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Paper Citation Record · LEDGER

Towards Applying Large Language Models to Complement Single-Cell Foundation Models

As of 7 August 2026, this Paper Citation Record lists 55 of 55 outbound references and 0 inbound Pith citation observations for arXiv:2507.10039.

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

pith.paper-citation-record.v1
2507.10039 v1

Coverage vector

measured 55 of 55 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-06T17:47:13.080183Z

measured 55 of 55 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-06T06:34:29.942622+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

55 of 55 outbound references displayed

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  • verified fuzzy33
  • unresolved21
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation bd233973-4b8b-4e2a-85ce-86c19561da93 · outbound

This paper cites https://huggingface.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models https://huggingface

Reference 1

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This paper cites https: //huggingface.co/sentence-transformers/all-MiniLM-L12-v2.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models https: //huggingface.co/sentence-transformers/all-MiniLM-L12-v2

Reference 2

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Observation fc506a9f-bb9f-44cc-a777-477e4a6ec740 · outbound

This paper cites Deep Learning using Rectified Linear Units (ReLU).

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Deep Learning using Rectified Linear Units (ReLU)

Reference 3

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Observation 5c207a8f-eb39-4f26-a756-3eb47f33edad · outbound

This paper cites Deepseek ai / deepseek r1 (fast).

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Deepseek ai / deepseek r1 (fast)

Reference 4

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Observation b3ae442e-db51-475b-9267-a1ba1bc7d496 · outbound

This paper cites Deepseek ai / deepseek v3.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Deepseek ai / deepseek v3

Reference 5

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Observation 4a2c98ca-a752-40cb-a02a-36206ff11db8 · outbound

This paper cites Flamingo: a visual language model for few-shot learning.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Flamingo: a visual language model for few-shot learning

Reference 6

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Observation 18577b56-bdf4-4138-a8a5-4f10cc7f4976 · outbound

This paper cites Decoding the transcriptome of calcified atherosclerotic plaque at single-cell resolution.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Decoding the transcriptome of calcified atherosclerotic plaque at single-cell resolution

Reference 7

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Observation 3a396ed1-46de-42bf-8291-a1067c3dd917 · outbound

This paper cites Genept: A simple but effective foundation model for genes and cells built from chatgpt.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Genept: A simple but effective foundation model for genes and cells built from chatgpt

Reference 8

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Observation 9d74c6e3-5d55-4907-a71a-a26868580b50 · outbound

This paper cites A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

Reference 9

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Observation f7192006-9539-462e-8165-2ede9ec2c640 · outbound

This paper cites Cellama: Foundation model for single cell and spatial transcriptomics by cell embedding leveraging language model abilities.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Cellama: Foundation model for single cell and spatial transcriptomics by cell embedding leveraging language model abilities

Reference 10

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Towards Applying Large Language Models to Complement Single-Cell Foundation Models Unresolved cited work

Reference 11

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Observation fdf16cb2-27ff-4f01-99e5-ed36cc22e444 · outbound

This paper cites Synovial cell cross-talk with cartilage plays a major role in the pathogenesis of osteoarthritis.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Synovial cell cross-talk with cartilage plays a major role in the pathogenesis of osteoarthritis

Reference 12

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Observation ae620480-e2ed-441b-8af1-976baf086f9f · outbound

This paper cites Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

Reference 13

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Observation 3b574c77-6fd4-4da4-8b6c-50b381449402 · outbound

This paper cites The tabula sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models The tabula sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Reference 14

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Observation 179efaf7-9ff2-4d85-bfa1-11d4868a0bd7 · outbound

This paper cites scgpt: toward building a foundation model for single-cell multi-omics using generative ai.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models scgpt: toward building a foundation model for single-cell multi-omics using generative ai

Reference 15

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Observation d0dddcf9-cfc0-43db-8f00-86841e330b64 · outbound

This paper cites Deepseek-r1.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Deepseek-r1

Reference 16

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Observation b2d26c08-1713-4d8f-a013-115248de59b4 · outbound

This paper cites The temperature parameter.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models The temperature parameter

Reference 17

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Observation fd148c2e-7e0d-4ac3-a7ae-07df75c3ca51 · outbound

This paper cites The Llama 3 Herd of Models.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models The Llama 3 Herd of Models

