Benchmarking AI Agents for Addressing Scientific Challenges Across Scales | Paper Citation Record

Observation b8259101-55f5-4db5-a8dd-d1f7ba06358e · outbound

This paper cites A Survey of Large Language Models.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales A Survey of Large Language Models

Reference 1

Resolution: verified exact; local_arxiv, observed 2026-07-03T11:28:04.338527Z

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Observation 1a195998-a7d6-4128-9d46-013431692892 · outbound

This paper cites Agentic AI for Scientific Discovery: A Survey of Progress, Challenges, and Future Directions.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Agentic AI for Scientific Discovery: A Survey of Progress, Challenges, and Future Directions

Reference 2

Resolution: verified exact; arxiv_id, observed 2026-07-03T11:28:04.348973Z

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Observation 088a97c0-14d2-497f-9984-1e607d3e5aa6 · outbound

This paper cites LitLLMs, LLMs for Literature Review: Are we there yet?.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales LitLLMs, LLMs for Literature Review: Are we there yet?

Reference 3

Resolution: verified exact; arxiv_id, observed 2026-07-03T11:28:04.343776Z

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Observation dd5bc914-07b7-4c27-a089-0ce97549ab87 · outbound

This paper cites Biomni: A general-purpose biomedical ai agent.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Biomni: A general-purpose biomedical ai agent

Reference 4

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Observation 600917a4-13a8-4f83-ab31-bb6312461346 · outbound

This paper cites Accelerating scientific discovery with autonomous goal-evolving agents.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Accelerating scientific discovery with autonomous goal-evolving agents

Reference 5

Resolution: verified exact; arxiv_id, observed 2026-07-03T11:28:04.346399Z

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Observation ba1a6bda-91d8-410c-b1ae-48d5ac888d87 · outbound

This paper cites Deep Research: A Survey of Autonomous Research Agents.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Deep Research: A Survey of Autonomous Research Agents

Reference 6

Resolution: verified exact; arxiv_id, observed 2026-07-03T11:28:04.336232Z

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Observation 8e008be9-ea43-4540-b451-d912f36af72a · outbound

This paper cites Deep research, 2026.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Deep research, 2026

Reference 7

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Observation b701393d-a93c-4efa-baa8-94a26fd38252 · outbound

This paper cites Towards an AI co-scientist.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Towards an AI co-scientist

Reference 8

Resolution: verified exact; local_arxiv, observed 2026-07-03T11:28:04.341255Z

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Observation 0f5d57e1-289b-4fba-acb2-687d1f7d06fe · outbound

This paper cites Towards end-to-end automation of ai research.Nature, 651(8107):914– 919, 2026.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Towards end-to-end automation of ai research.Nature, 651(8107):914– 919, 2026

Reference 9

Resolution: unresolved; no resolver link, observed 2026-06-27T09:34:09.347912Z

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Observation f0159f58-24b5-4553-9241-6c3ee423cf9e · outbound

This paper cites Sciarena: An open evaluation platform for foundation models in scientific literature tasks.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Sciarena: An open evaluation platform for foundation models in scientific literature tasks

Reference 10

Resolution: verified exact; arxiv_id, observed 2026-07-03T11:28:04.338521Z

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Observation f04ef476-8bc0-4a0f-a835-959f2171633b · outbound

This paper cites Evaluating Large Language Models in Scientific Discovery.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Evaluating Large Language Models in Scientific Discovery

Reference 11

Resolution: verified exact; local_arxiv, observed 2026-07-03T11:28:04.340950Z

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Observation 4a5d332b-b3ee-410f-93d2-9b9884877e8d · outbound

This paper cites SciAgentGym: Benchmarking Multi-Step Scientific Tool-use in LLM Agents.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales SciAgentGym: Benchmarking Multi-Step Scientific Tool-use in LLM Agents

Reference 12

Resolution: verified exact; local_arxiv, observed 2026-07-03T11:28:04.327347Z

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Observation ff7e7173-a328-489a-ab36-fd765d9adce3 · outbound

This paper cites Scienceagentbench: Toward rigorous assessment of lan- guage agents for data-driven scientific discovery.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Scienceagentbench: Toward rigorous assessment of lan- guage agents for data-driven scientific discovery

