PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects | Paper Citation Record

Observation 4583ad63-b771-47db-a862-9d273c9d33d3 · outbound

This paper cites Predicting cellular responses to perturbation across diverse contexts with state.BioRxiv, 2025.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Predicting cellular responses to perturbation across diverse contexts with state.BioRxiv, 2025

Reference 1

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Observation aa8e8a0c-4ef1-429d-8964-92ec3887115b · outbound

This paper cites Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines.Nature Methods, 22(8):1657–1661, 2025.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines.Nature Methods, 22(8):1657–1661, 2025

Reference 2

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Observation dd32c8c0-1475-4079-8949-bbe5d1d5e4d0 · outbound

This paper cites Bachman, Benjamin M.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Bachman, Benjamin M

Reference 3

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Observation a10a2af2-1614-4340-8bfa-9c9ee839c3b6 · outbound

This paper cites On the adaptive control of the false discovery rate in multiple testing with independent statistics.Journal of educational and Behavioral Statistics, 25(1):60–83, 2000.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects On the adaptive control of the false discovery rate in multiple testing with independent statistics.Journal of educational and Behavioral Statistics, 25(1):60–83, 2000

Reference 4

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Observation a5ff04c4-f80b-4864-b17b-054d0ee30048 · outbound

This paper cites Building a knowledge graph to enable precision medicine.Scientific data, 10(1):67, 2023.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Building a knowledge graph to enable precision medicine.Scientific data, 10(1):67, 2023

Reference 5

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Observation bb2b6485-b29e-4560-9401-69fbd32fba6d · outbound

This paper cites Scaling instruction-finetuned language models.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Scaling instruction-finetuned language models

Reference 6

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Observation b73e982f-9f72-441b-bb24-2bac40ab5430 · outbound

This paper cites scgpt: toward building a foundation model for single-cell multi-omics using generative ai.Nature methods, 21(8): 1470–1480, 2024.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects scgpt: toward building a foundation model for single-cell multi-omics using generative ai.Nature methods, 21(8): 1470–1480, 2024

Reference 7

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Observation c232dcbc-789b-42c0-838a-3e527551cf09 · outbound

This paper cites Interpretation, extrapolation and perturbation of single cells.Nature Reviews Genetics, pages 1–22, 2026.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Interpretation, extrapolation and perturbation of single cells.Nature Reviews Genetics, pages 1–22, 2026

Reference 8

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Observation 9825afce-0f88-4d48-9df7-077ff7db4467 · outbound

This paper cites Gene2vec: distributed representation of genes based on co-expression.BMC genomics, 20(Suppl 1):82, 2019.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Gene2vec: distributed representation of genes based on co-expression.BMC genomics, 20(Suppl 1):82, 2019

Reference 9

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This paper cites an unresolved cited work.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Unresolved cited work

Reference 10

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Observation d3ecf01a-a715-4402-a018-fce96266a620 · outbound

This paper cites scvae: variational auto-encoders for single-cell gene expression data.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects scvae: variational auto-encoders for single-cell gene expression data

Reference 11

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Observation 3882327b-c5c6-4cad-8bb3-da8d058d1bdc · outbound

This paper cites DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning

Reference 12

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Observation d7248a30-6205-4efd-99a1-feef3ba72eb8 · outbound

This paper cites Predicting cellular responses to novel drug perturbations at a single-cell resolution.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Predicting cellular responses to novel drug perturbations at a single-cell resolution

Reference 13

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Observation 8bb2365d-1194-4031-b5ae-1f45d0d598a2 · outbound

This paper cites Progressive Multi-Agent Reasoning for Biological Perturbation Prediction.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Progressive Multi-Agent Reasoning for Biological Perturbation Prediction

Reference 14

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Observation c891d55f-18eb-4bf0-8b97-3325d9aefa97 · outbound

This paper cites Biomistral: A collection of open-source pretrained large language models for medical domains,.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Biomistral: A collection of open-source pretrained large language models for medical domains,

Reference 15

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Observation 633e46a9-cacc-4ebe-a695-c5c4065b18d3 · outbound

This paper cites Cell2sentence: Teaching large language models the language of biology.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Cell2sentence: Teaching large language models the language of biology

Reference 16

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Observation cd608f7b-5e5f-4e6b-aa9b-17ca55550863 · outbound

This paper cites Retrieval- augmented generation for knowledge-intensive nlp tasks, 2021.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Retrieval- augmented generation for knowledge-intensive nlp tasks, 2021

