6 papers · ranked by Valyu relevance
Polina Bombina, Kevin R. Coombes
Comparative studies of trajectory inference (TI) methods evaluate complete computational pipelines, making it impossible to isolate how much distortion is introduced specifically by the dimensionality reduction (DR) step. To our knowledge, no study has directly and systematically evaluated how well DR methods alone…
Hao Ding, Nannan Wu, Tianyi Qiu
DNA foundation models such as Evo2 7B adopt hybrid Hyena/attention architectures (Striped-Hyena2) whose single-stream autoregressive decoding is bounded by weight bandwidth at ∼45 tok/s. Speculative decoding on such hybrids faces a systems problem that prior SSM work solves only partially: after a draft is verified…
Namasi G Sankar, Georgios Miliotis, Simon Caton
Genome assembly is important in infectious disease surveillance, antimicrobial resistance monitoring, and cancer genomics. The task of reconstructing full genomic sequences from fragmented reads, can be framed as a large scale combinatorial optimisation problem. Recent advances in quantum computing have introduced new…
Odin Zhang, Jiaqi Wang, Tuscan Rock Thompson, Ziyi You + 3 more
Biomolecular interactions, including protein–protein interactions, protein–nucleic acid recognition, and protein–small molecule binding, underlie a wide range of biological processes and therapeutic mechanisms. Although recent de novo design methods can generate candidate binders for diverse molecular targets…
Amélie Barozet, Vincent Cabeli, Jean Ogier du Terrail, Alexey Rukhovich + 6 more
The development of climate-resilient crops would be greatly accelerated by models able to reason directly over plant genomic sequences and to pinpoint trait-associated regions or loci. Anticipating the impact of DNA base changes (variants) remains challenging, and understanding regulatory mechanisms is still an active…
Luiz F. M. A. Benício, Érica C. M. Nascimento, Sonia M. de Freitas, João B. L. Martins
Context Bowman-Birk inhibitors (BBIs) are cysteine-rich proteins that inhibit trypsin and chymotrypsin proteases. Derived from soybeans, these natural BBIs have been identified as potential anticarcinogenic agents. Recent studies of the black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) demonstrated that peptides…