Reference 13

Resolution: unresolved; no resolver link, observed 2026-06-27T09:34:09.347912Z

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Observation 553f385b-2b83-4ad6-a73c-6cc75e7d4b7b · outbound

This paper cites DSAEval: Evaluating Data Science Agents on a Wide Range of Real-World Data Science Problems.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales DSAEval: Evaluating Data Science Agents on a Wide Range of Real-World Data Science Problems

Reference 14

Resolution: verified exact; local_arxiv, observed 2026-07-03T11:28:04.291631Z

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Observation 7e925725-5fc0-46b5-be9b-592b10bde736 · outbound

This paper cites Towards artificial intelligence research assistant for expert- involved learning.arXiv e-prints, pages arXiv–2505, 2025.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Towards artificial intelligence research assistant for expert- involved learning.arXiv e-prints, pages arXiv–2505, 2025

Reference 15

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Observation 9362f5de-c93a-4a7d-ae64-b221944a01d1 · outbound

This paper cites MLGym: A New Framework and Benchmark for Advancing AI Research Agents.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales MLGym: A New Framework and Benchmark for Advancing AI Research Agents

Reference 16

Resolution: verified exact; arxiv_id, observed 2026-07-03T11:28:04.333266Z

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Observation 56092da5-4202-4570-9163-10b947328fdd · outbound

This paper cites AstaBench: Rigorous Benchmarking of AI Agents with a Scientific Research Suite.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales AstaBench: Rigorous Benchmarking of AI Agents with a Scientific Research Suite

Reference 17

Resolution: verified exact; local_arxiv, observed 2026-07-03T11:28:04.310517Z

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Observation a10943d5-5986-47d0-b08f-af1485fff674 · outbound

This paper cites Math- arena: Evaluating llms on uncontaminated math competitions.Proceedings of the Neural In- formation Processing Systems Track on Datasets and Benchmark, 2025.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Math- arena: Evaluating llms on uncontaminated math competitions.Proceedings of the Neural In- formation Processing Systems Track on Datasets and Benchmark, 2025

Reference 18

Resolution: unresolved; no resolver link, observed 2026-06-27T09:34:09.347912Z

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Observation c96cd293-1f29-4ad6-9861-02b6fd469efc · outbound

This paper cites Folio: Natural language reasoning with first-order logic.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Folio: Natural language reasoning with first-order logic

Reference 19

Resolution: unresolved; no resolver link, observed 2026-06-27T09:34:09.347912Z

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Observation 21963a0a-9564-4c7f-aea3-eb4b14b5e50f · outbound

This paper cites Scicode: Aresearchcodingbenchmarkcurated by scientists.Advances in Neural Information Processing Systems, 37:30624–30650, 2024.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Scicode: Aresearchcodingbenchmarkcurated by scientists.Advances in Neural Information Processing Systems, 37:30624–30650, 2024

Reference 20

Resolution: unresolved; no resolver link, observed 2026-06-27T09:34:09.347912Z

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Observation 99da8693-c011-4921-b465-a555ee035378 · outbound

This paper cites Swe-bench: Can language models resolve real-world github issues? In12th International Conference on Learning Representations, ICLR 2024, 2024.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Swe-bench: Can language models resolve real-world github issues? In12th International Conference on Learning Representations, ICLR 2024, 2024

Reference 21

Resolution: unresolved; no resolver link, observed 2026-06-27T09:34:09.347912Z

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Observation 529876cb-7e68-4b3b-829f-3462d464144a · outbound

This paper cites Gpqa: A graduate-level google-proof q&a benchmark.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Gpqa: A graduate-level google-proof q&a benchmark

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Observation 9a08d040-a7a7-4200-91ae-a4f4aa5a038c · outbound

This paper cites Sci- enceqa: A novel resource for question answering on scholarly articles.International Journal on Digital Libraries, 23(3):289–301, 2022.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Sci- enceqa: A novel resource for question answering on scholarly articles.International Journal on Digital Libraries, 23(3):289–301, 2022

Reference 23

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Observation 50afc11a-25bb-4b6b-8cb1-10787b21df8c · outbound

