Quantitative Methods (Biology)
Mathematical and computational methods applied to biological systems.
q-bio.QM · 137 papersLetting the neural code speak: Automated characterization of monkey visual neurons through human language
A novel framework uses generative models and neural digital twins to characterize monkey visual neurons with concise, verifiable natural language descriptions.
Accounting for Missed Events in the Bayesian Modeling of IP3R Multimodal Gating
A Bayesian approach with missed event correction refines IP3R channel gating models, clarifying its multimodal behavior and kinetic parameters.
NORI: Fast probabilistic inference for ambiguous observation-entity mappings
NORI offers significantly faster probabilistic inference for ambiguous observation-entity mappings, enabling large-scale bioinformatics analysis.
EpiCastBench: Datasets and Benchmarks for Multivariate Epidemic Forecasting
EpiCastBench introduces 40 diverse multivariate epidemic datasets and a standardized benchmark for evaluating forecasting models.
Unlocking LLM Creativity in Science through Analogical Reasoning
Analogical Reasoning (AR) enables LLMs to generate significantly more diverse and novel solutions for scientific problems, mitigating mode collapse.
Beyond Manual Curation: Augmenting Targeted Protein Degradation Databases via Agentic Literature Extraction Workflows
A new expert-in-the-loop LLM workflow automates targeted protein degradation data extraction, significantly expanding databases with high accuracy.
AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents
AssayBench is a new benchmark for phenotypic screen prediction in virtual cell models, evaluating LLMs and agents on diverse cellular phenotypes.
Clin-JEPA: A Multi-Phase Co-Training Framework for Joint-Embedding Predictive Pretraining on EHR Patient Trajectories
Clin-JEPA is a multi-phase co-training framework for JEPA pretraining on EHR patient trajectories, enabling accurate forecasting and risk prediction.
LiteMedCoT-VL: Parameter-Efficient Adaptation for Medical Visual Question Answering
LiteMedCoT-VL enables compact 2B models to achieve advanced medical VQA reasoning by distilling chain-of-thought from a 235B teacher.
A putative, computationally stable structure of homotrimeric BP180/collagen XVII
This paper computationally predicts and validates a stable 3D structure for the homotrimeric BP180 protein, a key antigen in bullous diseases.
MicroFuse: Protein-to-Genome Expert Fusion for Microbial Operon Reasoning
MicroFuse integrates protein and genome context using a Mixture-of-Experts model to accurately predict microbial operons, outperforming baselines.
Automated Optical Density Normalization for Myelin Quantification: Cross-Modal Validation with 7T Ex Vivo MRI
This paper introduces an automated pipeline for normalizing optical density in myelin histopathology, improving quantitative analysis and cross-modal correlation with MRI.
VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design
VibeProteinBench is a new benchmark evaluating language-interfaced LLMs in generalist protein design across recognition, engineering, and generation.
MicroDiffuse3D: A Foundation Model for 3D Microscopy Imaging Restoration
MicroDiffuse3D is a foundation model that restores high-quality 3D microscopy images from degraded, low-resolution data, enabling faster volumetric chemical imaging.
PPI-Net connects molecular protein interactions to functional processes in disease
PPI-Net is a hierarchical GNN integrating protein interaction networks with pathway representations to model disease from molecular interactions to functional processes.
Flow Matching for Count Data
Introduces count-FM, a novel flow-matching framework for high-dimensional count data, achieving better sample quality and efficiency.
GoForth: Language Models for RNA Design under Structure, Sequence, and Coding Constraints
GoForth is a new RNA language model that efficiently designs RNA sequences under complex structure, sequence, and coding constraints.
Partitioning Neural Co-Variability
Introduces PMNLV, a novel model to partition neural co-variability, revealing shared population gain covariance peaks in primary visual cortex.
Better Protein Function Prediction by Modeling Survivorship Bias
Evo-PU improves protein function prediction by modeling survivorship bias in sequence data, outperforming existing methods.
Mathematical Modeling of Early Embryonic Cell Cycles of Drosophila melanogaster
This paper presents a mathematical model of Drosophila embryonic cell cycles, hypothesizing that CycB synthesis drives the observed period lengthening.
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