15 papers · ranked by Valyu relevance
Zhimeng Zhou, Yang Nan, Minjie Mou, Yuntao Qian + 16 more
Artificial intelligence (AI) is increasingly permeating the drug development pipeline. Numerous algorithms for accelerating this multi-stage and multi-task process have been constructed, which depends heavily on expert design and labor-intensive task-specific optimization. Given that AI-driven acceleration of drug…
Kangbien Park
Humans have long employed directed evolution (DE) to engineer desired biological traits. In this paper, I introduce an algebraic framework that provides a quantitative representation of the general phenotypic traits of asexual populations, enabling the systematic modeling of DE processes. Within this framework, key…
Manuel Corpas
Large language model (LLM) agents are typically deployed as clones: identical copies of a single configuration with no mechanism for heritable variation or population-level dynamics. Here we introduce Genomebook, a designed evolutionary system that encodes 26 behavioural traits across 60 diploid loci using additive…
João Sartori, Eduardo Krempser, Ana Carolina Ramos Guimarães, Lucas de Almeida Machado
The optimization of protein sequences for enhanced binding and stability remains a formidable challenge in bioengineering due to the vastness of sequence space. Existing state-of-the-art methods, including traditional structure-based design and protein language models, use fitness estimators as objective functions to…
Andrea Polo-Rodríguez, David R. Penas, Julio R. Banga
Parameter estimation is a central challenge in systems biology, particularly for large dynamic models described by nonlinear ordinary differential equations (ODEs). These global optimization problems exhibit landscapes which are topologically heterogeneous, often exhibiting a pathological mixture of stiff, smooth…
Ali M. Farhat, Lydia Freddolino
Understanding sequence specificity in transcription factor binding is a critical step in understanding gene regulation. DNA-protein binding experiments such as ChIP-chip and ChIP-seq can reveal where on the genome a particular transcription factor of interest is bound, and similar experiments such as ATAC-seq or DNase…
Iain G. Johnston, Ramon Diaz-Uriarte, James D. Boyko
Many scientific questions involve the coevolution of coupled, binary features over time – from phenotypes in evolutionary biology to mutations in cancer development. Evolutionary accumulation models (EvAMs) often neglect reversibility in these systems, uncertainty in observations, and/or phylogenetic connections…
Nhan Ly-Trong, Samuel Martin, Nick Goldman, Nicola De Maio + 1 more
Phylogenetic analysis is essential to genomic epidemiology, for example in tracing the origin and evolution of SARS-CoV-2 variants during the COVID-19 pandemic. We previously introduced CMAPLE, a single-threaded implementation of the MAPLE algorithm designed for large-scale epidemiological genomic datasets. CMAPLE can…
Niels Holtgrefe, Leo van Iersel, Ruben Meuwese, Yukihiro Murakami + 1 more
Phylogenetic diversity plays an important role in biodiversity, conservation, and evolutionary studies by measuring the diversity of a set of taxa based on their phylogenetic relationships. In phylogenetic trees, a subset of k taxa with maximum phylogenetic diversity can be found by a simple and efficient greedy…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…
Annabel Large, Ian Holmes
Most statistical phylogenetics analyses use relatively simple continuous-time finite-state Markov models of point substitution to describe molecular evolution, often keeping sequence length fixed, ignoring insertions and deletions (indels) entirely, and making little (if any) allowance for variations in selection…
Michael L. Helde, Alexander G. Dimitrov
We adapted an olfactory neuromorphic algorithm to image and sound recognition. To achieve this, we carried out specific preprocessing procedures that were tailored to each modality. For images, we used the NIST digits dataset directly. For sound, we used samples from the Google Speech Command dataset. A gammatone…
Nicolas Loeuille, Rudolf P. Rohr
Given the accumulation of evidence that evolution can affect ecological dynamics, especially under global change scenarios, a key question is how such ecoevolutionary dynamics may change the coexistence of species and biodiversity in general. In the present article, we propose a graphical approach allowing to…
Kimonas Provatas, Guliang Wang, Nikol Chantzi, Archit Patil + 4 more
H-DNA is a naturally occurring intramolecular DNA triplex structure formed by Hoogsteen hydrogen bonds at homopurine-homopyrimidine mirror repeats and has functional roles in gene regulation, genome instability, and human disease. The existing H-DNA detection tools capture only a subset of H-DNA sequences, often…
Vittorio Zampinetti, Harald Melin, Alva Hallin, Jens Lagergren
Phylogenetic tree reconstruction from single cell data based on copy-number alterations (CNAs) is an important problem in cancer genomics. Methods have been developed to address this problem by computing pairwise distances between copy-number profiles and employing a tree reconstruction algorithm. Despite the tight…