This paper cites Bioml-bench: Evaluation of ai agents for end-to-end biomedical ml.bioRxiv, pages 2025–09, 2025.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Bioml-bench: Evaluation of ai agents for end-to-end biomedical ml.bioRxiv, pages 2025–09, 2025

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Observation 315a4652-06d2-4831-b664-e6e93b8a9085 · outbound

This paper cites Laurent, Alex Andonian, Benjamin Tenmann, Siddharth Narayanan, Geemi P.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Laurent, Alex Andonian, Benjamin Tenmann, Siddharth Narayanan, Geemi P

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Resolution: metadata mismatch; arxiv_id, observed 2026-07-03T11:28:04.330097Z

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Observation 0748f54e-9bd7-4dd7-b87e-6396f5f72a73 · outbound

This paper cites Benchmarking AI scientists for omics data driven biological discovery, January 2026.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Benchmarking AI scientists for omics data driven biological discovery, January 2026

Reference 26

Resolution: verified exact; arxiv_id, observed 2026-07-03T11:28:04.324765Z

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Observation 8b664837-551b-459e-81df-26f25a486e02 · outbound

This paper cites Agentic systems are adept at solving well-scoped, verifiable problems in computational biol- ogy.bioRxiv, pages 2026–04, 2026.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Agentic systems are adept at solving well-scoped, verifiable problems in computational biol- ogy.bioRxiv, pages 2026–04, 2026

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Observation 3de0e178-5756-4c2a-a079-63bde3a98fdd · outbound

This paper cites Terminal-Bench: Benchmarking Agents on Hard, Realistic Tasks in Command Line Interfaces.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Terminal-Bench: Benchmarking Agents on Hard, Realistic Tasks in Command Line Interfaces

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Observation c8948f2d-7d86-43eb-a377-4739ecd912f1 · outbound

This paper cites Gpt-5.2 system card.https://openai.com/index/ gpt-5-system-card-update-gpt-5-2/, 2025.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Gpt-5.2 system card.https://openai.com/index/ gpt-5-system-card-update-gpt-5-2/, 2025

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Observation 6da83e22-cd74-44ba-bf2d-78effa85f7c6 · outbound

This paper cites Single cell analysis: the new frontier in ‘omics’.Trends in biotechnology, 28(6):281–290, 2010.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Single cell analysis: the new frontier in ‘omics’.Trends in biotechnology, 28(6):281–290, 2010

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Observation dfdd5bf7-a383-4c5e-9008-8f26cf163182 · outbound

This paper cites The dawn of spatial omics.Science, 381(6657):eabq4964, 2023.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales The dawn of spatial omics.Science, 381(6657):eabq4964, 2023

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Observation b1058408-fd27-4ac1-99cc-ead4eb2a48cb · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales The role of ai in drug discovery: challenges, opportunities, and strategies.Pharmaceuticals, 16(6):891, 2023

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Observation 330a8842-b1d8-4b29-8527-79d866c88594 · outbound

This paper cites From real-world electronic health record data to real- world results using artificial intelligence.Annals of the Rheumatic Diseases, 82(3):306–311, 2023.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales From real-world electronic health record data to real- world results using artificial intelligence.Annals of the Rheumatic Diseases, 82(3):306–311, 2023

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Observation 23434c61-7c97-42f9-a30c-39ee65ad8222 · outbound

This paper cites Engineeringaico-scientistsforstatisticalgeneticsapplications.NatureGenetics, pages 1–4, 2026.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Engineeringaico-scientistsforstatisticalgeneticsapplications.NatureGenetics, pages 1–4, 2026

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Observation 668bcba0-af3f-40f2-9183-a4f14f561020 · outbound

This paper cites Gemini 3 pro.https://storage.googleapis.com/deepmind-media/ Model-Cards/Gemini-3-Pro-Model-Card.pdf, 2025.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Gemini 3 pro.https://storage.googleapis.com/deepmind-media/ Model-Cards/Gemini-3-Pro-Model-Card.pdf, 2025

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Observation 77dfcb97-c447-4315-9375-1ee781235bef · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Claude sonnet 4.6.https://docs.anthropic.com/, 2025

