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.
Get the few papers worth your time in Quantitative Methods every morning.
Follow Quantitative Methods and ReadSearch reads its new papers each day, then brings you the few worth reading, each with its key finding in a sentence.
Newest papers, page 3
How Robust Are Prognostic Radiomic Features? Comparing Selection Techniques on Pooled Glioblastoma Cohorts
Radiomic survival studies in glioblastoma report heterogeneous prognostic features, but how much of this stems from the methodology itself is rarely examined.Small Average Error, Wide Individual Error: General-Purpose LLMs Estimating Energy Intake from Meal Photos in a Feeding Trial
Photo-based estimation of food energy could ease dietary assessment, and general-purpose multimodal large language models (LLMs) make such estimates easy to obtain.Bombadil: A Foundation Model for Plant Electrophysiology
Living plants, like animals, use electrical signals to carry information about their physiological state across their body, from roots to branches.What Language Adds, and at What Cost: Four Controlled Probes of Pathology Vision-Language Models
Vision--language models (VLMs) promise to make computational pathology queryable and able to draft reports, but how much language adds beyond the vision backbone is unclear, because almost every…Cross-disorder Learning of Imaging-derived Joint Mophometric Markers in Alzheimer's and Parkinson's Diseases
As two most prevalent neurodegenerative diseases (NDDs), Alzheimer's disease (AD) and Parkinson's disease (PD) shared commonalities both in symptomology and pathophysiology.EMBER: Predicting TCR--pMHC Binding Without a Docked Complex
We propose EMBER, a structure-based framework for TCR--pMHC binding prediction that eliminates the need for a predicted docked complex, and with it the placement error that dominates such predictions.QProtFuse: Query-Guided Layer Fusion for Retrieval-Augmented Protein Function Prediction
Predicting protein functions from amino acid sequences is essential to understanding biological processes.Label-Space Mismatch Distorts Cross-Cohort Evaluation in Breast Cancer Molecular Subtyping
Cross-cohort evaluation of breast cancer subtype classifiers is unreliable when source and target cohorts use different annotation standards: METABRIC labels six classes, PAM50 defines five, and a…CADS: Measuring the Incremental Contribution of LLM Proposers in Sequential Biological Screens
Large language models are increasingly used to guide sequential biological screens, yet standard evaluations rely on raw hit counts that conflate a proposer's value with the discovery capacity of…Aptamers as a sandbox for lab-in-the-loop agentic molecular discovery
Despite breakthroughs in AI-driven molecular generation, existing discovery pipelines operate largely in silico, with wet-lab feedback reserved for validation rather than iterative improvement.MultiPASE: Shape-Aware Comparative 3D Genome Analysis
3D genome structures reconstructed from Hi-C data provide valuable insights into chromatin organization, but comparing them across conditions and time points remains challenging because of noise…ProtoGTX: Prototype-Aligned Graph Transformer for Explainable Whole-Slide Image Analysis
Deep learning has achieved strong performance in computational pathology, but explaining whole-slide image (WSI) predictions remains challenging.Indirect Influences of Artificial Intelligence Advice on Complex Sepsis Treatment Decisions
Sepsis is a major public health concern, and many sepsis patients die due to ineffective hemodynamic management.OmicsBench: a long-horizon multi-turn benchmark of AI agents on research-study-scale bioinformatics
Computational biologists increasingly delegate substantial analyses to AI agents in long-horizon, multi-turn sessions, yet most benchmarks of agents' bioinformatics capabilities pose a single short…Poisoning the corpora of protein design systems during pre-training and retrieval
Protein foundation models increasingly support the generation of novel biological sequences, yet their reliance on large public datasets creates opportunities for adversarial manipulation of the…Documenting Trofinetide Treatment Phenotypes in Rett Syndrome with a Dual-LLM Consensus Pipeline
Trofinetide, approved in 2023 as the first Rett syndrome treatment, lacks scalable real-world monitoring because chart review is labor-intensive.Causal Integrated Gradients: Scalable Feature Attribution Along Causal Paths
Existing feature attribution methods that account for feature dependencies do not scale to high dimensions.Learning the Shared Latent Structure of Cryo-EM Inverse Problems
Understanding biomolecular function requires characterizing three-dimensional structure and conformational variability, for which cryogenic electron microscopy (cryo-EM) is a powerful tool.Harness-Driven Agentic Operation of Optical Pooled Screen Analysis
Optical pooled screens connect genetic perturbations to changes in cell morphology and behavior, but turning the microscopy data into interpretable results takes complex, multi-day analyses.Alert-List Concordance for Evaluating Imputation Strategies in ICU Sepsis Prediction
Preprocessing is an under-measured reliability risk in clinical prediction: a model can keep a similar AUROC and still change who receives an alert.