Reference 18

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Observation 0de6d984-fc82-4a69-b605-277095032878 · outbound

This paper cites How do large language models understand genes and cells.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models How do large language models understand genes and cells

Reference 19

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Observation 85f25fbb-d6b8-4839-867e-854d33034190 · outbound

This paper cites Panglaodb: a web server for explo- ration of mouse and human single-cell rna sequencing data.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Panglaodb: a web server for explo- ration of mouse and human single-cell rna sequencing data

Reference 20

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Observation 76f45997-cdba-42e9-9f15-6453938867cb · outbound

This paper cites Bias and fairness in large language models: A survey.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Bias and fairness in large language models: A survey

Reference 21

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Observation c90fbec2-7f81-44e7-8e08-d244a394a920 · outbound

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

Towards Applying Large Language Models to Complement Single-Cell Foundation Models DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning

Reference 22

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Observation d4d05716-3d6a-47da-af39-b3e4562b9dad · outbound

This paper cites Adam: A Method for Stochastic Optimization.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Adam: A Method for Stochastic Optimization

Reference 23

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Observation a86fe62f-19d9-49af-9b3e-c5372a53f376 · outbound

This paper cites A multimodal deep learning model using text, image, and code data for improving issue classification tasks.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models A multimodal deep learning model using text, image, and code data for improving issue classification tasks

Reference 24

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Observation cdd9558d-7f71-4d62-89fd-92b23caab98c · outbound

This paper cites Explanatory predictive model for covid-19 severity risk employing machine learning, shapley addition, and lime.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Explanatory predictive model for covid-19 severity risk employing machine learning, shapley addition, and lime

Reference 25

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Observation c73fd13a-14ad-4c62-bc6d-b8a3c0948d76 · outbound

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Towards Applying Large Language Models to Complement Single-Cell Foundation Models Open source strikes bread - new fluffy embeddings model, 2024

Reference 26

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Observation 280d8191-44ec-4e76-914c-4911ffe36514 · outbound

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Towards Applying Large Language Models to Complement Single-Cell Foundation Models Cell2sentence: Teaching large language models the language of biology

Reference 27

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Towards Applying Large Language Models to Complement Single-Cell Foundation Models AnglE-optimized Text Embeddings

Reference 28

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This paper cites Single-cell transcriptome analysis reveals dynamic cell populations and differential gene expression patterns in control and aneurysmal human aortic tissue.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Single-cell transcriptome analysis reveals dynamic cell populations and differential gene expression patterns in control and aneurysmal human aortic tissue

Reference 29

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Observation b46a30f2-bc36-4e4b-9f57-3dd2e3e22450 · outbound

This paper cites Towards General Text Embeddings with Multi-stage Contrastive Learning.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Towards General Text Embeddings with Multi-stage Contrastive Learning

Reference 30

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Observation b01131a0-8ce3-4eb1-b050-f78c8f190c2f · outbound

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Towards Applying Large Language Models to Complement Single-Cell Foundation Models Do Language Models Know the Way to Rome?

Reference 31

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This paper cites scelmo: Embeddings from language models are good learners for single-cell data analysis.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models scelmo: Embeddings from language models are good learners for single-cell data analysis

Reference 32

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Observation adf669d9-3a37-4034-9697-382459b94879 · outbound

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Towards Applying Large Language Models to Complement Single-Cell Foundation Models Decoupled Weight Decay Regularization

Reference 33

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Observation 12505c44-dbc0-4c35-b511-e97db2619056 · outbound

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

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Benchmarking atlas-level data integration in single-cell genomics.Nature methods, 19(1):41–50, 2022

Reference 34

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Source-reported events for the cited work

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Observation 4f585ed6-ed19-40cd-af55-a8d180bde60e · outbound

This paper cites Cellxgene: a performant, scalable exploration platform for high dimensional sparse matrices.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Cellxgene: a performant, scalable exploration platform for high dimensional sparse matrices

Reference 35

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raw_fallback, observed 2026-08-06T17:47:15.970743Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:11.404227Z digest=sha256:92104d33421180018189363d927687c93ec9386def362b6ecd0099d820befa54

Observation 212d01d1-1930-4d51-aadf-6e340e2f26ee · outbound

This paper cites Multi-modal classification using images and text.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Multi-modal classification using images and text