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Observation b1a5af43-ed15-4cd5-8cd4-84db79b8e9a7 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Democratizing ai scientists using tooluniverse

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Observation 4be6a72b-6657-4761-88c1-432abf119860 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales ChatGPT Codex.https://chatgpt.com/codex/, 2026

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Observation d0db7148-67a6-49b9-8983-f7a067bc59aa · outbound

This paper cites Claude Code Overview.https://code.claude.com/docs/en/overview,.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Claude Code Overview.https://code.claude.com/docs/en/overview,

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Observation 617f3523-3977-4070-89c5-ce9014c1d5c3 · outbound

This paper cites an unresolved cited work.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Unresolved cited work

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Observation adee86f9-1ec0-4355-9f90-69ac4221b11e · outbound

This paper cites Cellforge: Agentic design of virtual cell models.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Cellforge: Agentic design of virtual cell models

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Resolution: verified exact; arxiv_id, observed 2026-07-03T11:28:04.303818Z

Source-reported events for the cited work

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Observation 9bf35853-3532-4146-ac8b-c6506a539959 · outbound

This paper cites Stella: Towards a biomedical world model with self-evolving multimodal agents.bioRxiv, pages 2025–07, 2025.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Stella: Towards a biomedical world model with self-evolving multimodal agents.bioRxiv, pages 2025–07, 2025

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Observation e47f8139-7e4d-46a9-b4ee-6331d5daabe7 · outbound

This paper cites An aiagentforfullyautomatedmulti-omic analyses.Advanced Science, 11(44):2407094, 2024.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales An aiagentforfullyautomatedmulti-omic analyses.Advanced Science, 11(44):2407094, 2024

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Observation d783677c-0ca6-4653-a4dd-e3df20cff5d4 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Txagent: An ai agent for therapeutic reason- ing across a universe of tools, 2025

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Observation 7e12e0c1-88ca-48a9-a472-822d645d7391 · outbound

This paper cites Medea: An omics ai agent for therapeutic discovery.bioRxiv, pages 2026–01, 2026.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Medea: An omics ai agent for therapeutic discovery.bioRxiv, pages 2026–01, 2026

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Observation 04de898a-1581-4892-86fe-39d3b055811a · outbound

This paper cites McNaughton, Gautham Ramalaxmi, Agustin Kruel, Carter R.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales McNaughton, Gautham Ramalaxmi, Agustin Kruel, Carter R

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Resolution: unresolved; no resolver link, observed 2026-06-27T09:34:09.347912Z

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Observation 613b0965-c0f1-4d38-ae0f-f0dc55811996 · outbound

This paper cites Baker, Ziru Chen, Garrett Herb, Boyu Gou, Daniel Adu-Ampratwum, Xia Ning, and Huan Sun.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Baker, Ziru Chen, Garrett Herb, Boyu Gou, Daniel Adu-Ampratwum, Xia Ning, and Huan Sun

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Resolution: unresolved; no resolver link, observed 2026-06-27T09:34:09.347912Z

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Observation f510318c-5137-47d2-81f3-90951a675d28 · outbound

This paper cites Dru- gagent: Automating ai-aided drug discovery programming through llm multi-agent collabo- ration, 2025.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Dru- gagent: Automating ai-aided drug discovery programming through llm multi-agent collabo- ration, 2025

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Observation 64d3bb45-553a-4fa9-9a34-07ff4e60dfeb · outbound

This paper cites LIDDIA:Language-basedintelligent drug discovery agent.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales LIDDIA:Language-basedintelligent drug discovery agent

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Observation 8641f270-591d-43db-ae5f-ed3ca4757fc6 · outbound

This paper cites An auditable agent platform for automated molec- ular optimisation, 2025.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales An auditable agent platform for automated molec- ular optimisation, 2025

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Observation 4a4d8a91-1211-4b2c-ba66-65be7ec732fa · outbound

This paper cites Mragent: an llm-based automated agent for causal knowledge discovery in disease via mendelian randomization.Briefings in Bioinformat- ics, 26(2):bbaf140, 03 2025.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Mragent: an llm-based automated agent for causal knowledge discovery in disease via mendelian randomization.Briefings in Bioinformat- ics, 26(2):bbaf140, 03 2025

