Towards Applying Large Language Models to Complement Single-Cell Foundation Models | Paper Citation Record

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This paper cites https://huggingface.

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

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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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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)

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

Reference 4

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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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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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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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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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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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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

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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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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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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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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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This paper cites Deepseek-r1.

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

Reference 16

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

Reference 23

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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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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

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

Reference 33

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

Reference 36

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

Reference 37

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

Reference 38

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

Reference 39

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

Reference 40

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

Reference 41

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

Reference 42

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

Reference 43

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

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

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

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

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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

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

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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

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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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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

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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

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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

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