3 papers
q-bio.QM2026
Dual Triangle Attention: Effective Bidirectional Attention Without Positional Embeddings
Logan Hallee, Jason P. Gleghorn
Bidirectional transformers are the foundation of many sequence modeling tasks across natural, biological, and chemical language domains, but they are permutation-invariant without…
q-bio.BM2025
Diffusion Sequence Models for Enhanced Protein Representation and Generation
Logan Hallee, Nikolaos Rafailidis, David B. Bichara +1
Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials sci…
cs.LG2024
Contrastive Learning and Mixture of Experts Enables Precise Vector Embeddings
Logan Hallee, Rohan Kapur, Arjun Patel +2
The advancement of transformer neural networks has significantly elevated the capabilities of sentence similarity models, but they still struggle with highly discriminative tasks a…