Demo Data from EDBT 2026 / reviewers in the wild / expert
Ivan Vrkic
dblp:384/4238
· DBLP profile ↗
1ranked-venue papers
0as first author
1since 2021 · last 2024
—ORCID · none
Domains — the database's venue-derived domains; a paper can count in several
Artificial intelligence and machine learning · 1 · 1 since 2021
Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.
| Artificial intelligence
1 paper |
Language models and text generation · 100% | |
| Interdisciplinary, comprehensive, and emerging computing
1 paper |
Bioinformatics and computational biology · 100% |
Topics — the 2 heaviest of 3, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › single-cell analysis
single-cell transcriptomics |
0.8 | 1 | 2024 | Cell2Sentence: Teaching Large Language Models the Language of Biology · ICML 2024 |
Natural language and speech › Language models and text generation
text generation |
0.2 | 1 | 2024 | Cell2Sentence: Teaching Large Language Models the Language of Biology · ICML 2024 |
Methods — techniques the papers use, named apart from their topics
large language model fine-tuning · 1.5cell sentences · 1.5
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2024 | Cell2Sentence: Teaching Large Language Models the Language of BiologyabstractWe introduce Cell2Sentence (C2S), a novel method to directly adapt large language models to a biological context, specifically single-cell transcriptomics. By transforming gene expression data into "cell sentences," C2S bridges the gap between natural language processing and biology. We demonstrate cell sentences enable the fine-tuning of language models for diverse tasks in biology, including cell generation, complex cell-type annotation, and direct data-driven text generation. Our experiments reveal that GPT-2, when fine-tuned with C2S, can generate biologically valid cells based on cell type inputs, and accurately predict cell types from cell sentences. This illustrates that language models, through C2S fine-tuning, can acquire a significant understanding of single-cell biology while maintaining robust text generation capabilities. C2S offers a flexible, accessible framework to integrate natural language processing with transcriptomics, utilizing existing models and libraries for a wide range of biological applications. Daniel LeVine, Syed Asad Rizvi, Sacha Levy, Nazreen Pallikkavaliyaveetil, Sina Ghadermarzi, Ruiming Wu, Zihe Zheng, Ivan Vrkic, Anna Zhong, Daphne Raskin, Insu Han, Antonio H. O. Fonseca, Josue Ortega Caro, Amin Karbasi, Rahul Madhav Dhodapkar, David van Dijk |
ICML | 10 |