Reference 36

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:15.843465Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:11.470268Z digest=sha256:4c15221dafcfa3979247487264e30e65191d8e086d080ddf17dc3e8852b83f42

Observation db77f438-c09e-4a29-ada9-c752570b7418 · outbound

This paper cites MTEB: Massive Text Embedding Benchmark.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models MTEB: Massive Text Embedding Benchmark

Reference 37

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unresolved
no resolver link, observed 2026-08-06T17:47:11.540058Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-06T17:47:11.540058Z digest=sha256:65bb2b50c49d41e99365dbfc094cccca9f8a0bc8fc8bfa06a408d5ce0875f1b3

Observation 4f0e856a-a9f8-4302-a50e-eee0affd04b0 · outbound

This paper cites ember-v1: Sota embedding model, 2023.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models ember-v1: Sota embedding model, 2023

Reference 38

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:15.676074Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:11.606114Z digest=sha256:1f469bbf9feb360a803f962ceca735b1285388839b6279ab00f1d871d51d58ed

Observation c17a41b4-9442-4b51-802a-921a297a1ef2 · outbound

This paper cites Embeddings.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Embeddings

Reference 39

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:15.524100Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:11.674253Z digest=sha256:b2c4abff42dc81010abe38dfdf862d2a0dc41dd9a8d34ea5c3ce8f23c7953b15

Observation 2fd4a7d7-9a04-46e7-90fa-cac90702187e · outbound

This paper cites Reasoning models.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Reasoning models

Reference 40

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:15.363216Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:11.744504Z digest=sha256:0dd7c9d050fffa9413422bc3456fba50ed55ccdb455f15601c1276adbd5d442d

Observation 0f50b940-98b1-47f4-95a5-e1d4779ecf30 · outbound

This paper cites Pedregosa, G.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Pedregosa, G

Reference 41

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no resolver link, observed 2026-08-06T17:47:11.811450Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-06T17:47:11.811450Z digest=sha256:ace8b3a35a5aebe8930efcc803203c7ffce24732d173095c33cc6baf00ba6c21

Observation 0b3b72d2-c606-464c-8317-e7bd7b93ce5c · outbound

This paper cites Replicate.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Replicate

Reference 42

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:15.120299Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:11.910800Z digest=sha256:ad8ba70561eecd34b7fca0f8004a1ed97ba69aaa97518f718b881781d7a32e28

Observation 83b5fb9b-b4c9-4b92-be2c-6716d6158287 · outbound

This paper cites why should i trust you?.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models why should i trust you?

Reference 43

Resolution
unresolved
no resolver link, observed 2026-08-06T17:47:12.012737Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-06T17:47:12.012737Z digest=sha256:17bb821a0644e76891ebda2d3b17ec05f329b0bf4b8725579e1fcd59c9a07d58

Observation 7765b27a-2251-48ef-9bf7-d52d6bae4344 · outbound

This paper cites Scaling large language models for next-generation single-cell analysis.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Scaling large language models for next-generation single-cell analysis

Reference 44

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:14.841007Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:12.113879Z digest=sha256:4dacf6979754999c158f698c4d934ce9e959916023a1a1f45a93728c66f311a6

Observation 19a6449c-d0f0-4f7e-9165-b97ef15567ab · outbound

This paper cites Neuronal vulnerability and multilineage diversity in multiple sclerosis.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Neuronal vulnerability and multilineage diversity in multiple sclerosis

Reference 45

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:14.555182Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:12.192516Z digest=sha256:7f6f1aafab4c933b92a4a39d6e23750675fdcf17609cd8b9d00a0743af81d5ed

Observation bbecffe1-14ba-4667-8522-57cb0fbc3067 · outbound

This paper cites GISTEmbed: Guided In-sample Selection of Training Negatives for Text Embedding Fine-tuning.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models GISTEmbed: Guided In-sample Selection of Training Negatives for Text Embedding Fine-tuning

Reference 46

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unresolved
no resolver link, observed 2026-08-06T17:47:12.268371Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-06T17:47:12.268371Z digest=sha256:e1bba3979909b0e7654623ba700d4bf967f27193dddaf19096426a7ee792f9ec

Observation 63d70e99-0678-4b5b-822e-e2964314fa37 · outbound

This paper cites Multimodal data fusion for cancer biomarker discovery with deep learning.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Multimodal data fusion for cancer biomarker discovery with deep learning

