10 papers · ranked by Valyu relevance
Rob Patro, Siddhant Bharti, Prajwal Singhania, Rakrish Dhakal + 2 more
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compressed fastq.gz files has become a substantial scalability bottleneck in the modern world of fast and massively parallel…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
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Recent advances in machine learning force fields (MLFF) have significantly extended the reach of atomistic simulations. Continuous progress in this field requires reliable reference datasets, accurate MLFF architectures, and efficient active learning strategies to enable robust modeling of complex molecular and…
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Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…
Simone Krogh, Liina Pylkkänen
The neural basis of syntax is notoriously difficult to study without working memory and lexico-semantic confounds. To tackle these challenges, we presented dependencies in minimal Danish two-word sentences using Rapid Parallel Visual Presentation (RPVP), which eliminated the tem-poral delay between a filler and gap.…
Charles Tapley Hoyt, Klas Karis, Benjamin M. Gyori
Hundreds of resources assign identifiers to biomedical concepts including genes, small molecules, biological processes, diseases, and cell types. Often, these resources overlap by assigning identifiers to the same or related concepts. This creates a data interoperability bottleneck, as integrating data sets and…
Gina F. Humphreys, Matthew A. Lambon Ralph
This study integrates three literatures typically examined in isolation: single-concept semantics, combinatorial semantics, and theory of mind (ToM). We argue that these domains share overlapping computational principles and neuroanatomical networks. Here, we report three major investigations with converging…
Carlo Y. Meloni, Chundra A. Cathcart, Erik J. Ringen, Jessica K. Ivani + 1 more
We examine the syntax-semantics interface in clause linkage using a cross-linguistic sample of nearly 700 constructions from Indo-European, Sino-Tibetan, and Tupí-Guaraní. To evaluate predictions from the Interclausal Relations Hierarchy, we model the phylogenetic dynamics of how semantic relations influence the degree…
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Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
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Step-by-step thinking is essential in all domains of chemical sciences and engineering. While machine learning tools are broadly used, algorithms that automate reasoning are far less common. We elaborate on seven categories of human reasoning activities and connect each to applications in chemical science and…