Reference 17

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Observation 298ca102-6f9e-47ef-8266-7727c11622cc · outbound

This paper cites The molecular signatures database hallmark gene set collection.Cell systems, 1(6):417–425, 2015.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects The molecular signatures database hallmark gene set collection.Cell systems, 1(6):417–425, 2015

Reference 18

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Observation e594d734-8117-412a-bf87-16d96fa1c07f · outbound

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

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Deep generative modeling for single-cell transcriptomics.Nature methods, 15(12):1053–1058, 2018

Reference 19

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Observation 2b3f3297-78f4-4417-819f-3c5c2ba54fdb · outbound

This paper cites Predicting cellular responses to complex perturbations in high-throughput screens.Molecular Systems Biology, page e11517, 2023.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Predicting cellular responses to complex perturbations in high-throughput screens.Molecular Systems Biology, page e11517, 2023

Reference 20

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Observation 37f59868-fbd2-40b9-b4c0-83b149ffb4ef · outbound

This paper cites Biogpt: generative pre-trained transformer for biomedical text generation and mining.Briefings in Bioinformatics, 23(6), September 2022.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Biogpt: generative pre-trained transformer for biomedical text generation and mining.Briefings in Bioinformatics, 23(6), September 2022

Reference 21

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Observation f7a89469-efcd-43c1-82b7-77b0bb71fa0a · outbound

This paper cites Teaching small language models to reason.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Teaching small language models to reason

Reference 22

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Observation cd807c83-319f-49cb-a4f9-93d02abeb9bb · outbound

This paper cites Orca 2: Teaching Small Language Models How to Reason.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Orca 2: Teaching Small Language Models How to Reason

Reference 23

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Observation bfff660f-46e5-44ae-9ff5-389ff2ba1d05 · outbound

This paper cites Replogle, Angela N.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Replogle, Angela N

Reference 24

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Observation cdc05ae7-9b02-4c40-bd20-2cd053a9166a · outbound

This paper cites Identifying compound-protein interactions with knowledge graph embedding of perturbation transcriptomics.Cell genomics, 4(10), 2024.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Identifying compound-protein interactions with knowledge graph embedding of perturbation transcriptomics.Cell genomics, 4(10), 2024

Reference 25

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This paper cites URL https://www.biorxiv.org/content/early/2024/0 7/03/2024.07.03.601903.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects URL https://www.biorxiv.org/content/early/2024/0 7/03/2024.07.03.601903

Reference 26

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Observation d6377424-957c-44f1-8abd-51189d026a60 · outbound

This paper cites Obtaining genetics insights from deep learning via explainable artificial intelligence.Nature Reviews Genetics, 24(2):125–137, 2023.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Obtaining genetics insights from deep learning via explainable artificial intelligence.Nature Reviews Genetics, 24(2):125–137, 2023

Reference 27

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Observation cb50a269-d91b-467c-9477-e96544367eff · outbound

This paper cites Capabilities of GPT-4 on Medical Challenge Problems.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Capabilities of GPT-4 on Medical Challenge Problems

Reference 28

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Observation 95b33ef1-7291-4499-a07c-5ec7edbcd5bf · outbound

This paper cites scperturb: harmonized single-cell perturbation data.Nature Methods, 21(3):531–540, 2024.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects scperturb: harmonized single-cell perturbation data.Nature Methods, 21(3):531–540, 2024

Reference 29

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Observation 2fe3b507-3cb5-4e63-bfe5-1e5d5dcafb3f · outbound

This paper cites Paull, Daniel E.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Paull, Daniel E

Reference 30

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Observation dcecc708-2312-44ff-a1a1-f93df4579c55 · outbound

This paper cites Tracking biological hallucinations in single-cell perturbation predictions using scarchon, a comprehensive benchmarking platform.bioRxiv, 2025.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Tracking biological hallucinations in single-cell perturbation predictions using scarchon, a comprehensive benchmarking platform.bioRxiv, 2025

Reference 31

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Observation eabf3c39-65fe-4db4-8ca6-a809b27e5dd2 · outbound

This paper cites Prada-Medina, Rory Donovan-Maiye, and Kaspar Märtens.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Prada-Medina, Rory Donovan-Maiye, and Kaspar Märtens

Reference 32

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Observation 0fdb41cf-fbd5-4670-ac7e-012afa3729d2 · outbound

