523577e7e19c406ac3f64fd857c8509
+size 49953

var_dims.pkl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a6ffd1b9eb4e1e36cd329c3d24950d272eae7010b93e2e8907622c4f454daeb4
+size 25675

wandb_path.txt

@@ -0,0 +1 @@
+arcinstitute/vci1/7t6pdont