Search · four archives
Search · four archives
19 papers · ranked by Valyu relevance
Huan Feng, YanJin Li, XiaoYi Wang, QingChuan Wang + 1 more
Background Rural older adult populations face significant disparities in sports participation compared to urban areas. Traditional linear analytical approaches often fail to capture the complex configurational nature of effective public service delivery in rural contexts, necessitating sophisticated methodological…
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We present a new method for fingerprint- ing atomic configurations relevant to ML-IAM training and application, utilizing the ChIMES descriptor. These fingerprints enable rigor- ous analysis of statistical distinguishability be- tween configurations. Sample applications in- clude assessing diversity within ML-IAP…
Nina Javerzat, Gerhard Jung, Jorge Kurchan, Misaki Ozawa
We compute the low-temperature configurational entropy of a two-dimensional supercooled liquid. Our method, based on a higher-dimensional version of the Grassberger--Procaccia algorithm, can be implemented in a manner that is entirely agnostic with respect to both the dynamics and the theoretical framework, as any…
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The consideration of transition state (TS) conformer ensembles is required to accurately model a reaction, and thus plays a key role in computational catalyst design. While CREST and GOAT are established methods for TS conformer ensemble generation, the associated computational cost remains a major bottleneck in…
Nikolay Fedorov, Akito Monden, Hiroki Inayoshi, Haruaki Tamada + 1 more
Software birthmarks provide a robust approach to detecting code plagiarism even under substantial modifications, while distinguishing independently developed software. Existing similarity measures are typically applied at the module level (e.g., source or class files). However, in practice, software reuse often occurs…
Gabriel Bounias, Sabine Ploux
This work examines the semantic geometry underlying NLP models. We compare supervised vector embeddings, such as CamemBERT, with lexical co-occurrence graphs that encode semantic relations more directly. While transformer-based embeddings achieve strong performance, their induced geometries often display unsatisfactory…
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Subtle stereoelectronic effects can play an important role in drug discovery and other application areas, with atropisomerism gaining increasing interest recently. This raises the question which level of theory is required to model such phenomena accurately by computational means, i.e., are classical mechanics (MM)…
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Predicting how chemical modifications affect drug binding is central to rational drug design. Free Energy Perturbation (FEP) calculations provide accurate estimates of these binding affinity changes, but existing methods often require substantial computational resources and expert knowledge. Here we present QligFEP…
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Cold regulated protein 15A (COR15A) is a late embryogenesis abundant (LEA) protein from Arabidopsis thaliana which is expressed in response to low temperatures and dehydration. Here we use a combination of ion mobility-mass spectrometry (IM-MS) and molecular dynamics (MD) simulations with elevated temperature for…
Kalen Clifton, Vivien Jiang, Rafael dos Santos Peixoto, Srujan Singh + 3 more
Comparative analysis of spatial transcriptomics (ST) data is needed to identify genes that spatially change in their expression patterns between conditions, such as in diseased versus healthy tissues. Existing methods, including those developed for and adapted from non-spatial transcriptomics, generally focus on…
Leonard Bohnenkämper, Luca Parmigiani, Cedric Chauve, Jens Stoye
Genomic rearrangements are major drivers of evolution and genetic disease. However, studying rearrangements requires segmenting the genomes of interest into conserved regions, called synteny blocks, that highlight structural differences between genomes. Synteny blocks are typically defined from annotated genes or…
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…
Xin Wang, Ming Liu, Jun-E. Zhang, Renli Deng + 7 more
When performing fuzzy-set qualitative comparative analysis, researchers face a considerable margin of discretion in setting parameters that can influence the results. Therefore, it is necessary to conduct robustness checks based on the set-theoretic method. This study achieves robustness checks by adjusting the…
Franjo Ivankovic, Dongmei Yu, James Shen, Lingyu Zhan + 10 more
Cross-Array Experiment (CAE) results are summarized in [btag341-T5] and [btag341-T6], [sup1]. Briefly, similarly to WAE, Full Sets in both the OEE and GSA1 array resulted in the most CNV calls (low-stringency QC 14 587 calls and 19 396 calls; medium-stringency QC 2293 and 1818 calls on GSA1 and OEE, respectively) and…
Marieke Stolte, Jörg Rahnenführer, Andrea Bommert
Quantifying the similarity of two or more datasets has widespread applications in statistics and machine learning. The method choice is, however, difficult due to the abundance of proposed methods and the lack of neutral comparison studies, especially for categorical data. Here, the most promising methods are compared…
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Atomistic simulations provide essential mechanistic insights into chemical processes, yet many important phenomena in chemistry and materials science occur on timescales that are inaccessible to molecular dynamics. Existing computational approaches force a choice between atomic resolution on relatively short timescales…
Luca Franco, Matteo Migliarini, Matteo Tommaso Ungaro, Egnald Çela + 5 more
Accurate evaluation of genome assemblies within highly repetitive regions, such as centromeres, remains a major open challenge in genomics. Conventional benchmarking relies on sequence alignment, which becomes problematic in regions of high homogeneity and divergence. Here, we framed centromere assembly evaluation as a…
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Quantitative Structure Activity Relationship (QSAR) remains an effective tool for early-stage chemical modelling and virtual screening in drug design. The advancements in this field are led by two core paradigms, 1) descriptor engineering, where complex fixed-length vectors of compounds are generated and conventional…
Mark S. Hibbins, Cassandre Pyne, Mykhailo Sukmaniuk, Emily Glasgow + 4 more
Chromosomal rearrangements are a major driver of evolutionary innovation, shaping processes including local adaptation, speciation, and sex chromosome evolution. Multispecies synteny datasets are rich in information on the drivers of genomic rearrangement, but statistical approaches that enable insights to be obtained…