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Observation 17343a56-8c74-42e7-ad42-aa166b8dabfa · outbound

This paper cites an unresolved cited work.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Unresolved cited work

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Observation fab4e75a-be5e-4d9b-85f5-f2fb9b1be29d · outbound

This paper cites Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development

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Observation bfb616ab-e596-4eed-bc2a-6377649a02dd · outbound

This paper cites Patrícia Bento, Jon Chambers, Marleen De Veij, Eloy Félix, María Paula Magariños, Juan F.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Patrícia Bento, Jon Chambers, Marleen De Veij, Eloy Félix, María Paula Magariños, Juan F

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Observation 102f6667-1697-49a8-9603-1ba3cd6f4499 · outbound

This paper cites Gilson, Tiqing Liu, Michael Baitaluk, George Nicola, Linda Hwang, and Jenny Chong.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Gilson, Tiqing Liu, Michael Baitaluk, George Nicola, Linda Hwang, and Jenny Chong

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Observation f7db43d9-64de-4c1d-b255-d6d033d859cf · outbound

This paper cites Baell and Georgina A.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Baell and Georgina A

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Observation 52544215-78bc-4bff-b560-a82e66694bd4 · outbound

This paper cites Guacamol: bench- marking models for de novo molecular design.Journal of chemical information and modeling, 59(3):1096–1108, 2019.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Guacamol: bench- marking models for de novo molecular design.Journal of chemical information and modeling, 59(3):1096–1108, 2019

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Observation d25ba20f-586f-49c8-9dd7-e780175ead72 · outbound

This paper cites Clustering with the average silhouette width.Computa- tional Statistics & Data Analysis, 158:107190, 2021.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Clustering with the average silhouette width.Computa- tional Statistics & Data Analysis, 158:107190, 2021

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Observation 3731c4e3-fd97-4cb0-9013-4d41747f0551 · outbound

This paper cites Fast, sensitive and accu- rate integration of single-cell data with harmony.Nature methods, 16(12):1289–1296, 2019.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Fast, sensitive and accu- rate integration of single-cell data with harmony.Nature methods, 16(12):1289–1296, 2019

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Observation c0df6c65-78fa-4f84-8671-38fb5698cca2 · outbound

This paper cites Deep genera- tive modeling for single-cell transcriptomics.Nature methods, 15(12):1053–1058, 2018.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Deep genera- tive modeling for single-cell transcriptomics.Nature methods, 15(12):1053–1058, 2018

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Observation c36c01c4-ee24-4ba4-9b37-e1ac4617c036 · outbound

This paper cites Moderated estimation of fold change and dispersion for rna-seq data with deseq2.Genome biology, 15(12):550, 2014.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Moderated estimation of fold change and dispersion for rna-seq data with deseq2.Genome biology, 15(12):550, 2014

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Observation c3e2b1d2-05b6-4441-b792-ba9aa3fc270c · outbound

This paper cites Modelingandpredicting single-cell multi-gene perturbation responses with sclambda.bioRxiv, 2024.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Modelingandpredicting single-cell multi-gene perturbation responses with sclambda.bioRxiv, 2024

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Observation 4b532c6b-43b2-4a10-850f-d11566b74b98 · outbound

This paper cites Ibarra, Olle Holmberg, Isaac Virshup, Mohammad Lotfollahi, Sabrina Richter, and Fabian J.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Ibarra, Olle Holmberg, Isaac Virshup, Mohammad Lotfollahi, Sabrina Richter, and Fabian J

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Observation 9ec60ada-d6b1-4b21-8988-c3e3c81eb109 · outbound

This paper cites Jensen, Lars J.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Jensen, Lars J

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Observation 8c40edc0-b1f5-40d2-9369-f91eec6f6acf · outbound

This paper cites an unresolved cited work.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Unresolved cited work

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Observation ee1970ea-252e-4d0c-af3e-f07904250025 · outbound

This paper cites an unresolved cited work.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Unresolved cited work

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Observation 67aecde7-0822-4000-abf6-709abef1fd1e · outbound

This paper cites Polygenic prediction via bayesian regression and continuous shrinkage priors.Nature communications, 10(1):1776, 2019.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Polygenic prediction via bayesian regression and continuous shrinkage priors.Nature communications, 10(1):1776, 2019

