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A central goal in systems biology and drug discovery is to predict the transcriptional response of cells to perturbations. This task is challenging due to the noisy and sparse nature of single-cell measurements, as well as the fact that…

Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far…

Flow cytometry is a technology that rapidly measures antigen-based markers associated to cells in a cell population. Although analysis of flow cytometry data has traditionally considered one or two markers at a time, there has been…

The biomedical imaging world is notorious for working with small amounts of data, frustrating state-of-the-art efforts in the computer vision and deep learning worlds. With large datasets, it is easier to make progress we have seen from the…

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed…

We introduce Flux Matching, a new paradigm for generative modeling that generalizes existing score-based models to a broader family of vector fields that need not be conservative. Rather than requiring the model to equal the data score, the…

In silico, cell based approaches for modeling biological morphogenesis are used to test and validate our understanding of the biological and mechanical process that are at work during the growth and the organization of multi-cell tissues.…

Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…

The dynamics of cellular aggregates is driven by the interplay of mechanochemical processes and cellular activity. Although deterministic models may capture mechanical features, local chemical fluctuations trigger random cell responses,…

Cell motility is one of the most fundamental phenomena underlying biological processes that maintain living organisms alive. Here we introduce a simple model to describe the motility of cells which include not only time-correlated internal…

Flow matching has emerged as a promising generative approach that addresses the lengthy sampling times associated with state-of-the-art diffusion models and enables a more flexible trajectory design, while maintaining high-quality image…

Most biological tissues grow by the synthesis of new material close to the tissue's interface, where spatial interactions can exert strong geometric influences on the local rate of growth. These geometric influences may be mechanistic, or…

Biochemical processes in cells are governed by complex networks of many chemical species interacting stochastically in diverse ways and on different time scales. Constructing microscopically accurate models of such networks is often…

Simulating trajectories of dynamical systems is a fundamental problem in a wide range of fields such as molecular dynamics, biochemistry, and pedestrian dynamics. Machine learning has become an invaluable tool for scaling physics-based…

Fast and realistic coupling of blood flow and vessel wall is of great importance to virtual surgery. In this paper, we propose a novel data-driven coupling method that formulates physics-based blood flow simulation as a regression problem,…

Autologous chemotaxis is the process in which cells secrete and detect molecules to determine the direction of fluid flow. Experiments and theory suggest that autologous chemotaxis fails at high cell densities because molecules from other…

Solvent-based techniques usually involve preparing dilute blends of electron-donor and electron-acceptor materials dissolved in a volatile solvent. After some form of coating onto a substrate, the solvent evaporates. An initially…

Microfluidics-based biochips are soon expected to revolutionize clinical diagnosis, DNA sequencing, and other laboratory procedures involving molecular biology. Most microfluidic biochips are based on the principle of continuous fluid flow…

While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cell, an environment densely packed with diverse macromolecules. Here, we revise…

Recent diffusion and flow matching models have demonstrated strong capabilities in image generation and editing by progressively removing noise through iterative sampling. While this enables flexible inversion for semantic-preserving edits,…