5 papers · 1 filter
seqme: a Python library for evaluating biological sequence design
Rasmus Møller-Larsen, Adam Izdebski, Jan Olszewski +4
Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity o…
Freeze, Diffuse, Decode: Task-Aware Adaptation of Transformer Embeddings for Antimicrobial Peptide Design
Pankhil Gawade, Adam Izdebski, Myriam Lizotte +4
Pretrained transformers provide rich, general-purpose embeddings, which are transferred to downstream tasks. However, current transfer strategies: fine-tuning and probing, either d…
Mamba Goes HoME: Hierarchical Soft Mixture-of-Experts for 3D Medical Image Segmentation
Szymon Płotka, Gizem Mert, Maciej Chrabaszcz +2
In recent years, artificial intelligence has significantly advanced medical image segmentation. Nonetheless, challenges remain, including efficient 3D medical image processing acro…
ProSpero: Active Learning for Robust Protein Design Beyond Wild-Type Neighborhoods
Michal Kmicikiewicz, Vincent Fortuin, Ewa Szczurek
Designing protein sequences of both high fitness and novelty is a challenging task in data-efficient protein engineering. Exploration beyond wild-type neighborhoods often leads to…
Synergistic Benefits of Joint Molecule Generation and Property Prediction
Adam Izdebski, Jan Olszewski, Pankhil Gawade +5
Modeling the joint distribution of data samples and their properties allows to construct a single model for both data generation and property prediction, with synergistic benefits…