Paper Citation Record · LEDGER

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis

As of 9 August 2026, this Paper Citation Record lists 40 of 40 outbound references and 0 inbound Pith citation observations for arXiv:2509.10575.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2509.10575 v1

Coverage vector

measured 40 of 40 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-04T18:49:01.866423Z

measured 40 of 40 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-09T06:31:02.800959+00:00

measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: cited_works

Reference resolution

40 of 40 outbound references displayed

verified exact0
verified fuzzy0
unresolved40
parse uncertain0
malformed identifier0
metadata mismatch0

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation a969a4f3-a10e-4fcd-a352-6371e233c62d · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 1

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:55.245012Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 2bce98b4-5d56-4ac0-b042-f38089ac63f2 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 2

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:55.344490Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation ff302772-3fb7-4690-b689-343978bf2dae · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 3

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:55.483102Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 62e40044-4aff-4390-94ac-59e34486fe38 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:55.691799Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation dc019283-79da-42bf-b68d-3303f1ac6938 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 5

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:55.827430Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation df222f29-a41f-45ad-9cd0-6473ae33f81c · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 6

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:55.953636Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 02327807-6275-4889-8b0d-525d772dc17a · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 7

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:56.166781Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 86e53841-9d3a-4316-97f3-29d930b66d7a · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 8

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:56.366979Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 5c48abb3-9cbf-4956-8b2e-2a2017b9c983 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 9

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:56.491517Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation b641b337-5d47-4315-afbd-928bf37c8f14 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 10

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:56.698320Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 2bb5b29c-62dc-44a1-9b82-23c0a1270e95 · outbound

This paper cites DeepSeek-V3 Technical Report.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis DeepSeek-V3 Technical Report

Reference 11

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:56.826530Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation f6de14a0-8c3c-4d9f-8122-411a12bff687 · outbound

This paper cites OpenAI o1 System Card.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis OpenAI o1 System Card

Reference 12

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:57.031639Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 7d10c08a-7b60-433a-9b55-4d4673dad54a · outbound

This paper cites Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine

Reference 13

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:57.241906Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a5a5d1b8-dea6-4c57-b57d-142c8c8562aa · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 14

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:57.429877Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 4a7b16cc-72cd-4fe9-866e-2709309cbdc7 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 15

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:57.578256Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e8130233-b89f-4f30-ba84-b90345c91fb6 · outbound

This paper cites Online DPO: Online Direct Preference Optimization with Fast-Slow Chasing.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Online DPO: Online Direct Preference Optimization with Fast-Slow Chasing

Reference 16

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:57.769300Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation b34fd9ac-5359-42ff-b090-8b7daafcdd04 · outbound

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

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models

Reference 17

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:58.006648Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 77bee413-4074-43fa-a385-6ac201ac0077 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 18

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:58.175377Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation bbdd4f3a-f142-4ead-a466-ae1f4859f75d · outbound

This paper cites Injecting Domain-Specific Knowledge into Large Language Models: A Comprehensive Survey.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Injecting Domain-Specific Knowledge into Large Language Models: A Comprehensive Survey

Reference 19

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:58.299011Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 77a98633-642d-4e2b-99bc-03fcf912bbe2 · outbound

This paper cites V., Jones, M.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis V., Jones, M

Reference 20

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:58.463890Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 1405bc9b-28c7-4b24-9e4d-412eb1ca3342 · outbound

This paper cites Genegpt: Augmenting large language models with domain tools for improved access to biomedical information.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Genegpt: Augmenting large language models with domain tools for improved access to biomedical information

Reference 21

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:58.654921Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 56f07a28-9c4b-4366-934a-f338be558e34 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 22

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:58.811811Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e01a863c-7009-4274-8f97-81750cdd71f7 · outbound

This paper cites MedAlpaca -- An Open-Source Collection of Medical Conversational AI Models and Training Data.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis MedAlpaca -- An Open-Source Collection of Medical Conversational AI Models and Training Data

Reference 23

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:58.983514Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 025fdf09-bb81-44d0-9aaf-1bb596f0096c · outbound

This paper cites Clinical Camel: An Open Expert-Level Medical Language Model with Dialogue-Based Knowledge Encoding.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Clinical Camel: An Open Expert-Level Medical Language Model with Dialogue-Based Knowledge Encoding

Reference 24

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:59.145988Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 1199c7a7-8294-4a41-83ee-432bcbb57bb0 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 25

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:59.305578Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 54b53c84-6c26-4691-aa86-a5f4d4b154f9 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 26

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:59.466814Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 931a8e8e-ad3b-42e9-a1f7-a90113ca7e37 · outbound

This paper cites Cell-o1: Training LLMs to Solve Single-Cell Reasoning Puzzles with Reinforcement Learning.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Cell-o1: Training LLMs to Solve Single-Cell Reasoning Puzzles with Reinforcement Learning

Reference 27

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:59.629102Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 4eefdb4c-f992-4100-9306-bb45fd808f32 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 28

Resolution: unresolved; no resolver link, observed 2026-08-04T18:48:59.828394Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation cd3a6642-f6d6-43d7-8b3f-5090a633811e · outbound

This paper cites Annotation of biologically relevant ligands in UniProtKB using ChEBI.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Annotation of biologically relevant ligands in UniProtKB using ChEBI

Reference 29

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:00.007498Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 4e00d07f-44f9-438b-8b57-5ffde915d05d · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 30

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:00.155783Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 8ad97293-4895-4c79-a92e-785ec8fffb58 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 31

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:00.320833Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 809d4868-e8ab-4ee2-9995-7fc72938b702 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 32

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:00.478819Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a2bcb3c0-b8d1-48ab-b141-b67b186b12dc · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 33

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:00.699540Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 88b0c986-997f-4ead-8618-4fb9de89bb63 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 34

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:00.907004Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 150df6e2-cbb1-4215-bc36-d4d195857e79 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 35

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:01.090994Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation b9192cec-476b-405d-ae1f-eb01cea80d27 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 36

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:01.243496Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a9a3d7aa-533b-4ea0-bbdb-50ff49f53057 · outbound

This paper cites Rouge: A package for automatic evaluation of summaries.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Rouge: A package for automatic evaluation of summaries

Reference 37

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:01.396949Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 28f89e0a-f13e-4ca6-834a-1ee5272a639a · outbound

This paper cites Sentence -BERT: Sentence Embeddings using Siamese BERT - Networks.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Sentence -BERT: Sentence Embeddings using Siamese BERT - Networks

Reference 38

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:01.548506Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation cf9cf861-7613-4d29-a116-716f063d2e65 · outbound

This paper cites an unresolved cited work.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis Unresolved cited work

Reference 39

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:01.700129Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 302b39df-b24c-4412-9f49-45b17205bc13 · outbound

This paper cites LLaMA: Open and Efficient Foundation Language Models.

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis LLaMA: Open and Efficient Foundation Language Models

Reference 40

Resolution: unresolved; no resolver link, observed 2026-08-04T18:49:01.866423Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Pith citing papers

No inbound Pith citation observations are available.