Quantitative Biology
Stochastic burst-like oscillations are common in physiological signals, yet there are few compact generative models that capture their transient structure. We propose a numerical-twin framework that represents transient narrowband activity…
Complex systems produce high-dimensional signals that lack macroscopic variables analogous to entropy, temperature, or free energy. This work introduces a thermoinformational formulation that derives entropy, internal energy, temperature,…
Attractor dynamics are a fundamental computational motif in neural circuits, supporting diverse cognitive functions through stable, self-sustaining patterns of neural activity. In these lecture notes, we review four key examples that…
The pursuit of strategies that minimize the number of individuals needing vaccination to control an outbreak is a well-established area of study in mathematical epidemiology. However, for certain diseases, public policy tends to prioritize…
Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…
Accurate forecasting of infectious disease incidence is critical for public health planning and timely intervention. While most data-driven forecasting approaches rely primarily on historical data from a single country, such data are often…
Enabling natural communication through brain-computer interfaces (BCIs) remains one of the most profound challenges in neuroscience and neurotechnology. While existing frameworks offer partial solutions, they are constrained by…
The spatial structure of populations may promote the emergence and maintenance of cooperation. Cooperation in the prisoner's dilemma is favored under specific update rules in evolutionary graph theory models with one individual per node of…
Each T cell typically carries a specific T-cell receptor (TCR) that determines its specificity against an epitope presented by the HLA complex on a target cell. Antigenic challenge triggers the expansion of reactive cells within a diverse…
Identifying the effects of mechanical ventilation strategies and protocols in critical care requires analyzing data from heterogeneous patient-ventilator systems within the context of the clinical decision-making environment. This research…
Diffusion MRI (dMRI) tractography is currently the only method for in vivo mapping of the brain's white matter (WM) connections. Tractometry is an advanced tractography analysis technique for along-tract profiling to investigate the…
Tumor growth is constrained by spatial, mechanical, and metabolic factors whose alignment progressively breaks down across cellular, mesoscopic, and tissue scales as tumors expand. We hypothesize that this misalignment drives tumors toward…
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an…
Molecular representation learning aims to learn vector embeddings that capture molecular structure and geometry, thereby enabling property prediction and downstream scientific applications. In many AI for science tasks, labeled data are…
Designing enzymes with substrate-binding pockets is a critical challenge in protein engineering, as catalytic activity depends on the precise interaction between pockets and substrates. Currently, generative models dominate functional…
Visual illusions provide a window into the mechanisms underlying visual processing, and dynamical neural circuit models offer a natural framework for proposing and testing theories of their emergence. We propose and analyze a delay-coupled…
There are few, if any, algorithms in statistical phylogenetics which are used more heavily than Felsenstein's 1973 pruning method for computing the likelihood of a tree. We present LvD, (Likelihood via Decomposition), an alternative to…
Vehicle movements, including vehicle cabs and trailers, play a role in disseminating disease in swine production. However, there are many information gaps about vehicle movements patterns that increase the probability of disease…
Global biodiversity loss is accelerating, prompting international efforts such as the Kunming-Montreal Global Biodiversity Framework (GBF) and the United Nations Sustainable Development Goals to direct resources toward halting species…
Diseases originating from wildlife pose a significant threat to global health, causing human and economic losses each year. The transmission of disease from animals to humans occurs at the interface between humans, livestock, and wildlife…