Pennsylvania State University

Phylogeny-informed transformer that detects episodic diversifying selection in codon alignments, amortizing maximum-likelihood dN/dS tests.

Contrastive multimodal model for perturbation screens, aligning transcriptomic signatures with text and cell-painting image embeddings.

Photoplethysmography foundation model pretrained by reconstructing masked ECG from PPG, learning cardiac timing structure for wearable health tasks.

Protein-protein binding affinity prediction from sequence alone, pairing frozen protein language model embeddings with gradient-boosted trees.

DNA sequence embedding model that approximates edit distance via contrastive fine-tuning of DNABERT-2, improving similar-sequence search accuracy.

De novo small-molecule generation inside a protein pocket, diffusing ligand atoms and pocket side chains together so the site adapts as it binds.

Graph neural network that reconstructs chemical bonds and bond orders from 3D coordinates, distorted generated geometries, or bare 2D connectivity.

Protein-ligand binding affinity prediction for Kd, Ki and IC50 from a pocket structure and a SMILES string, with no docked complex required.

Self-supervised masked autoencoder for functional MRI that learns representations from BOLD time-series with per-ROI embeddings and graph attention.