8 papers · ranked by Valyu relevance
Fabio Cumbo, Kabir Dhillon, M. Hassan Najafi, Sercan Aygun + 1 more
The exponential growth of genomic databases necessitates alignment-free methods for comparing genomes. While MinHash-based tools have revolutionized this field by efficiently estimating the Average Nucleotide Identity based on k-mer sets, they inherently discard structural genomic information. We introduce HyperSketch…
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…
Xianshengjie Lang, Changbin Zhang, Jingxuan Lin, Zhe Zhang + 3 more
Cell-free protein synthesis (CFPS) systems are a powerful platform with immense potential in fundamental research, biotechnology, and synthetic biology. Conventional prokaryotic CFPS systems, particularly those derived from Escherichia coli, often rely on complex reaction buffers containing up to 35 components…
Eliezer Masliah
How transient neural representations become integrated and stable enough to function as internal neural models remains incompletely understood. Grounded in efficient coding, Bayesian and predictive frameworks, recurrent and attractor dynamics, neural state-space models, and systems neuroscience, the Principle of…
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…
Phillip M. Gray, Phoebe Perham, Ben Andrews
Data were collected through focus groups, which were selected to maximize time efficiency and provide rich data through the snowballing of ideas. Sessions were conducted on one occasion between May and June 2023, either face-to-face or online via Teams or Zoom. Online focus groups offered participants logistical…
Yuesong Wu, Haohao Su, Yuehua Cui
Cell-cell communication (CCC) is essential for maintaining tissue organization and driving biological progression, yet its inference from transcriptomic data has long been limited by the absence of spatial context. Advances in spatial transcriptomics (ST) now enable mechanistically grounded analyses of CCC by…
Nishan Shettigar, Ling-Qi Zhang, Jessica Teran, Luisa Schuster + 3 more
In the wild, a mouse must flexibly perform multiple computations at once, rapidly navigating, sampling its environment, forming and using memories, and balancing internal needs. Capturing the self-paced, low-repetition, complex nature of decision making in the wild while preserving the experimental control needed to…