Reference 47

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:14.312657Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:12.357978Z digest=sha256:b0621a276692f1e422a82623ba3658db37b6b709bc0bfb265a2b1a66e17c7143

Observation 22b037bd-5b9f-4169-bc0a-ee58969434ca · outbound

This paper cites Axiomatic attribution for deep networks.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Axiomatic attribution for deep networks

Reference 48

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no resolver link, observed 2026-08-06T17:47:12.473684Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-06T17:47:12.473684Z digest=sha256:a6b77a73eb8627dfea1c098d4e8e83d50f29d6ae9a7481a17ebf65412e95a6c2

Observation d5510b38-c155-4e58-9d7f-c96ab0d05e81 · outbound

This paper cites Exploring the performance and explainability of fine-tuned bert models for neuro- radiology protocol assignment.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Exploring the performance and explainability of fine-tuned bert models for neuro- radiology protocol assignment

Reference 49

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:14.059793Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:12.575126Z digest=sha256:92be15cb945297011247d1176b97413d97d2a43672df40037e0191e3da4327c2

Observation 47df759a-46ab-4a8c-8a5a-bb536f6d6245 · outbound

This paper cites Attention is all you need.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Attention is all you need

Reference 50

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no resolver link, observed 2026-08-06T17:47:12.624094Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-06T17:47:12.624094Z digest=sha256:5e0dbbe65b8a2435f7d9470d32b58c4b409ff0e7b97ad2eb59a071f999321a80

Observation 031ee8be-a965-4012-b2ab-6b46def223fb · outbound

This paper cites Interpretable machine learning for personalized medical recommendations: A lime-based approach.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Interpretable machine learning for personalized medical recommendations: A lime-based approach

Reference 51

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:13.832626Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:12.731775Z digest=sha256:660d35feb0f9ca42ec36ae3b81d65114fa6eee2e5f2c8c49f8ee498743a95865

Observation 9be3982a-7d82-4462-9635-4180b9be0b59 · outbound

This paper cites C-pack: Packaged resources to advance general chinese embedding, 2023.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models C-pack: Packaged resources to advance general chinese embedding, 2023

Reference 52

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unresolved
no resolver link, observed 2026-08-06T17:47:12.816143Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-06T17:47:12.816143Z digest=sha256:0c9733e9df40c950c97f1b5192c02860510b49998ed168f8bc1a75d9062be540

Observation 037826d6-c03d-4993-bc52-98dd94ac6a57 · outbound

This paper cites scbert as a large-scale pretrained deep language model for cell type annotation of single-cell rna-seq data.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models scbert as a large-scale pretrained deep language model for cell type annotation of single-cell rna-seq data

Reference 53

Resolution
verified fuzzy
raw_fallback, observed 2026-08-06T17:47:13.653330Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-06T06:34:29.942622+00:00.

source=pdf_text observed=2026-08-06T17:47:12.898753Z digest=sha256:4e247d28c6ada31bcd8ae49f9437534e99fb5b88e0a8d7171246e184101293d7

Observation f67ee5c3-3ca3-4590-8289-b0825378c85d · outbound

This paper cites Scientific Large Language Models: A Survey on Biological & Chemical Domains.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models Scientific Large Language Models: A Survey on Biological & Chemical Domains

Reference 54

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unresolved
no resolver link, observed 2026-08-06T17:47:12.986499Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-06T17:47:12.986499Z digest=sha256:f51be045352496f656cadefa355d2a847ee8ecab51069563761cd57ee37aceec

Observation 099be64c-d9a5-4848-9860-f2b10bde3e41 · outbound

This paper cites mGTE: Generalized Long-Context Text Representation and Reranking Models for Multilingual Text Retrieval.

Towards Applying Large Language Models to Complement Single-Cell Foundation Models mGTE: Generalized Long-Context Text Representation and Reranking Models for Multilingual Text Retrieval

Reference 55

Resolution
unresolved
no resolver link, observed 2026-08-06T17:47:13.080183Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-06T17:47:13.080183Z digest=sha256:2dda2ce60caed626c0ba858ca25b94a3663fe2d56917e43e3dadc84729fa7156

Pith citing papers

No inbound Pith citation observations are available.