Merge pull request #31 from moritzschaefer/patch-2

Add link to preprint and GitHub repository for 'CellWhispererer' method

README.md

@@ -47,7 +47,7 @@ We welcome contributions to this repository. Please open a pull request or an is
 | Model          | Paper                                                                                                                                                                     | Code                                                        | Omic Modalities                    | Pre-training Dataset                                                                                                                                                                                                                                                                                                                                       | Input Embedding                                                                                                                  | Architecture                                                                                                        | SSL Tasks                                                           | Supervised Tasks                                                       | Zero-shot Tasks                                                                                          |
 |----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------|------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------|------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------|
 | CELLama        | 📝[Choi et al. 2024](https://www.biorxiv.org/content/10.1101/2024.05.08.593094v1.full#ref-16)                                                                             | [🛠GitHub](https://github.com/portrai-io/CELLama)           | scRNA-seq, Spatial transcriptomics | Natural Language [SBERT](https://fq.pkwyx.com/default/https/aclanthology.org/D19-1410.pdf)                                                                                                                                                                                                                                                                 | Other: Ordering with embedding of the natural language representation, additional cell annotations are added in natural language | Siamese encoders ([SBERT](https://fq.pkwyx.com/default/https/aclanthology.org/D19-1410.pdf))                        | Contrastive loss                                                    | Cell type annotation                                                   | Cell type annotation, niche cell type featuring                                                          |
-| CellWhisperer  | 📝[Schaefer et al. 2024](https://openreview.net/forum?id=yWiZaE4k3K)                                                                                                      | Soon                                                        | Bulk/scRNA-seq                     | Transcriptome data paired with natural language annotations                                                                                                                                                                                                                                                                                                | Geneformer- and BioBERT-based embedding models (contrastively fine-tuned)                                                        | Multimodal contrastive training of embedding models (CLIP) and transcriptome instruction fine-tuning of LLM (LLaVA) | None                                                                | Transcriptome-aware question-answering                                 | Reference-free cell property prediction (cell types & states, disease states, organ of cell origin, ...) |
+| CellWhisperer  | 📝[Schaefer et al. 2024](https://www.biorxiv.org/content/10.1101/2024.10.15.618501v1)                                                                                                      | [🛠GitHub](https://github.com/epigen/cellwhisperer)                                                        | Bulk/scRNA-seq                     | Transcriptome data paired with natural language annotations                                                                                                                                                                                                                                                                                                | Geneformer- and BioBERT-based embedding models (contrastively fine-tuned)                                                        | Multimodal contrastive training of embedding models (CLIP) and transcriptome instruction fine-tuning of LLM (LLaVA) | None                                                                | Transcriptome-aware question-answering                                 | Reference-free cell property prediction (cell types & states, disease states, organ of cell origin, ...) |
 | scInterpreter  | 📝[Li et al. 2024](https://arxiv.org/abs/2402.12405)                                                                                                                      | None                                                        | scRNA-seq                          | Natural Language [GPT-3.5](https://api.openai.com/) and [Llama-13b](https://arxiv.org/abs/2302.13971)                                                                                                                                                                                                                                                      | Other: Ordering with embedding of the natural language representation                                                            | Decoder, [GPT-3.5](https://api.openai.com/) and [Llama-13b](https://arxiv.org/abs/2302.13971)                       | NTP with CE loss and instruction finetuning (GPT-3.5 closed-source) | None                                                                   | Cell type annotation (LLMs frozen, only small MLP trained)                                               |
 | ChatCell       | 📝❌[Fang et al. 2024](https://arxiv.org/abs/2402.08303)                                                                                                                   | [🛠GitHub](https://github.com/zjunlp/ChatCell)              | scRNA-seq                          | Natural Language [T5](https://huggingface.co/docs/transformers/en/model_doc/t5) and [natural language instructions](https://huggingface.co/datasets/zjunlp/ChatCell-Instructions)                                                                                                                                                                          | Other: Ordering with embedding as natural language with additional terms                                                         | Encoder-Decoder, [T5](https://huggingface.co/docs/transformers/en/model_doc/t5)                                     | NTP with CE loss                                                    | None (conditional sequence generation, prompting)                      | Simulation, cell type annotation, drug sensitivity prediction                                            |
 | MarkerGeneBERT | 📝[Cheng et al. 2023](https://www.biorxiv.org/content/10.1101/2024.01.30.578115v1)                                                                                        | None                                                        | scRNA-seq                          | Natural Language, [PubMed](https://pubmed.ncbi.nlm.nih.gov/) and [PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/)                                                                                                                                                                                                                                       | Other: Natural language preprocessed with [SciBERT](https://arxiv.org/abs/1903.10676)                                            | Encoder                                                                                                             | MLM                                                                 | Named Entity Recognition (NER), cell-biomarker sentence classification | None                                                                                                     |