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Ivan Vrkic

dblp:384/4238 · DBLP profile ↗
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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

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › single-cell analysis
single-cell transcriptomics
0.812024
Cell2Sentence: Teaching Large Language Models the Language of Biology · ICML 2024
Natural language and speech › Language models and text generation
text generation
0.212024
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
YearPublicationVenuePosition
2024 Cell2Sentence: Teaching Large Language Models the Language of Biology
abstract
We 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
ICML10