Quantitative Biology
Over the past two decades, quantum-like modeling (QLM) has emerged as a powerful framework for describing non-classical features of cognition and decision-making. Rather than assuming physical quantum processes in the brain, QLM employs the…
We present a memory-augmented transformer in which attention serves simultaneously as a retrieval, consolidation, and write-back operator. The core update, $A^\top A V W$, re-grounds retrieved values into persistent memory slots via the…
Manual measurement of muscle morphology from ultrasound during speech is time-consuming and limits large-scale studies. We present SMMA, a fully automated framework that combines deep-learning segmentation with skeleton-based thickness…
In this work we analyze the emergence of phase transitions in a quantum brain model inspired by the Lipkin-Meshkov-Glick framework, where biologically motivated synaptic feedback modulates the collective interaction in a nonlinear and…
We propose NEURONA, a neuro-symbolic framework for fMRI decoding and concept grounding in neural activity. Leveraging image- and video-based fMRI question-answering datasets, NEURONA learns to decode interacting concepts from visual stimuli…
The Bayesian brain hypothesis has been a leading theory in understanding perceptual decision-making under uncertainty. While extensive psychophysical evidence supports the notion of the brain performing Bayesian computations, how…
Decoded Neurofeedback (DecNef) is a flourishing non-invasive approach to brain modulation with wide-ranging applications in neuromedicine and cognitive neuroscience. However, progress in DecNef research remains constrained by…
Retinal detachment (RD) is a vision-threatening condition that requires prompt intervention to preserve sight. A critical factor in treatment urgency and visual prognosis is macular involvement -- whether the macula is intact or detached.…
Biological systems operate under persistent noise, which can alter system states and induce transitions between attractors. Here, we study the attractor dynamics of Boolean networks focusing on the transitions between attractors induced by…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
Background: Single-cell foundation models such as Geneformer and scGPT encode rich biological information, but whether this includes causal regulatory logic rather than statistical co-expression remains unclear. Sparse autoencoders (SAEs)…
The interplay between tumor cells and macrophages plays a central regulatory role in cancer progression. In this study, we developed a mathematical model that incorporates tumor cells, M1 type macrophages, M2 type macrophages and an M3 type…
Stochastic modeling of movement behavior provides a valuable way to understand how complex motion can be generated from relatively simple building blocks. Ants demonstrate sophisticated social behavior ranging from foraging to nest…
The Reduction Principle states that, near a stable equilibrium under fixed viability selection, a selectively neutral modifier allele that reduces recombination rate among selected loci is favored, whereas one that increases recombination…
Understanding how decision making changes across the lifespan is a central challenge for neuroscience, yet research on cognitive aging has remained largely disconnected from the theoretical and computational advances that now shape modern…
Species growing in environments that change in time and space will vary in their abundance across locations, even in the absence of persistent location preferences. Here we quantify this non-equilibrium effect by studying a minimal model of…
Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…
In order to develop association studies and to improve the phenotypic description for abiotic and biotic stress related traits, nested core collections of 48, 96, 144 and 384 sunflower lines were built from a set of 752 diverse, public or…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
This study establishes a benchmark for Caenorhabditis elegans neuron classification, comparing four graph methods (GCN, GraphSAGE, GAT, GraphTransformer) against four non-graph methods (Logistic Regression, MLP, LOLCAT, NeuPRINT). Using the…