Quantitative Biology
Low vision involves a range of visual impairments that significantly impact daily activities, particularly navigation in urban environments. Individuals with low vision often develop adaptive strategies to compensate for visual deficits,…
Medulloblastoma is a malignant pediatric brain cancer, and the discovery of molecular subgroups is enabling personalized treatment strategies. In 2019, a consensus identified eight novel subtypes within Groups 3 and 4, each displaying…
Objective: To develop an explainable multimodal large language model (MM-LLM) that (1) screens optic nerve head (ONH) OCT circle scans for quality and (2) generates structured clinical reports that include glaucoma diagnosis and sector-wise…
Neural recording technologies now enable simultaneous recording of population activity across many brain regions, motivating the development of data-driven models of communication between brain regions. However, existing models can struggle…
Predicting the future evolutionary trajectory of SARS-CoV-2 remains a critical challenge, particularly due to the pivotal role of spike protein mutations. It is therefore essential to develop evolutionary models capable of continuously…
With the advent of diffusion models, new proteins can be generated at an unprecedented rate. The motif scaffolding problem requires steering this generative process to yield proteins with a desirable functional substructure called a motif.…
Data-Independent Acquisition (DIA) was introduced to improve sensitivity to cover all peptides in a range rather than only sampling high-intensity peaks as in Data-Dependent Acquisition (DDA) mass spectrometry. However, it is not very clear…
A central feature of complex systems is the relevance and entanglement of different levels of description. For instance, the dynamics of ecosystems can be alternatively described in terms of large ecological processes and classes of…
A fundamental question in the field of molecular computation is what computational tasks a biochemical system can carry out. In this work, we focus on the problem of finding the maximum likelihood estimate (MLE) for log-affine models. We…
Background: The existence of different basal cell carcinoma (BCC) clinical criteria cannot be objectively validated. An adequate ground-truth is needed to train an artificial intelligence (AI) tool that explains the BCC diagnosis by…
Bioinformatics tools are essential for complex computational biology tasks, yet their integration with emerging AI-agent frameworks is hindered by incompatible interfaces, heterogeneous input-output formats, and inconsistent parameter…
Automated semantic segmentation of whole-slide images (WSIs) stained with hematoxylin and eosin (H&E) is essential for large-scale artificial intelligence-based biomarker analysis in breast cancer. However, existing public datasets for…
Understanding how subjective experience arises from information processing remains a central challenge in neuroscience, cognitive science, and AI research. The Modular Consciousness Theory (MCT) proposes a biologically grounded and…
Chronic upper extremity (UE) impairment is common after stroke. This study evaluated Boost, a novel wheelchair-mounted rehabilitation device designed to assist individuals in UE motor recovery during inpatient rehabilitation. Thirty-five…
Effective recognition of foreign antigens by the adaptive immune system relies on T cells being activated by antigen-presenting cells (APCs) in lymph nodes. Here, diffusing T cells may encounter cognate APCs that present matching antigen…
Chikungunya (CHIK) is a viral disease transmitted to humans through the bites of {\it Aedes} mosquitoes infected with the chikungunya virus (CHIKV). CHIKV has been imported annually to Florida in the last decade due to Miami's crucial…
We study a bi-virus susceptible-infected-susceptible (SIS) epidemic model in which individuals are either susceptible or infected with one of two virus strains, and consider mutation-driven transitions between strains. The general case of…
The integration of artificial intelligence (AI) in early-stage drug discovery offers unprecedented opportunities for exploring chemical space and accelerating hit-to-lead optimization. However, docking optimization in generative approaches…
Recent advances in large language models (LLMs) and biomedical foundation models (BioFMs) have achieved strong results in biological text reasoning, molecular modeling, and single-cell analysis, yet they remain siloed in disjoint embedding…
Malaria remains a major public health concern in Ethiopia, particularly in the Amhara Region, where seasonal and unpredictable transmission patterns make prevention and control challenging. Accurately forecasting malaria outbreaks is…