🔄 In a Training Loop

Dan Ofer

GrimSqueaker

29 25 581

https://scholar.google.co.il/citations?user=uDx2ItYAAAAJ&hl=en

AI & ML interests

Bioinformatics, Neurobiology, AutoML, AI, Feature engineering, Proteins, Biological foundation models, ML healthcare, NLP

Recent Activity

updated a dataset about 4 hours ago

GrimSqueaker/cath43-eat

published a dataset about 4 hours ago

GrimSqueaker/cath43-eat

new activity 1 day ago

Oxer11/Protein-Function-Annotation:Datasets not viewable

View all activity

Organizations

upvoted a collection 12 days ago

JEPA

Collection

https://www.biorxiv.org/content/10.64898/2026.04.02.716255v1.full.pdf • 15 items • Updated 12 days ago • 1

upvoted 2 papers 12 days ago

ProteinJEPA: Latent prediction complements protein language models

Paper • 2605.07554 • Published May 8 • 1

JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures

Paper • 2602.17162 • Published May 25 • 1

upvoted 2 collections 2 months ago

AminoWeb

Collection

AminoWeb is the biggest (~8TB) collection of high quality protein (sequence, structure, function) datasets available in the whole web. • 29 items • Updated May 28 • 5

📊 DNA benchmarks

Collection

Zero-shot DNA benchmarks for Variant Effect prediction, Sequence Recovery and Perturbation tasks. • 5 items • Updated May 19 • 14

upvoted a collection 3 months ago

Hebrew Semantic Retrieval Competition Winners

Collection

3 items • Updated May 10 • 1

upvoted an article 5 months ago

Article

Train 400x faster Static Embedding Models with Sentence Transformers

tomaarsen

•

Jan 15, 2025

• 233

upvoted a paper 5 months ago

Evaluating Protein Transfer Learning with TAPE

Paper • 1906.08230 • Published Jun 19, 2019 • 1

upvoted 2 collections 5 months ago

PPI Datasets

Collection

Dayhoff Atlas

Collection

The models and datasets that comprise the Dayhoff Atlas • 10 items • Updated Jul 28, 2025 • 13

upvoted a collection 9 months ago

Omni-DNA

Collection

A family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. • 14 items • Updated Feb 20, 2025 • 1

upvoted a collection 10 months ago

DNA language models

Collection

11 items • Updated Apr 17 • 10

upvoted a collection 11 months ago

GPN-Star

Collection

paper: https://www.biorxiv.org/content/10.1101/2025.09.21.677619v1 code: https://github.com/songlab-cal/gpn • 32 items • Updated 11 days ago • 10

upvoted an article 12 months ago

Article

Training and Finetuning Reranker Models with Sentence Transformers

tomaarsen

•

Mar 26, 2025

• 197

upvoted 2 articles about 1 year ago

Article

Ettin Suite: SoTA Paired Encoders and Decoders

orionweller, kdricci, mmarone, NohTow, dlawrie, vandurme

•

Jul 16, 2025

• 81

Article

Arc Virtual Cell Challenge: A Primer

FL33TW00D-HF, abhinadduri

•

Jul 18, 2025

• 66

upvoted a collection about 1 year ago

Encoders vs Decoders: the Ettin Suite

Collection

A collection of SOTA, open-data, paired encoder-only and decoder only models ranging from 17M params to 1B. See the paper at https://arxiv.org/abs/250 • 30 items • Updated Mar 2 • 31

upvoted a paper over 1 year ago

The Open Medical-LLM Leaderboard: Benchmarking Large Language Models in Healthcare

aaditya, pminervini, clefourrier

•

Apr 19, 2024

• 202

upvoted a collection almost 2 years ago

Llama 3.2

Collection

Meta's new Llama 3.2 vision and text models including 1B, 3B, 11B and 90B. Includes GGUF, 4-bit bnb and original versions. • 25 items • Updated 15 days ago • 69

Dan Ofer

AI & ML interests

Recent Activity

Organizations

GrimSqueaker's activity

Train 400x faster Static Embedding Models with Sentence Transformers

Training and Finetuning Reranker Models with Sentence Transformers

Ettin Suite: SoTA Paired Encoders and Decoders

Arc Virtual Cell Challenge: A Primer

The Open Medical-LLM Leaderboard: Benchmarking Large Language Models in Healthcare