457 citations · 462 across the 9 of their papers we have counts for
10 papers
VANDAM: Viewing a nucleotide sequence with DNA molecular priors
Jeremy Levy, Ariel Larey, Yury Nahshan +18
Contemporary Genomic Foundation Models (GFMs) rely on a DNA-as-a-string paradigm that employs masked token prediction objectives for pretraining. However, this abstraction does not…
ProteinJEPA: Latent prediction improves protein language model pretraining
Dan Ofer, Dafna Shahaf, Michal Linial
Protein language models are trained primarily with masked language modeling (MLM), which predicts masked amino-acid identities. Joint-embedding predictive architectures (JEPA) inst…
ProtSent: Protein Sentence Transformers
Dan Ofer, Oriel Perets, Michal Linial +1
Protein language models produce rich per-residue representations, but the sequence embeddings obtained by mean-pooling them are never trained to place related proteins near one ano…
JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures
Ariel Larey, Elay Dahan, Amit Bleiweiss +15
Genomic Foundation Models (GFMs) typically rely on Masked Language Modeling (MLM) or Next-Token Prediction (NTP) to learn the "Laws of Nature". While effective at capturing local s…
InterFeat: A Pipeline for Finding Interesting Scientific Features
Dan Ofer, Michal Linial, Dafna Shahaf
Finding interesting phenomena is the core of scientific discovery, but it is a manual, ill-defined concept. We present an integrative pipeline for automating the discovery of inter…
Optothermal needle-free injection of vaterite nanocapsules
Denis Kislov, Daniel Ofer, Andrey Machnev +4
The propulsion and acceleration of nanoparticles with light have both fundamental and applied significance across many disciplines. Needle-free injection of biomedical nano cargoes…
Whats next? Forecasting scientific research trends
Dan Ofer, Michal Linial
Scientific research trends and interests evolve over time. The ability to identify and forecast these trends is vital for educational institutions, practitioners, investors, and fu…
Cards Against AI: Predicting Humor in a Fill-in-the-blank Party Game
Dan Ofer, Dafna Shahaf
Humor is an inherently social phenomenon, with humorous utterances shaped by what is socially and culturally accepted. Understanding humor is an important NLP challenge, with many…
Machine Learning for Protein Function
Dan Ofer
Systematic identification of protein function is a key problem in current biology. Most traditional methods fail to identify functionally equivalent proteins if they lack similar s…
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Yuxiang Jiang, Tal Ronnen Oron, Wyatt T Clark +144
Background: The increasing volume and variety of genotypic and phenotypic data is a major defining characteristic of modern biomedical sciences. At the same time, the limitations i…