Quantitative Biology
A kernel density estimator (KDE) is one of the most popular non-parametric density estimators. In this paper we focus on a best bandwidth selection method for use in an analogue of a classical KDE using the tropical symmetric distance,…
Sensory prediction (SP) is a fundamental mechanism of perception that supports cognitive development. Atypical SP has been reported across multiple neurodevelopmental disorders (ND), suggesting it may constitute an early cross-syndromic…
We introduce a biologically inspired, multilayer neural architecture composed of Rectified Spectral Units (ReSUs). Each ReSU projects a recent window of its input history onto a canonical direction obtained via canonical correlation…
Decision paralysis, i.e. hesitation, freezing, or failure to act despite full knowledge and motivation, poses a challenge for choice models that assume options are already specified and readily comparable. Drawing on qualitative reports in…
Dynamical modeling of multisite human intracranial neural recordings is essential for developing neurotechnologies such as brain-computer interfaces (BCIs). Linear dynamical models are widely used for this purpose due to their…
Cortical surface parcellation is a fundamental task in both basic neuroscience research and clinical applications, enabling more accurate mapping of brain regions. Model-based and learning-based approaches for automated parcellation…
Routine histology contains rich prognostic information in stage II/III colorectal cancer, much of which is embedded in complex spatial tissue organisation. We present INSIGHT, a graph neural network that predicts survival directly from…
In contrast to their remarkable performance on general knowledge QA, the true abilities of Large Language Models (LLMs) in tasks demanding deep, specialized reasoning, such as in protein biology, have yet to be thoroughly investigated.…
Kinetic theory frameworks are widely used for modeling stochastic interacting systems, where the evolution primarily depends on binary interactions. Recently, in this framework the action of the external force field has been introduction in…
The extraction of structured knowledge from scientific literature remains a major bottleneck in nutraceutical research, particularly when identifying microbial strains involved in compound biosynthesis. This study presents a domain-adapted…
Over the last decade several attempts have been made to extend biodiversity studies in ways that would allow researchers to explore how biodiversity-ecosystem functioning relationships may change across different spatial and temporal…
We introduce a method for approximating posterior probabilities of phylogenetic trees and reconstructing ancestral sequences under models of sequence evolution with site-dependence, where standard phylogenetic likelihood computations…
Life demonstrates remarkable homochirality of its major building blocks: nucleic acids, amino acids, sugars, and phospholipids. We propose a mechanism that places the root of life homochirality in the formation of phospholipid bilayer…
Functional brain networks exhibit topological structures that reflect neural organization; however, statistical comparison of these networks is challenging for several reasons. This paper introduces a topologically invariant permutation…
Acidosis in tumors arises from reprogrammed metabolism and compromised vasculature, creating a harsh, acidic microenvironment that drives the evolutionary selection of acid-resistant cell phenotypes. A mathematical model is proposed to…
Autism spectrum disorder (ASD) has been associated with structural alterations across cortical and subcortical regions. Quantitative neuroimaging enables large-scale analysis of these neuroanatomical patterns. This project used structural…
In recent years, the alignment between artificial neural network (ANN) embeddings and blood oxygenation level dependent (BOLD) responses in functional magnetic resonance imaging (fMRI) via neural encoding models has significantly advanced…
Higher-order brain connectivity (HOBC), which captures interactions among three or more brain regions, provides richer organizational information than traditional pairwise functional connectivity (FC). Recent studies have begun to infer…
Emergence during mammalian evolution of concordant and divergent traits of genomic regulatory networks encompassing ubiquitous, qualitatively nearly identical yet quantitatively distinct arrays of sequences of transcription factor binding…
High resolution volumetric neuroimaging datasets from electron microscopy (EM) and x-ray micro and holographic-nano tomography (XRM/XHN) are being generated at an increasing rate and by a growing number of research teams. These datasets are…