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ychuest authored Aug 27, 2024
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Expand Up @@ -59,7 +59,8 @@ Awesome-LLMs-meet-genomes is a collection of state-of-the-art, novel, exciting L
| 2024.05 | **Are Genomic Language Models All You Need? Exploring Genomic Language Models on Protein Downstream Tasks** | bioRxiv | [link](https://www.biorxiv.org/content/10.1101/2024.05.20.594989v1) | [link](https://huggingface.co/InstaDeepAI/nucleotide-transformer-v2-50m-3mer-multi-species) |
| 2024.04 | **DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome** | ICLR'24 | [link](https://openreview.net/pdf?id=oMLQB4EZE1) | [link](https://github.com/MAGICS-LAB/DNABERT_2) |
| 2024.04 | **Species-aware DNA language models capture regulatory elements and their evolution** | Genome Biology | [link](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03221-x) | [link](https://github.com/gagneurlab/SpeciesLM) |
| 2024.02 | **GenomicLLM: Exploring Genomic Large Language Models: Bridging the Gap between Natural Language and Gene Sequences** | bioRxiv | [link](https://www.biorxiv.org/content/10.1101/2024.02.26.581496v1) | [link](https://github.com/Huatsing-Lau/GenomicLLM) [data](https://zenodo.org/records/10695802) |
| 2024.02 | **GenomicLLM: Exploring Genomic Large Language Models: Bridging the Gap between Natural Language and Gene Sequences** | bioRxiv | [link](https://www.biorxiv.org/content/10.1101/2024.02.26.581496v1) | [link](https://github.com/Huatsing-Lau/GenomicLLM)
[data](https://zenodo.org/records/10695802) |
| 2024.02 | **Sequence modeling and design from molecular to genome scale with Evo** | bioRxiv | [link](https://www.biorxiv.org/content/10.1101/2024.02.27.582234v1) | [link](https://github.com/evo-design/evo) |
| 2024.01 | **ProkBERT family: genomic language models for microbiome applications** | Frontiers in Microbiology | [Link](https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1331233/full) | [link](https://github.com/nbrgppcu/prokbert) |
| 2023.09 | **The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics** | bioRxiv | [link](https://www.biorxiv.org/content/10.1101/2023.01.11.523679v3) | [link](https://github.com/instadeepai/nucleotide-transformer) |
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