This paper cites Replogle, Reuben A.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Replogle, Reuben A

Reference 33

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Observation b6214258-b8d6-4378-9e17-7bbb02dfe053 · outbound

This paper cites Deepspeed: System optimizations enable training deep learning models with over 100 billion parameters.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Deepspeed: System optimizations enable training deep learning models with over 100 billion parameters

Reference 34

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Observation 643be723-6c21-45c3-bf5b-4ba03509fabe · outbound

This paper cites Universal cell embeddings: A foundation model for cell biology.BioRxiv, 2023.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Universal cell embeddings: A foundation model for cell biology.BioRxiv, 2023

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This paper cites Predicting transcriptional outcomes of novel multigene perturbations with gears.Nature Biotechnology, 42(6):927–935, 2024.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Predicting transcriptional outcomes of novel multigene perturbations with gears.Nature Biotechnology, 42(6):927–935, 2024

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Observation bdded0a2-939f-46ef-b672-af3a59736e8d · outbound

This paper cites Large Language Models Encode Clinical Knowledge.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Large Language Models Encode Clinical Knowledge

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Observation 66622f37-56d7-4fed-bf2c-fc86398bd4e6 · outbound

This paper cites DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models

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Observation d7d4c596-46a5-4d03-976e-1ad5dbe67c49 · outbound

This paper cites Srivatsan, José L.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Srivatsan, José L

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Observation 8cd87fc9-062e-47f8-8649-48c06afc7fa0 · outbound

This paper cites Pfohl, Heather Cole-Lewis, Darlene Neal, Qazi Mamunur Rashid, Mike Schaekermann, Amy Wang, Dev Dash, Jonathan H.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Pfohl, Heather Cole-Lewis, Darlene Neal, Qazi Mamunur Rashid, Mike Schaekermann, Amy Wang, Dev Dash, Jonathan H

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Observation c991fa16-2fd6-4ce5-b3d2-4b51b082c51c · outbound

This paper cites Mas-Rosario, Rico Meinl, Jalil Nourisa, Jared Tumiel, Tin M.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Mas-Rosario, Rico Meinl, Jalil Nourisa, Jared Tumiel, Tin M

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Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:19.915979Z

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Observation 9f1ee291-8cbd-4d8e-ae1f-04d3f6aad519 · outbound

This paper cites KGARevion: An AI agent for knowledge-intensive biomedical QA.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects KGARevion: An AI agent for knowledge-intensive biomedical QA

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Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:19.803087Z

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Observation f88f7fb6-94ff-48c7-83b4-8354aa1d3e12 · outbound

This paper cites Theodoris, Ling Xiao, Anant Chopra, Mark D.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Theodoris, Ling Xiao, Anant Chopra, Mark D

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Observation 92d3de41-ea69-451f-9a62-e47603c0fcd6 · outbound

This paper cites Inductive relation prediction by subgraph reasoning.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Inductive relation prediction by subgraph reasoning

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Observation 72073491-82de-4b20-a121-4aa5d68b2df8 · outbound

This paper cites TRL: Transformers Reinforcement Learning,.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects TRL: Transformers Reinforcement Learning,

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Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:20.414913Z

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Observation c383d808-55cc-49ac-9efd-8cd5d9c01e01 · outbound

This paper cites Omnipath: guidelines and gateway for literature-curated signaling pathway resources.Nature methods, 13(12):966–967, 2016.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Omnipath: guidelines and gateway for literature-curated signaling pathway resources.Nature methods, 13(12):966–967, 2016

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Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:20.280967Z

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Observation feaf4de5-3917-4641-99e5-7f21562a0ff2 · outbound

This paper cites Benchmarking algorithms for generalizable single-cell perturbation response prediction.Nature Methods, pages 1–14, 2025.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Benchmarking algorithms for generalizable single-cell perturbation response prediction.Nature Methods, pages 1–14, 2025

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Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.037047Z

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Observation 737f72ec-558c-421d-b15d-acb33a8984ee · outbound

This paper cites TxPert: Leveraging Biochemical Relationships for Out-of-Distribution Transcriptomic Perturbation Prediction.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects TxPert: Leveraging Biochemical Relationships for Out-of-Distribution Transcriptomic Perturbation Prediction

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Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.134900Z

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Observation 5b6b2890-f688-4a9b-a602-84a17e774a0f · outbound

