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Most neural networks assume that input images have a fixed number of channels (three for RGB images). However, there are many settings where the number of channels may vary, such as microscopy images where the number of channels changes…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Biomedical research results are being published at a high rate, and with existing search engines, the vast amount of published work is usually easily accessible. However, reproducing published results, either experimental data or…
Cell types are at the root of modern biology, and describing them is a core task of the Human Cell Atlas project. Surprisingly, there are no standards for reporting new cell types, leading to a gap between classes mentioned in biomedical…
While Large Language Models (LLMs) achieve superhuman performance on standardized medical licensing exams, these static benchmarks have become saturated and increasingly disconnected from the functional requirements of clinical workflows.…
Ageing of lithium-ion batteries results in irreversible reduction in performance. Intrinsic variability between cells, caused by manufacturing differences, occurs throughout life and increases with age. Researchers need to know the minimum…
For Application Specific Integrated Circuits (ASIC) and System-on-Chip (SOC) designs, Cell - Based Design (CBD) is the most prevalent practice as it guarantees a shorter design cycle, minimizes errors and is easier to maintain. In modern…
The modeling of bio-molecular system across molecular scales remains a central challenge in scientific research. Large language models (LLMs) are increasingly applied to bio-molecular discovery, yet systematic evaluation across multi-scale…
The turn of the millennium has seen a growing interest in the study of live cells by infrared (IR) spectroscopy, driven by the versatility, wealth of molecular information, and potential for high-throughput screening of the technique.…
Lymphocyte populations, stimulated in vitro or in vivo, grow as cells divide. Stochastic models are appropriate because some cells undergo multiple rounds of division, some die, and others of the same type in the same conditions do not…
Summary: Cell population plots are visualizations showing cell population distributions in biological samples with single-cell data, traditionally shown with stacked bar charts. Here, we address issues with this approach, particularly its…
Single-object tracking is a well-known and challenging research topic in computer vision. Over the last two decades, numerous researchers have proposed various algorithms to solve this problem and achieved promising results. Recently,…
We investigate the use of self-tracking data and unsupervised mixed-membership models to phenotype endometriosis. Endometriosis is a systemic, chronic condition of women in reproductive age and, at the same time, a highly enigmatic…
In vitro cellular experimentation with genetic interventions, using for example CRISPR technologies, is an essential step in early-stage drug discovery and target validation that serves to assess initial hypotheses about causal associations…
To help accelerate progress in multi-target, multi-camera tracking systems, we present (i) a new pair of precision-recall measures of performance that treats errors of all types uniformly and emphasizes correct identification over sources…
An accurate modelling of bio-electrochemical processes that govern Microbial Fuel Cells (MFCs) and mapping their behaviour according to several parameters will enhance the development of MFC technology and enable their successful…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
In biological cells and novel diagnostic devices biochemical receptors need to be sensitive to extremely small concentration changes of signaling molecules. The accuracy of such molecular signaling is ultimately limited by the counting…