bioRxiv

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Trustworthy detection of exencephaly in high-throughput micro-CT embryo screens with focal-loss transformers

bioRxiv Jan 1, 2025
Lethal and sub-viable knockout mouse lines require whole-embryo 3D imaging to connect genotype to phenotype (Dickinson et al., 2016; Cacheiro et al., 2022). There are often far fewer samples of in-class (e.g., homozygous knockouts) than wildtype or n...
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Scaling down protein language modeling with MSA Pairformer

bioRxiv Jan 1, 2025
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use multiple sequence alignments (MSA), such as MSA Tr...
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Depositing biological segmentation datasets FAIRly

bioRxiv Jan 1, 2025
Segmentation of biological images identifies regions of an image which correspond to specific features of interest, which can be analysed quantitatively to answer biological questions. This task has long been a barrier to conducting large-scale biolo...
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Divergent spatiotemporal integration of whole-field visual motion in medaka and zebrafish

bioRxiv Jan 1, 2025
Animals in different ecological niches have evolved different sensory capacities to detect behaviorally relevant sensory signals. How behavioral algorithms and neural networks adapt to environmental demands remains unknown. We compared spatiotemporal...
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scELMo: Embeddings from Language Models are Good Learners for Single-cell Data Analysis

bioRxiv Jan 1, 2025
Various Foundation Models (FMs) have been built based on the pre-training and fine-tuning framework to analyze single-cell data with different degrees of success. In this manuscript, we propose a method named scELMo (Single-cell Embedding from Langua...
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Subtype-Specific Roles of Nigrostriatal Dopaminergic Neurons in Motor and Associative Learning

bioRxiv Jan 1, 2025
Nigrostriatal dopaminergic neurons (DANs) in the substantia nigra pars compacta (SNc) comprise distinct subtypes defined by unique gene expression profiles and anatomical characteristics. However, their specific contributions to motor and non-motor f...
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Peripheral immune patterns enable robust cross-platform prediction of ALS onset and progression

bioRxiv Jan 1, 2025
Amyotrophic lateral sclerosis (ALS) progression rates vary dramatically between patients, yet the basis of this heterogeneity remains elusive, with no prognostic biomarkers existing to guide clinical decisions or stratify patients for therapeutic tri...
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BRAVE: a highly accurate method for predicting HIV-1 antibody resistance using large language models for proteins

bioRxiv Jan 1, 2025
Broadly neutralizing antibodies (bNAbs) that target the envelope glycoprotein (Env) of human immunodeficiency virus-1 (HIV-1) have been utilized in clinical trials aimed at preventing and treating HIV-1 infections. However, the emergence of neutraliz...
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PAM adenine methylation and flanking sequence regulate SaCas9 activity in bacteria

bioRxiv Jan 1, 2025
Cas9 nucleases are the effectors of the class 2 type II CRISPR system in bacteria and function to restrict invading DNA. They can also be used with single guide RNAs (sgRNAs) as antimicrobials and genome engineering tools in bacteria, yet application...
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Neural network-assisted analysis of tube vocal tract models

bioRxiv Jan 1, 2025
We present a pipeline for deep neural network assisted modeling and analysis of tube vocal tract models. Such models are composed of a series of cylindrical tube segments, each characterized by length and cross-sectional area. A large synthetic datas...
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