12 papers · ranked by Valyu relevance
Aial Sobeh, Simone Shamay-Tsoory, Bruno Kluwe-Schiavon, Giorgio Manenti
Human behavior is shaped by a pervasive motive to align with others, manifesting across a wide range of tendencies-from motor synchrony and emotional contagion to convergence in beliefs and choices. Existing accounts explain how alignment arises through predictive coding and observation-execution mechanisms, but they…
Toshitake Asabuki, Claudia Clopath
Recurrent neural circuits often face inherent complexities in learning and generating their desired outputs, especially when they initially exhibit chaotic spontaneous activity. While the celebrated FORCE learning rule can train chaotic recurrent networks to produce coherent patterns by suppressing chaos, it requires…
Samantha Petti, Nicholas Bhattacharya, Roshan Rao, Justas Dauparas + 5 more
Multiple Sequence Alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any…
Toshitake Asabuki, Claudia Clopath
Recurrent neural circuits often face inherent complexities in learning and generating their desired outputs, especially when they initially exhibit chaotic spontaneous activity. While the celebrated FORCE learning rule can train chaotic recurrent networks to produce coherent patterns by suppressing chaos, it requires…
Tao Fang, Damian Szklarczyk, Radja Hachilif, Christian von Mering
Protein-protein interactions (PPIs) play essential roles in most biological processes. The binding interfaces between interacting proteins impose evolutionary constraints that have successfully been employed to predict PPIs from multiple sequence alignments (MSAs). To construct MSAs, critical choices have to be made…
Tao Fang, Damian Szklarczyk, Radja Hachilif, Christian von Mering
Protein-protein interactions play essential roles in almost all biological processes. The binding interfaces between interacting proteins impose evolutionary constraints, leading to co-evolutionary signals that have successfully been employed to predict protein interactions from multiple sequence alignments (MSAs).…
Maryam Gillani, Gianluca Pollastri
Alignments in bioinformatics refer to the arrangement of sequences to identify regions of similarity that can indicate functional, structural, or evolutionary relationships. They are crucial for bioinformaticians as they enable accurate predictions and analyses in various applications, including protein subcellular…
Nimrod Serok, Ksenia Polonsky, Haim Ashkenazy, Itay Mayrose + 2 more
Multiple sequence alignment (MSA) inference is a central task in molecular evolution and comparative genomics, and the reliability of downstream analyses, including phylogenetic inference, depends critically on alignment quality. Despite this importance, most widely used MSA methods optimize the sum-of-pairs (SP)…
Nimrod Serok, Ksenia Polonsky, Haim Ashkenazy, Itay Mayrose + 3 more
Multiple sequence alignment (MSA) inference is a central task in molecular evolution and comparative genomics, and the reliability of downstream analyses, including phylogenetic inference, depends critically on alignment quality. Despite this importance, most widely used MSA methods optimize the sum-of-pairs (SoP)…
Andreas Grigorjew, Artur Gynter, Fernando Dias, Benjamin Buchfink + 2 more
Sequence alignments have become the foundation of life science research by unlocking biological mechanisms through protein comparisons. Despite its methodological success, most algorithmic innovation in the past decades focused on the optimal alignment problem, while often ignoring information derived from suboptimal…
Daniel Wolf, Gasser Farrag, Tabea Flügge, Lan Huong Timm + 4 more
'Vincenzo Grassia' 'Letizia Perillo' 'Fabrizia d’Apuzzo' 'Juan Martin Palomo'] Background/Objectives: Machine learning (ML) models predicting the risk of refinement (i.e., a subsequent course of treatment being necessary) in clear aligner therapy (CAT) were developed and evaluated. Methods: An anonymized sample of 9942…
Vanessa Ferdinand, Amy Yu, Sarah Marzen
Organisms can solve complex tasks despite having limited cognitive resources when those resources are used optimally. Doing so optimally makes an organism “resource-rational”. In this paper, we show for the first time that humans are resource-rational at prediction. In a novel sequence learning experiment, participants…