This paper cites Chain-of-thought prompting elicits reasoning in large language models.Advances in neural information processing systems, 35:24824–24837, 2022.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Chain-of-thought prompting elicits reasoning in large language models.Advances in neural information processing systems, 35:24824–24837, 2022

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Observation e77c2f46-154a-4601-936e-0a6fff24194a · outbound

This paper cites Individual comparisons by ranking methods.Biometrics bulletin, 1(6):80–83, 1945.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Individual comparisons by ranking methods.Biometrics bulletin, 1(6):80–83, 1945

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Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.270541Z

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Observation f6cb5a3d-1745-4d4c-8c4b-1b746cab2f7d · outbound

This paper cites Contextualizing biological perturbation experiments through language.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Contextualizing biological perturbation experiments through language

Reference 51

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.352463Z

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Observation 66faa4d1-7cf7-40e4-9f55-cfa31c540838 · outbound

This paper cites Perteval-scFM: Benchmarking single-cell foundation models for perturbation effect prediction.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Perteval-scFM: Benchmarking single-cell foundation models for perturbation effect prediction

Reference 52

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.217238Z

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Observation 287b58f8-9a0a-4fc9-a0c0-160744aba11b · outbound

This paper cites Nature Language Model: Deciphering the Language of Nature for Scientific Discovery.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Nature Language Model: Deciphering the Language of Nature for Scientific Discovery

Reference 53

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.523345Z

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Observation 7a0ca055-16a6-4fd3-aea8-fb73e931098d · outbound

This paper cites Qwen3 Technical Report.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Qwen3 Technical Report

Reference 54

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.586223Z

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Observation a844978b-93ce-457b-afd9-ccc46b9dce23 · outbound

This paper cites Perturbench: Benchmarking machine learning models for cellular perturbation analysis.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Perturbench: Benchmarking machine learning models for cellular perturbation analysis

Reference 55

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.438642Z

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Unavailable: canonical work link unavailable.

Observation e65290c7-37a5-4264-9824-e0b7674345f2 · outbound

This paper cites Making large language models perform better in knowledge graph completion.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Making large language models perform better in knowledge graph completion

Reference 56

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.817264Z

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Observation 6a19ab28-b5a1-43ca-a94b-e083b10794c8 · outbound

This paper cites BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning

Reference 57

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.884837Z

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Observation 19b08a65-d1a8-4ad0-b1e4-0e08eefb0b55 · outbound

This paper cites scbert as a large-scale pretrained deep language model for cell type annotation of single-cell rna-seq data.Nature machine intelligence, 4(10):852–866, 2022.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects scbert as a large-scale pretrained deep language model for cell type annotation of single-cell rna-seq data.Nature machine intelligence, 4(10):852–866, 2022

Reference 58

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:21.718992Z

Source-reported events for the cited work

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Observation 6a939d6c-5daf-4dfa-a134-8e077243327d · outbound

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PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects cannot be explained

Reference 61

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Observation a301c5ad-8589-43f9-bd69-a14719f6cded · outbound

This paper cites Reducing a drug to its top-2 targets ignores significant off-target effects and downstream modulation that define the drug’s actual transcriptomic footprint.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Reducing a drug to its top-2 targets ignores significant off-target effects and downstream modulation that define the drug’s actual transcriptomic footprint

Reference 62

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:22.010516Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 0419dec0-8e18-493a-b12c-3c6b4dce36f7 · outbound

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PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects up", "down

Reference 63

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:22.070388Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 9c954b33-72d8-4c81-8616-cc0d738514f9 · outbound

This paper cites Alogliptin.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Alogliptin

Reference 66

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:22.365761Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a42524bf-e371-4ea3-8f9e-62cc86e67354 · outbound

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PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Unresolved cited work

Reference 67

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:22.477460Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 2b5a9bed-dbab-43f8-aa77-c313ce660b30 · outbound

This paper cites an unresolved cited work.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Unresolved cited work

Reference 68

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:22.589439Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 195cb816-c24e-4499-af02-6b458bf8bdd4 · outbound

This paper cites Alogliptin.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Alogliptin

Reference 69

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:22.645595Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation f4a83b21-ba69-422e-bb0c-04ebf9720829 · outbound

This paper cites an unresolved cited work.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects Unresolved cited work

Reference 2020

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:20.584922Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e512823e-57e5-411c-8e5f-cef798fd5c45 · outbound

This paper cites BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains.

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains

Reference 2024

Resolution: unresolved; no resolver link, observed 2026-08-01T14:28:17.483266Z

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