Cell Behavior Video Classification Challenge, a benchmark for computer vision methods in time-lapse microscopy

The classification of microscopy videos capturing complex cellular behaviors is crucial for understanding and quantifying the dynamics of biological processes over time. However, it remains a frontier in computer vision, requiring approaches that effectively model the shape and motion of objects without rigid boundaries, extract hierarchical spatiotemporal features from entire image sequences rather than static frames, and account for multiple objects within the field of view. To this end, we organized the Cell Behavior Video Classification Challenge (CBVCC), benchmarking 35 methods based on three approaches: classification of tracking-derived features, end-to-end deep learning architectures to directly learn spatiotemporal features from the entire video sequence without explicit cell tracking, or ensembling tracking-derived with image-derived features. We discuss the results achieved by the participants and compare the potential and limitations of each approach, serving as a basis to foster the development of computer vision methods for studying cellular dynamics.

Implementing Immune Repertoire Models Using Weighted Finite State Machines

The adaptive immune system's T and B cells can be viewed as large populations of simple, diverse classifiers. Artificial immune systems (AIS) $\unicode{x2013}$ algorithmic models of T or B cell repertoires $\unicode{x2013}$ are used in both computational biology and natural computing to investigate how the immune system adapts to its changing environments. However, researchers have struggled to build such systems at scale. For string-based AISs, finite state machines (FSMs) can store cell repertoires in compressed representations that are orders of magnitude smaller than explicitly stored receptor sets. This strategy allows AISs with billions of receptors to be generated in a matter of seconds. However, to date, these FSM-based AISs have been unable to deal with multiplicity in input data. Here, we show how weighted FSMs can be used to represent cell repertoires and model immunological processes like negative and positive selection, while also taking into account the multiplicity of input data. We use our method to build simple immune-inspired classifier systems that solve various toy problems in anomaly detection, showing how weights can be crucial for both performance and robustness to parameters. Our approach can potentially be extended to increase the scale of other population-based machine learning algorithms such as learning classifier systems.