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Observation 0dcf3c46-6da8-487b-bf77-98479149e3c7 · outbound

This paper cites Martin, Shengying Qin, Hail- iang Huang, and Tian Ge.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Martin, Shengying Qin, Hail- iang Huang, and Tian Ge

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Observation 0d42cd2d-fd76-4a08-bea6-9b0e22f788d6 · outbound

This paper cites The gtex consortium atlas of genetic regulatory effects across human tissues.Science, 369(6509):1318–1330, 2020.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales The gtex consortium atlas of genetic regulatory effects across human tissues.Science, 369(6509):1318–1330, 2020

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Observation e454e79f-712d-402d-b502-46cca5057be1 · outbound

This paper cites On the art of compilingandusing’drug-like’chemicalfragmentspaces.ChemMedChem, 3(10):1503–1507, October 2008.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales On the art of compilingandusing’drug-like’chemicalfragmentspaces.ChemMedChem, 3(10):1503–1507, October 2008

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Observation 67aabd72-7739-46bb-880c-98eb1c069449 · outbound

This paper cites conda: Asystem-level,binarypackageandenvironmentmanagerrunning on all major operating systems and platforms.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales conda: Asystem-level,binarypackageandenvironmentmanagerrunning on all major operating systems and platforms

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Observation 41524d9a-e7ef-4319-9bec-7cd0b7606044 · outbound

This paper cites an unresolved cited work.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Unresolved cited work

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Observation f48e4184-02e9-4d6d-b491-b8f92ab13a3b · outbound

This paper cites Shoemaker, Paul A.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Shoemaker, Paul A

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Observation 04549f40-8815-416c-bd01-356d7725b572 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales ChEBI in 2016: Improved services and an expanding collection of metabolites.Nucleic Acids Research, 44(D1):D1214–1219, January 2016

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Observation c1a3a50f-027b-4795-8fe2-e0943d777f6e · outbound

This paper cites Irwin and Brian K.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Irwin and Brian K

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Observation 6a56dd84-a1af-438f-899f-4633387692a6 · outbound

This paper cites A clinical road map for single-cell omics.Cell, 188(14):3633–3647, 2025.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales A clinical road map for single-cell omics.Cell, 188(14):3633–3647, 2025

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Observation c03d2ab1-6a30-4cac-9b0f-5e7ff764a0ae · outbound

This paper cites Single- cell rna sequencing technologies and applications: a brief overview.Clinical and translational medicine, 12(3):e694, 2022.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Single- cell rna sequencing technologies and applications: a brief overview.Clinical and translational medicine, 12(3):e694, 2022

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Observation 0c0b2c54-31fd-419f-a2aa-23cc7e028f4c · outbound

This paper cites Scanpy: large-scale single-cell gene expression data analysis.Genome biology, 19(1):15, 2018.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Scanpy: large-scale single-cell gene expression data analysis.Genome biology, 19(1):15, 2018

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Observation 24bebf7e-9378-4f0d-8e1c-fb4e0df90e6c · outbound

This paper cites Benchmarking atlas-level data integration in single-cell genomics.Nature methods, 19(1):41–50, 2022.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Benchmarking atlas-level data integration in single-cell genomics.Nature methods, 19(1):41–50, 2022

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Observation fd99c5b7-4140-4bf9-a806-d7bcc158efb2 · outbound

This paper cites Scikit- learn: Machine learning in python.the Journal of machine Learning research, 12:2825–2830, 2011.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Scikit- learn: Machine learning in python.the Journal of machine Learning research, 12:2825–2830, 2011

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Observation 980f398e-abf9-449d-b9a5-40608757f5e8 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales A single- cell transcriptomic map of the human and mouse pancreas reveals inter-and intra-cell popu- lation structure.Cell systems, 3(4):346–360, 2016

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Observation 33c79c83-26b0-4989-9f87-864fbc8d9d7a · outbound

This paper cites A single-cell transcriptome atlas of the human pancreas.Cell systems, 3(4):385–394, 2016.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales A single-cell transcriptome atlas of the human pancreas.Cell systems, 3(4):385–394, 2016

