Marcus N. Boon

Patrik Reiske, Marcus N. Boon, Niek Andresen et al.

Machine learning and computer vision methods have a major impact on the study of natural animal behavior, as they enable the (semi-)automatic analysis of vast amounts of video data. Mice are the standard mammalian model system in most research fields, but the datasets available today to refine such methods focus either on simple or social behaviors. In this work, we present a video dataset of individual mice solving complex mechanical puzzles, so-called lockboxes. The more than 110 hours of total playtime show their behavior recorded from three different perspectives. As a benchmark for frame-level action classification methods, we provide human-annotated labels for all videos of two different mice, that equal 13% of our dataset. Our keypoint (pose) tracking-based action classification framework illustrates the challenges of automated labeling of fine-grained behaviors, such as the manipulation of objects. We hope that our work will help accelerate the advancement of automated action and behavior classification in the computational neuroscience community. Our dataset is publicly available at https://doi.org/10.14279/depositonce-23850

Olaf Hellwich, Niek Andresen, Katharina Hohlbaum et al.

Tracking mouse body parts in video is often incomplete due to occlusions such that - e.g. - subsequent action and behavior analysis is impeded. In this conceptual work, videos from several perspectives are integrated via global exterior camera orientation; body part positions are estimated by 3D triangulation and bundle adjustment. Consistency of overall 3D track reconstruction is achieved by introduction of a 3D mouse model, deep-learned body part movements, and global motion-track smoothness constraint. The resulting 3D body and body part track estimates are substantially more complete than the original single-frame-based body part detection, therefore, allowing improved animal behavior analysis.

Marcus N. Boon, Lorenzo Cassola, Hans-Christian Ruiz Euler et al.

Deep learning, a multi-layered neural network approach inspired by the brain, has revolutionized machine learning. One of its key enablers has been backpropagation, an algorithm that computes the gradient of a loss function with respect to the weights and biases in the neural network model, in combination with its use in gradient descent. However, the implementation of deep learning in digital computers is intrinsically energy hungry, with energy consumption becoming prohibitively high for many applications. This has stimulated the development of specialized hardware, ranging from neuromorphic CMOS integrated circuits and integrated photonic tensor cores to unconventional, material-based computing system. The learning process in these material systems, realized, e.g., by artificial evolution, equilibrium propagation or surrogate modelling, is a complicated and time-consuming process. Here, we demonstrate a simple yet efficient and accurate gradient extraction method, based on the principle of homodyne detection, for performing gradient descent on a loss function directly in a physical system without the need of an analytical description. By perturbing the parameters that need to be optimized using sinusoidal waveforms with distinct frequencies, we effectively obtain the gradient information in a highly robust and scalable manner. We illustrate the method in dopant network processing units, but argue that it is applicable in a wide range of physical systems. Homodyne gradient extraction can in principle be fully implemented in materia, facilitating the development of autonomously learning material systems.