arXiv preprints from January 1, 2026 through September 23, 2026 — 07:58:16 EST
Local chemical perception and property reasoning are both essential for understanding how molecular structure determines properties. Current LLM-based chemical reasoning methods either receive SMILES/molecular images together with descriptions of local motifs, or reason directly from molecular images. Neither approach enables the...
Fast pixelated detectors are driving 4D-STEM toward microsecond dwell times, a regime in which the finite response of the scan deflection coils becomes comparable to the dwell time itself. Using direct probe imaging and sub-frame diffraction analysis, we document a significant intra-dwell scan-coil delay that systematically smears the...
The field of bioinformatics struggles with legacy code - old code that is commonly used but may no longer have a maintainer, or may be written in an now-unfamiliar language (e.g. Perl, Fortran). This incurs maintenance cost (technical debt), but dynamically typed languages also negatively impacts the environment and fail to make use...
Highly pathogenic avian influenza (HPAI) outbreaks require rapid control during active transmission and evidence-based decisions on the safe restocking of depopulated farms. We developed a stochastic spatial SEIR-based metapopulation model for a synthetic HPAI outbreak on the fictional Jolly Island. Farms were classified as...
Neurodegenerative diseases can be viewed as spreading processes on brain networks, in which pathological proteins propagate between anatomically connected brain regions. Mathematical models have been used to study this process, but they generally ignore the influence of neuronal activity, even though experimental studies show that...
Microbial populations generally evolve in fluctuating environments under time-varying conditions. These are often described by binary switching models, sometimes seen as coarse-grained feast-famine cycles, in which resource availability switches abruptly between abundant and scarce conditions. However, experimental studies suggest...
Biochemical reaction networks have become a central theoretical framework for implementing molecular computation. A key challenge is finite time computational accuracy, as computation outputs are encoded in limiting steady states (LSSs) of species concentrations while practical implementations operate for only finite time. This work...
Protein language models (PLMs) have transferred the latest advances from natural language processing to computational biology. These models, trained on large corpora of protein sequence data, are widely used to translate amino acid sequences into latent-space embeddings, ready for use in diverse downstream tasks (DTs). By a common...
A predictive model can fit its data even when its information set is insufficient; fit alone cannot establish sufficiency. This Perspective introduces Level II-A, a new design-based inference framework to test this distinction, illustrated in anticipatory EEG using contingent negative variation. A pre-event endpoint is committed...
The classical problem of Other Minds has dogged philosophers for millennia; asking if we have any way to truly understand the experience of another mind. We know our own intrinsic experience by acquaintance, but can only ever hope to possess an extrinsic description of another's, with the two separated by an acquaintance gap....
Identifying individual learning styles optimizes pedagogical efficacy. While traditional questionnaires are structured, behavioral tracking methods require prolonged interaction log accumulation. To overcome these temporal constraints, this paper proposes an objective Electroencephalography (EEG) approach evaluating Phase Locking...
Scaling relations linking species size, abundance, and resource availability are among the most robust empirical regularities in ecology. However, a mechanistic explanation for how these community-level laws emerge from ecological processes remains elusive. Here, we address this gap by developing a minimal spatially explicit dynamical...
SVPLEX is a Nextflow pipeline for cohort-level structural variant detection from short-read whole-genome sequencing data. The pipeline implements six different structural variant callers with different strengths and weaknesses, integrating different levels of evidence for SVs, and generates a merged consensus callset across the...
Congruency effects, observed in conflict tasks such as Stroop and flanker tasks, have been investigated for nearly a century in psychology and neuroscience, but their mechanistic basis is not fully understood. We introduce a verbal-only LLM conflict task in which a prompt stem elicits a default same-color completion and an explicit...
Hit-to-lead optimization requires iterative design of hit analogs across competing potency, selectivity, physicochemical, pharmacokinetic, safety, and synthetic constraints. We present SABLE (Synthetically-accessible Agentic Bayesian Ligand Exploration), an open-source framework that employs natural-language orchestration to guide...
AlphaFold3-class structure predictors pair a representational trunk, which processes sequence and context, with a diffusion module, which generates atomic coordinates. How biological information changes as it crosses this architectural boundary remains poorly understood. We analyze per-residue activations from the Pairformer trunk and...
Drug response prediction (DRP) models are an active area of research in pharmacogenomics, with growing potential to accelerate the identification of effective anticancer drugs. However, their predictive performance is often constrained by limited dataset scale and insufficient coverages of cancer and chemical spaces. In addition,...
To be conscious is to have an experience - not a collection of phenomenal atoms, but a structured whole composed of distinctions and the relations that bind them. Integrated Information Theory (IIT) identifies the essential properties of every experience (axioms), formulates them operationally as postulates that a substrate must...
Predicting how molecular changes affect large-scale brain activity is a difficult task because of the lack of appropriate methods to link scales. In this perspective, we review a class of mean-field models that can integrate biophysical details such as synaptic receptors or membrane ion channels. This leads to a multi-scale modeling...
Active-quiescent switching occurs in biological populations in which growth is confined to a proliferative active state, while cells may reversibly enter a nonproliferative quiescent state. Experiments often observe only part of this process, through active-state markers, aggregate population measurements, or aggregate data...
Representational similarity analysis (RSA) is increasingly used to ask which learning rules give convolutional networks brain-like representations. Because biologically plausible rules such as feedback alignment, predictive coding and STDP do not scale, studies that include them train small networks on small images (typically 32x32...
Reproductive hormones regulate a wide range of physiological processes throughout the human lifespan. Estrogen, in particular, varies substantially across the menstrual cycle and is widely used in contraceptives and hormone replacement therapies. Despite its physiological importance, few experimental studies and even fewer...
Neural tracking - the time-locking of neural responses to continuous stimuli such as speech, music, and video - is widely used to study how the brain processes natural input. Tracking strength is typically quantified as the correlation between the recorded neural response and the stimulus, decoded and/or encoded through data-driven...
A key issue in using AI for pathology diagnosis is what image information should be given to the AI and how limited analysis resources should be used. This study compares two ways of processing different types of images under limited resources. The first is WSI-AI, in which AI automatically compresses information from the whole slide...
Let $f_{\ell}(n)$ be the largest size of a family $\mathcal{A}\subseteq2^{[n]}$ such that no member has size divisible by $\ell$, while the intersection of every two distinct members has size divisible by $\ell$, and let $ω(\ell)$ denote the number of distinct prime divisors of $\ell$. For any prime power $\ell$, the classical answer...