Quantitative Biology
The study of shapes is one of the most fundamental problems in life sciences. Although numerous methods have been developed for the morphometry of planar biological shapes over the past several decades, most of them focus solely on either…
The two-thirds power law of human motor control ($v \propto \kappa^{-1/3}$) is geometrically equivalent to constant equi-affine speed. In classical differential geometry, however, the equi-affine metric is not a tensor: it depends on…
Network topology excels at structural predictions but fails to capture functional semantics encoded in biomedical literature. We present RAG-GNN, an end-to-end trainable retrieval-augmented graph neural network framework that integrates GNN…
There is little debate about the importance of the ancestral recombination graph in population genetics. An important theoretical tool, the main obstacle to its widespread usage is the computational cost required to match the…
Humans systematically misrepresent probability in a stereotyped inverse-S pattern. It has been documented for decades, but its origin remains unexplained. We propose a Bayesian encoding-decoding account in which probabilities are…
Current video foundation models, including the strongest self-supervised models such as V-JEPA2, fail to capture how humans organize social information in dynamic scenes. For example, across a range of diverse vision models tested, none…
This paper gives an overview of a theory for modelling the interaction between geometric image transformations and receptive field responses for a visual observer that views objects and spatio-temporal events in the environment. This…
Characterizing in-utero brain development is essential for understanding typical and atypical neurodevelopment. Building on prior spatiotemporal fetal brain MRI atlases, we present the CRL-2025 fetal brain atlas, a spatiotemporal (4D) atlas…
Understanding the intricate interplay among sequence, structure, and function remains a fundamental challenge in proteomics. The sequence-structure-function paradigm posits that biological roles are governed by the tertiary geometric…
Strongly coupled, recurrent, balanced network models have been successful in describing and predicting many phenomena observed in cortical neural recordings. However, most balanced network models use current-based synapse models in place of…
Microbiome functions are encoded within the genes of the community-wide metagenome. A natural question is whether properties of a microbial community can be predicted just from knowing the raw DNA sequences of its members. In this work, we…
The spatial and functional organization of the primate visual cortex is a fundamental problem in neuroscience. While recent computational frameworks like the Topographic Deep Artificial Neural Network (TDANN) have successfully modeled…
The Inositol 1,4,5-trisphosphate receptor channel (IP 3 R) is an important calcium channel involved in calcium-induced calcium release, playing a prominent role in intracellular calcium signaling. However, accurately characterizing its…
NORI performs probabilistic inference to resolve ambiguous mappings between experimental observations and biological entities orders of magnitude faster than state-of-the-art methods. This makes large-scale analysis and extensive…
Topological data analysis (TDA) has established itself as a useful tool for capturing multiscale structures in complex networks, such as connected components, cycles, and cavities. Although Vietoris-Rips (VR) filtering is widely used in…
Predictive models in biomedicine depend on structured assay data locked in the text, tables, and supplements of primary publications. This bottleneck is especially acute in targeted protein degradation (TPD), where each assay record must…
Regression to the Mean and Regression Dilution are often viewed as unrelated issues in the clinical and ecological literatures. In reality, they are different names for the same problem: measurement error in an independent variable that…
One of the great phytogeography zones of semi-arid lands in the world is the Kurdistan region of Iraq which hosts many important fruit species due to its geographical location and ecology. Mountain Hawthorn (Crataegus spp.) is a vital wild…
Identifying operons is a fundamental step in understanding prokaryotic gene regulation, as classifying genes into operons supports the reconstruction of regulatory networks, functional annotation of unannotated genes, and drug candidate…
Learning in artificial neural networks usually relies on continuous, externally driven weight updates, in which parameters are modified at every step in response to incoming data, error signals or reward feedback. In this setting, routine…