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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Newest papers
How Deep is the Signal? Time-Context up to 30 Years for Colorectal Cancer Prediction in a Primary-Care EHR Model
EHR foundation models read medical events within a fixed context window, and long context has so far been measured only in tokens.PharmAgents2: Towards Autonomous End-to-End Drug Discovery
Drug discovery requires continuous scientific decision-making across a vast research space.Interpretable many-body interaction laws for collective motion from few trajectories
Models of collective motion usually reduce social interactions to pairwise forces, despite empirical evidence for many-body effects.A low-rank decoder bottleneck bounds reliability in foundation-model perturbation prediction
Foundation-model predictors of perturbation response are evaluated primarily by aggregate accuracy.CellCanon: An Agentic Cellular World Model for Prediction, Explanation, and Observation-Driven Updating
Biological discovery requires using molecular knowledge and new measurements to infer responses beyond the conditions already observed.The DynaCell Evaluation Suite for Dynamic 3D Virtual Staining of Live Cells
Understanding how cells respond to perturbations over time is central to cell biology and drug discovery.Attribution-based diagnostics for single-cell foundation models
Single-cell RNA foundation models (scFMs) are increasingly used for in-silico biological discovery, yet predictive performance alone does not reveal whether their decisions rely on biologically…A Scientific Claim Stability Framework for Evaluating MRI Morphometry Pipelines
MRI morphometry pipelines are often evaluated by measurement agreement or downstream accuracy, yet their scientific value depends on the conclusions they support.HistoTx: Early fusion of H&E images and spatial transcriptomics at varying spatial transcriptomics resolution with self-supervised learning
Spatial transcriptomics maps gene expression across tissue sections and, when integrated with whole slide images, jointly captures both morphological architecture and molecular activity to provide a…From FAIR to AI-FAIR Metadata-First Infrastructure for AI-Enabled Science
Artificial intelligence (AI) technologies and their capabilities have advanced rapidly over the past few years, leading to widespread interest and adoption in the biological and ecological sciences.BEND 2.0: Benchmarking the Capabilities Needed to Design DNA
Genomic foundation models are increasingly used to propose DNA sequences and edits.One Mistake, Three Layers: Persistence Rules Under Depth Correlation
Probing frozen representations layer by layer is now standard practice, but reporting when a signal first becomes decodable requires a rule for reading a depth curve, and the obvious rule is wrong.From Tool State to Scientific Action: Auditing Decision Provenance in Biomedical Research Agents
A scientific agent can give the same verdict while reading and citing different evidence.Accurate automated photo-identification of Near Eastern and European fire salamanders
Photo-identification underpins non-invasive capture-recapture monitoring of amphibians, but manual identification becomes slow and error-prone as reference libraries grow.Stand-In Effects and Pooling Amplification: Design-Based Tests of Whether Biological World Models Use Actions
Action-conditioned world models are increasingly trained on data from randomized experiments, and whether their predictions respond to actions is usually checked by replacing or removing the actions…Comparative Strategies for Handling Imbalanced QSAR Regression: A Case Study on hERG Activity Prediction
Data imbalance frequently occurs in QSAR modeling, yet most studies focus on classification tasks, and few address regression tasks, as it is challenging to determine which regions of the data are…Governing Equations of Human Sleep Macro-Structure:Symbolic Discovery from 1,106 Nights
Human sleep is organized into a small number of cycles per night: deep sleep dominates early cycles, REM lengthens toward morning, and light sleep clusters at cycle boundaries.Can agents reliably design therapeutic antibodies?
Recent work has demonstrated agents driving protein design workflows, either through orchestration of specialized tools or direct manipulation of sequences.FACET: Feasibility-Automaton Complete Enumeration and Truncation-Free Scoring of Molecular Formulas from MS/MS
Determining the neutral molecular formula of a precursor ion from its tandem mass (MS/MS) spectrum is the first step in identifying an unknown small molecule.Co$^2$ODE: Conditionally Coarse-Grained Model Discovery for Rewiring in Biochemical Networks
Biochemical networks propagate the signals that regulate cellular behaviour, and which routes carry them depends on cellular context: a shift in context rewires the network's effective dynamics.