Quantitative Biology
The turn of the millennium has seen a growing interest in the study of live cells by infrared (IR) spectroscopy, driven by the versatility, wealth of molecular information, and potential for high-throughput screening of the technique.…
When people pursue rewards in stochastic environments, they often match their choice frequencies to the observed target frequencies, even when this policy is demonstrably sub-optimal. We used a ``hide and seek'' task to evaluate this…
Single-cell RNA sequencing (scRNA-seq) technology enables systematic delineation of cellular states and interactions, providing crucial insights into cellular heterogeneity. Building on this potential, numerous computational methods have…
Large-language models (LLMs) are rapidly being applied to radiology, enabling automated image interpretation and report generation tasks. Their deployment in clinical practice requires both high diagnostic accuracy and low inference…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
In realistic neural circuits, both neurons and synapses are coupled in dynamics with separate time scales. The circuit functions are intimately related to these coupled dynamics. However, it remains challenging to understand the intrinsic…
This work addresses multistationarity of fully open reaction networks equipped with mass action kinetics. We improve upon the existing results relating existence of positive feedback loops in a reaction network and multistationarity; and we…
The anti-cancer immune response relies on the bindings between T-cell receptors (TCRs) and antigens, which elicits adaptive immunity to eliminate tumor cells. This ability of the immune system to respond to novel various neoantigens arises…
Transcription commonly occurs in bursts, with alternating productive (ON) and quiescent (OFF) periods, governing mRNA production rates. Yet, how transcription is regulated through bursting dynamics remains unresolved. Here, we conduct…
Travelling waves of neural firing activity are observed in brain tissue as a part of various sensory, motor and cognitive processes. They represent an object of major interest in the study of excitable networks, with analysis conducted in…
The integration of artificial intelligence (AI) into pathology is advancing precision medicine by improving diagnosis, treatment planning, and patient outcomes. Digitised whole-slide images (WSIs) capture rich spatial and morphological…
RNA-based vaccination has been broadly applied in the COVID pandemic. A characteristic of the immunization was fast waning immunity. However, the time scale of this process varied considerable for virus subtypes and among individuals.…
Background and Objectives: This paper focuses on using AI to assess the cognitive function of older adults with mild cognitive impairment or mild dementia using physiological data provided by a wearable device. Cognitive screening tools are…
The motor cortex (MC) is often described as an autonomous dynamical system during movement execution. In an autonomous dynamical system, flexible movement generation depends on reconfiguring the initial conditions, which then unwind along…
We extend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall \& D'Souza, 2025). That work showed that time itself is multifractal -- not a universal background dimension, but an…
Benchmarking models is a key factor for the rapid progress in machine learning (ML) research. Thus, further progress depends on improving benchmarking metrics. A standard metric to measure the behavioral alignment between ML models and…
Real-time decoding of neural activity is central to neuroscience and neurotechnology applications, from closed-loop experiments to brain-computer interfaces, where models are subject to strict latency constraints. Traditional methods,…
Modern neural recording techniques such as two-photon imaging or Neuropixel probes allow to acquire vast time-series datasets with responses of hundreds or thousands of neurons. Contrastive learning is a powerful self-supervised framework…
Basic and instantaneous reproduction numbers, "R" _"0" and "R" _"t" , are important metrics to assess progress of an epidemic and effectiveness of preventative interventions undertaken, and also to estimate coverage needed for vaccination.…
Functional brain graphs are often characterized with separate graph-theoretic or spectral descriptors, overlooking how these properties covary and partially overlap across brains and conditions. We anticipate that dense, weighted functional…