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Inspired by natural evolution, evolutionary search algorithms have proven remarkably capable due to their dual abilities to radiantly explore through diverse populations and to converge to adaptive pressures. A large part of this behavior…
The support vector machine (SVM) is one of the most successful learning methods for solving classification problems. Despite its popularity, SVM has a serious drawback, that is sensitivity to outliers in training samples. The penalty on…
In order to clarify phase relation of Zn2SiO4 system, first-principles DFT calculations of 11 phases were conducted. We confirmed that phases III and IV are retrograde phases. Instead, Na2CrO4- and Ag2CrO4-structured phases are most likely…
Reinforcement Learning with Verifiable Rewards (RLVR) enhances reasoning of Large Language Models (LLMs) but usually exhibits limited generation diversity due to the over-incentivization of positive rewards. Although methods like Negative…
The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has ushered panic responses around the world due to its contagious and vaccine escape mutations. The essential infectivity and antibody…
The activation/repression of a given gene is typically regulated by multiple transcription factors (TFs) that bind at the gene regulatory region and recruit RNA polymerase (RNAP). The interactions between the promoter region and TFs and…
The PTPN11 gene encodes the Src homology 2 domain-containing protein tyrosine phosphatase (SHP2), a key regulator of cell growth, differentiation, and apoptosis through its modulation of various signaling pathways, including the RAS/MAPK…
We consider a general mathematical model of a within-host viral infection with $n$ virus strains and explicit age-since-infection structure for infected cells. In the model, multiple virus strains compete for a population of target cells.…
Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to…
The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…
The brain encodes external stimuli through patterns of neural activity, forming internal representations of the world. Recent experiments show that neural representations for a given stimulus change over time. However, the mechanistic…
Many single-stranded (ss) RNA viruses self assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively…
The SARS-CoV-2 spike (S) protein facilitates viral infection, and has been the focus of many structure determination efforts. Its flexible loop regions are known to be involved in protein binding and may adopt multiple conformations. This…
While solid-state protein junctions have shown efficient electron transport over lengths that surpass those of conventional organic semiconducting systems, interfacial or contact effects may obscure the intrinsic protein charge transport…
One of the most important challenges in the analysis of high-throughput genetic data is the development of efficient computational methods to identify statistically significant Single Nucleotide Polymorphisms (SNPs). Genome-wide association…
COVID-19 is an infection caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2), which has caused a global outbreak. Current research efforts are focused on the understanding of the molecular mechanisms involved in…
A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we show that the two most commonly used methods to disentangle the…
Automated detection of sclerotic metastases (bone lesions) in Computed Tomography (CT) images has potential to be an important tool in clinical practice and research. State-of-the-art methods show performance of 79% sensitivity or…
Decoding how linear DNA encodes regulatory information remains a central challenge. Existing decoding approaches lack interpretability and struggle to reveal the underlying coding principles. Here, we present the interpretability-first,…
The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function,…