Quantitative Biology
Designing proteins that satisfy natural language functional requirements is a central goal in protein engineering. A straightforward baseline is to fine-tune generic instruction-tuned LLMs as direct text-to-sequence generators, but this is…
MLE-Toolbox is a comprehensive open-source MATLAB toolbox for end-to-end analysis of magnetoencephalography (MEG) and electroencephalography (EEG) data. Inspired by widely used neuroimaging platforms such as Brainstorm and FieldTrip, it…
We investigate the longitudinal behaviour of blood markers from common haematological tests as a marker of disease and as a function of disease progression in a variety of conditions including cancer, cardiovascular disease, and infections.…
We continue recent attempts to put together concepts and results of Chemical Reaction Networks theory (CRNT) and Mathematical Epidemiology (ME), for solving problems of stability of positive ODEs. We provide first an elegant CRN-flavored…
High-dimensional omics datasets are routinely visualized as heatmaps, where color intensities reveal co-expression patterns and correlations. However, modern omics technologies increasingly generate matrices so large that existing visual…
Recovering unbiased kinetic and thermodynamic observables from the enhanced sampling simulations is a central challenge in rare-event sampling. Classical Girsanov Reweighting (GR) offers a principled solution by yielding exact pathwise…
Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico…
Tree-grass coexistence is a defining feature of savanna ecosystems, which play an important role in supporting biodiversity and human populations worldwide. While recent advances have clarified many of the underlying processes, how these…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Statistical physics can describe the behavior of microbial populations consisting of many heterogeneous individuals. A direct consequence is the existence of phase transitions, where the behavior of a population changes discontinuously upon…
Experimental evidence indicates that intracellular chloride concentration regulates the excitation and inhibition (EI) balance, yet the mechanisms by which activity-dependent chloride dynamics drive seizure evolution and stage transitions…
Motivation: Statistical analysis of microbial count data derived from 16S rRNA or metagenomics sequencing poses unique challenges due to the sparse, compositional, and high-dimensional nature of the data. While QIIME 2 already provides many…
Biological agents navigate complex environments by combining long-term memory of successful actions with short-term suppression of recently visited locations-a capability that remains difficult to replicate in artificial systems, especially…
Recent progress in visual brain decoding from fMRI has been enabled by large-scale datasets such as the Natural Scenes Dataset (NSD) and powerful diffusion-based generative models. While current pipelines are primarily optimized for…
Motivated behaviour relies on the brain's capacity to evaluate effort and reward. Dysregulation within these processes contributes to a spectrum of conditions, from hyperactivity in attention-deficit/hyperactivity disorder (ADHD) to…
Gradient saliency from deep sequence models surfaces candidate biomarkers efficiently, but the resulting gene lists can be contaminated by tissue-composition confounders that degrade downstream classifiers. We study whether LLM…
Integrated information theory (IIT) starts from the existence of consciousness and characterizes its essential properties: every experience is intrinsic, specific, unitary, definite, and structured. IIT then formulates existence and its…
(Im)balance indices can be used to quantify the (im)balance of trees by assigning numerical scores to them. An easy way to generate a new index is to construct a compound index, e.g., a linear combination of established indices. Two of the…
Eukaryotic cells generally sense chemical gradients using the binding of chemical ligands to membrane receptors. In order to perform chemotaxis effectively in different environments, cells need to adapt to different concentrations. We…
Living cells inherently reorganize their intracellular structures in response to mechanical cues from their environment. Among these responses, the formation of actin-based stress fibers exhibits a series of structural transitions depending…