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Predicting evolution of expanding populations is critical to control biological threats such as invasive species and cancer metastasis. Expansion is primarily driven by reproduction and dispersal, but nature abounds with examples of…
A Recurrent Neural Network (RNN) was used to perform video frame prediction of microbial growth for a population of two mutants of Pseudomonas aeruginosa. The RNN was trained on videos of 20 frames that were acquired using fluorescence…
Anatomy shape modeling is a fundamental problem in medical data analysis. However, the geometric complexity and topological variability of anatomical structures pose significant challenges to accurate anatomical shape generation. In this…
Metapopulation epidemic models are a valuable tool for studying large-scale outbreaks. With the limited availability of epidemic tracing data, it is challenging to infer the essential constituents of these models, namely, the epidemic…
A spacially extended model of the collective behavior of a large number of locally acting organisms is proposed in which organisms move probabilistically between local cells in space, but with weights dependent on local morphogenetic…
Understanding how internal community structure shapes the course of epidemics remains a fundamental challenge in modeling real-world populations. Standard metapopulation models often assume uniform mixing within communities, overlooking how…
Biofilms inhabit a range of environments, such as dental plaques or soil micropores, often characterized by intricate, non-even surfaces. However, the impact of surface irregularities on the population dynamics of biofilms remains elusive…
An antibiogram is a periodic summary of antibiotic resistance results of organisms from infected patients to selected antimicrobial drugs. Antibiograms help clinicians to understand regional resistance rates and select appropriate…
Antibiotics are a vital class of drugs closely associated with the prevention and treatment of bacterial infections. Accurate prediction of molecular antimicrobial activity remains a key challenge in the pursuit of novel antibiotic…
The evolutionary success of bacteria lies in their ability to form complex surface-associated communities in diverse biophysical settings. However, it remains poorly understood how compliance of soft surfaces, measured in terms of their…
Antimicrobial resistance (AMR) poses a mounting global health crisis, requiring rapid and reliable prediction frameworks that capture its complex evolutionary dynamics. Traditional antimicrobial susceptibility testing (AST), while accurate,…
The size and shape of the region affected by an outbreak is relevant to understand the dynamics of a disease and help to organize future actions to mitigate similar events. A simple extension of the SIR model is considered, where agents…
Locust infestation of some regions in the world, including Africa, Asia and Middle East has become a concerning issue that can affect the health and the lives of millions of people. In this respect, there have been attempts to resolve or…
Insect swarms are a model system for understanding collective behavior where the collective motion appears in disorder. To initiate and maintain a swarm in place, flying insects often use a visual external cue called a marker. In…
Morphology of mitochondria plays critical roles in mediating their physiological functions. Accurate segmentation of mitochondria from 3D electron microscopy (EM) images is essential to quantitative characterization of their morphology at…
Representation learning on static graph-structured data has shown a significant impact on many real-world applications. However, less attention has been paid to the evolving nature of temporal networks, in which the edges are often changing…
Propagating interfaces are ubiquitous in nature, underlying instabilities and pattern formation in biology and material science. Physical principles governing interface growth are well understood in passive settings; however, our…
A rising research challenge is running costly machine learning (ML) networks locally on resource-constrained edge devices. ML networks with large convolutional layers can easily exceed available memory, increasing latency due to excessive…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…
Behavioural differences across organisms, whether healthy or pathological, are closely tied to the structure of their neural circuits. Yet, the fine-scale synaptic changes that give rise to these variations remain poorly understood, in part…