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Observation 74429ba3-2bbb-49e2-9dac-4eeb073735a4 · outbound

This paper cites Single-celltranscriptomeprofilingofhumanpancreaticisletsinhealthandtype 2 diabetes.Cell metabolism, 24(4):593–607, 2016.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Single-celltranscriptomeprofilingofhumanpancreaticisletsinhealthandtype 2 diabetes.Cell metabolism, 24(4):593–607, 2016

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Observation fb150495-64c9-49db-84ef-0eb28ee74c9a · outbound

This paper cites Single-cell transcriptomics of the human endocrine pancreas.Diabetes, 65(10):3028–3038, 2016.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Single-cell transcriptomics of the human endocrine pancreas.Diabetes, 65(10):3028–3038, 2016

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Observation 0aa1aec8-36c4-4206-be04-d5c19c51b206 · outbound

This paper cites Rnasequencingofsinglehumanislet cells reveals type 2 diabetes genes.Cell metabolism, 24(4):608–615, 2016.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Rnasequencingofsinglehumanislet cells reveals type 2 diabetes genes.Cell metabolism, 24(4):608–615, 2016

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Observation 97a6c801-f9f1-4754-8f3b-dd082921c988 · outbound

This paper cites Massively parallel digital transcriptional profiling of single cells.Nature communications, 8(1):14049, 2017.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Massively parallel digital transcriptional profiling of single cells.Nature communications, 8(1):14049, 2017

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Observation ca31f499-820f-4662-88c0-b79af47e388c · outbound

This paper cites Cells of the adult human heart.Nature, 588(7838):466–472, 2020.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Cells of the adult human heart.Nature, 588(7838):466–472, 2020

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Observation 6feb7bce-06b3-4ccd-9657-065facf245f9 · outbound

This paper cites Cellmarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scrna-seq data.Nucleic acids research, 51(D1):D870–D876, 2023.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Cellmarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scrna-seq data.Nucleic acids research, 51(D1):D870–D876, 2023

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Observation 9cd7ddcd-a1b3-43e0-9363-acea5e4f0ba1 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Beyond visual inspection: Principled benchmarkingofsingle-celltrajectoryrepresentationswithscTRAM

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Observation 3a184e11-0187-461f-bee8-dd8309b3a583 · outbound

This paper cites Mapping the developing human immune system across organs.Science, 376(6597):eabo0510, 2022.

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Mapping the developing human immune system across organs.Science, 376(6597):eabo0510, 2022

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Observation 5470faf5-a35f-4c42-8f62-b014f05832eb · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Evaluating the utilities of foundation models in single-cell data analysis.Advanced Science, page e14490, 2026

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Observation ee1700f3-2b89-4678-8476-97241784c320 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Exploring genetic interaction manifolds con- structed from rich single-cell phenotypes.Science, 365(6455):786–793, 2019

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Observation 9eb5fe85-e85e-4307-85ca-90888530569d · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales A multiplexed single-cell crispr screening platform enables systematic dissection of the unfolded protein re- sponse.Cell, 167(7):1867–1882, 2016

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Observation 5ee31a12-6aca-4df4-a8af-77099e0e51b4 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Mapping information-rich genotype-phenotype landscapes with genome-scale perturb- seq.Cell, 185(14):2559–2575, 2022

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Observation 78b84fb2-feb0-4e0f-9907-487fd2120bc9 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Fischer, Anna C

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Observation 2883c955-171f-4085-8178-251e4bb7c028 · outbound

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Observation 23c9c5c4-cf50-4aa9-8d8d-1710f76f7a06 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Spotiphy enables single-cell spatial whole transcriptomics across an entire section.Nature Methods, 22(4):724–736, 4 2025

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Observation 4071ec9f-c393-4b6c-a482-11358f70579a · outbound

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Observation a8a02bfa-e247-4ec6-98fe-155b871e1631 · outbound

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Benchmarking AI Agents for Addressing Scientific Challenges Across Scales Huuki-Myers, Abby Spangler, Nicholas J

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Observation 0b6be691-0a2f-45dd-9e4c-049771da2d1f · outbound

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Pith citing papers