Biophysics & Systems Biology · Life Sciences
Quantitative Methods
The newest papers in Quantitative Methods that ReadSearch has read, newest first. Each links to its own page, with its authors, date, where it was published and the original.
140 papers, from 4 September 2026 to 5 November 2026: 140 arXiv preprints.
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A two-stage diffusion-driven morphogenesis model with evolving connectivity
Morphogenesis of diatom silica shells involves a sequence of topological transitions: initially separate ribs grow and branch, then merge through bridges, leaving a regular network of pores.A richness-sensitive Acoustic Biodiversity Index from species-level detections: classifier benchmarking, false-positive control and validation against standard soundscape indices in an African savanna and an urban zoo
Acoustic indices are widely used as rapid proxies for biodiversity, but they summarise the distribution of sound energy rather than the species producing it and often track richness poorly.Physiological Trajectories and Observation Patterns in ICU Mortality Prediction: Transportability Under Changing Measurement Conditions
To distinguish the transferable predictive value of physiological trajectories from that of observation patterns in ICU mortality prediction, and to assess whether measurement timing affects…Confidence Filtering in Video-Based Gait Assessment: Measurement Error versus Selection Shift
Video-based gait assessment often keeps only high-confidence pose observations, which can lower measurement error but change the movement assessed.Agentic LLM reasoning in pediatric diabetes outcome prediction from multimodal medical records
Large language model (LLM) agents are proposed for clinical prediction but are untested in pediatrics, where cohorts are small and outcomes are uncommon.Learning developmental dynamics from lineage context
A central goal of biology is to predict the dynamics of multicellular systems.GraphTFactor: A graph-based approach for proteins transcription factor prediction
Transcription factors (TFs) play an important role in regulating gene expression, making their identification a fundamental task in computational biology.Morpheus.AI: agents autonomously generate, execute and refine virtual tissue models
Virtual tissue models link observations to mechanistic hypotheses, but building them demands expertise in biology, mathematics and programming.Who Called? V33DA: A Physically Verified Multimodal Benchmark for Vocal Attribution in Zebra Finch Groups
Deciding which member of an animal group produced a vocalization and where that vocalization was produced are central to studying social communication but are rarely evaluated with physically…What to randomize matters: a controlled study of volume, axis and representation in low-data molecular generation
Chemical language models can struggle to generate new molecules when trained on small datasets, where a model may reproduce training examples rather than learn a useful generative distribution.Automatic Construction of Strong Simple Baselines
To rigorously establish the value of a novel deep learning method, it must be compared against appropriate baselines.Stationary Action Principles for Neuronal Growth
Neuronal growth is guided by biochemical, mechanical, and geometrical cues while being influenced by stochastic fluctuations in cytoskeletal dynamics, adhesion, and growth cone sensing.HGPRGDel: GPR-Aware Learning and Ranking for Growth-Coupled Gene Deletion Design
Designing microbial strains for growth-coupled production, in which cellular growth is linked to the synthesis of a target compound through genetic interventions, is a fundamental goal in metabolic…A Differentiable, GPU-Accelerated Finite-Element Formulation in JAX for Large-Deformation Shells with Contact: Application to Patient-Specific Aortic Valve Simulation
Patient-specific aortic-valve models can help assess how tissue properties and geometry influence leaflet deformation and coaptation, with potential to inform intervention planning.Structure, Not Sequence: Tracking and Validating Folding Mechanisms in ESMFold's Trunk with Sparse Autoencoders
Structure predictors like ESMFold fold proteins using neural network computation and have transformed structural biology.ProtAgent: Post-Training Compact Protein Tool Agents with Interaction-Level Credit Assignment
Protein annotation agents must choose suitable bioinformatics tools, interpret their outputs, and use the resulting evidence in the final answer.Automated screening of Parkinson's Disease using Smooth Pursuit Eye Movements
Smooth pursuit eye movements are frequently altered in Parkinson's disease, but previous studies have relied mainly on conventional parameters that describe the relationship between gaze and target.Kinetic Proofreading Activation Times Beyond the Weibull Limit
T cells can detect a few foreign peptide-major histocompatibility complexes (pMHCs) among a far larger number of self pMHCs.VGL-stGen: Learning a shared multimodal model for lung histology and spatial transcriptomics
VGL-stGen is a multimodal large language model adapted from a pretrained medical vision-language model using paired lung H&E and spatial transcriptomics with single-cell references.Spatially Informed and Direction Sensitive Representation Learning for Spatial Transcriptomics
Cellular states are shaped by both intrinsic gene expression programs and the spatial microenvironment in which cells reside.