15 papers · ranked by Valyu relevance
Kathryn Dover, Zixuan Cang, Anna Ma, Qing Nie + 1 more
- We propose a framework for the simultaneous alignment and dimension reduction of coupled high-dimensional datasets without any knowledge of common features. - By accomplishing both the dimension reduction and alignment simultaneously, AVIDA is better able to preserve fine-scale structures unique to individual data…
Joshua Franklin, Thomas LaBar, Christoph Adami
Populations exposed to a high mutation rate harbor abundant deleterious genetic variation, leading to depressed mean fitness. This reduction in mean fitness presents an opportunity for selection to restore adaptation through the evolution of mutational robustness. In extreme cases, selection for mutational robustness…
C G Nitash, Thomas LaBar, Arend Hintze, Christoph Adami
While all organisms on Earth descend from a common ancestor, there is no consensus on whether the origin of this ancestral self-replicator was a one-off event or whether it was only the final survivor of multiple origins. Here we use the digital evolution system Avida to study the origin of self-replicating computer…
Thomas LaBar, Christoph Adami, Arend Hintze
The most prominent property of life on Earth is its ability to evolve. It is often taken for granted that self-replication– the characteristic that makes life possible–implies evolvability, but many examples such as the lack of evolvability in computer viruses seem to challenge this view. Is evolvability itself a…
Bhaskar Kumawat, Ramray Bhat
Asexually reproducing populations of single cells evolve through mutation, natural selection, and genetic drift to enhance their reproductive fitness. The environment provides the contexts that allow and regulate their fitness dynamics. In this work, we used Avida - a digital evolution framework - to uncover the effect…
Raúl Ortega, Enrique Wulff, Miguel A. Fortuna
The Ontology for Avida (OntoAvida) aims to develop an integrated vocabulary for the description of Avida, the most widely used computational approach for performing experimental evolution using digital organisms-self-replicating computer programs that evolve within a user-defined computational environment. The lack of…
Chase W Nelson, John C Sanford
Background Avida is a computer program that performs evolution experiments with digital organisms. Previous work has used the program to study the evolutionary origin of complex features, namely logic operations, but has consistently used extremely large mutational fitness effects. The present study uses Avida to…
Bhaskar Kumawat, Ramray Bhat
Background Asexually reproducing populations of single cells evolve through mutation, natural selection, and genetic drift. Environmental conditions in which the evolution takes place define the emergent fitness landscapes. In this work, we used Avida-a digital evolution framework-to uncover a hitherto unexplored…
Daniel R O’Donnell, Jordan A Fish, Abhijna Parigi, Ian Dworkin + 1 more
Standing genetic variation and the historical environment in which that variation arises (evolutionary history) are both potentially significant determinants of a population’s capacity for evolutionary response to a changing environment. We evaluated the relative importance of these two factors in influencing the…
Hirofumi Tsuruta, Hiroyuki Yamazaki, Ryota Maeda, Ryotaro Tamura + 1 more
Language Models Authors: ['Hirofumi Tsuruta' 'Hiroyuki Yamazaki' 'Ryota Maeda' 'Ryotaro Tamura' 'Akihiro Imura'] Antibodies are crucial proteins produced by the immune system to eliminate harmful foreign substances and have become pivotal therapeutic agents for treating human diseases. To accelerate the discovery of…
Dehua Hang, Eric Torng, Charles Ofria, Thomas M Schmidt
Background Maximum parsimony is one of the most commonly used and extensively studied phylogeny reconstruction methods. While current evaluation methodologies such as computer simulations provide insight into how well maximum parsimony reconstructs phylogenies, they tell us little about how well maximum parsimony…
Tiancheng Liu, Jessica Hsiung, Su Zhao, Jessica Kost + 11 more
The outbreak and rapid spread of SARS-CoV-2 virus has led to a dire global pandemic with millions of people infected and ~ 400,000 deaths thus far. Highly accurate detection of antibodies for COVID-19 is an indispensable part of the effort to combat the pandemic^1,2^. Here we developed two-plex antibody detection…
Hong Gao, Yiming Bao, Xuezhen Tu, Yutong Xu + 5 more
Video understanding requires not only visual recognition but also complex reasoning. While Vision-Language Models (VLMs) demonstrate impressive capabilities, they typically process videos largely in a single-pass manner with limited support for evidence revisit and iterative refinement. While recently emerging…
Holger Stitz, Stefan Luger, Marc Streit, Nils Gehlenborg
A major challenge of data-driven biomedical research lies in the collection and representation of data provenance information to ensure reproducibility of findings. In order to communicate and reproduce multi-step analysis workflows executed on datasets that contain data for dozens or hundreds of samples, it is crucial…
Guillaume Croville, Mathilda Walch, Laetitia Lèbre, Sonia Silva + 2 more
During the recent avian influenza epizootics that occurred in France in 2020/21 and 2021/22, the virus was so contagiousness that it was impossible to control its spread between farms. The preventive slaughter of millions of birds consequently was the only solution available. In an effort to better understand the…