Tobias Senoner

Pseudoperplexity Probes Memorization in Protein Language Models

This study uses pseudoperplexity to assess whether ProtT5 memorizes its training data, finding detectable but limited memorization.

ProtSpace: Protein Universe in Your Browser

ProtSpace visualizes protein language model embeddings interactively, enabling hypothesis generation across biological scales without installation.

UdonPred: Untangling Protein Intrinsic Disorder Prediction

UdonPred predicts per-residue protein disorder from sequence using embeddings from ProstT5, showing that annotation quality, not model capacity, drives performance in continuous disorder prediction.

Which pLM to choose?

This study benchmarks fourteen protein-language models (pLMs) to determine which best captures biological properties, finding that mid-scale models often outperform larger ones for general tasks.

FlatProt: 2D visualization eases protein structure comparison

FlatProt provides 2D visualizations for comparing protein structures, enabling scalable and standardized analysis of large protein sets.

ProtSpace: a tool for visualizing protein space

ProtSpace visualizes protein embeddings in 2D/3D to reveal functional patterns and challenges existing classifications in phage and venom protein analyses.

Domain loss enabled evolution of novel functions in a gene superfamily

The paper reconstructs the evolutionary history of three-finger toxins (3FTxs) and identifies their non-toxin ancestor as a non-secretory Ly6 in squamate reptiles.