Ann Kennedy

Ruize Yang, Ann Kennedy, R. James Cotton

Advances in markerless motion capture are expanding access to biomechanical movement analysis, making it feasible to obtain high-quality movement data from outpatient clinics, inpatient hospitals, therapy, and even home. Expanding access to movement data in these diverse contexts makes the challenge of performing downstream analytics all the more acute. Creating separate bespoke analysis code for all the tasks end users might want is both intractable and does not take advantage of the common features of human movement underlying them all. Recent studies have shown that fine-tuning language models to accept tokenized movement as an additional modality enables successful descriptive captioning of movement. Here, we explore whether such a multimodal motion-language model can answer detailed, clinically meaningful questions about movement. We collected over 30 hours of biomechanics from nearly 500 participants, many with movement impairments from a variety of etiologies, performing a range of movements used in clinical outcomes assessments. After tokenizing these movement trajectories, we created a multimodal dataset of motion-related questions and answers spanning a range of tasks. We developed BiomechGPT, a multimodal biomechanics-language model, on this dataset. Our results show that BiomechGPT demonstrates high performance across a range of tasks such as activity recognition, identifying movement impairments, diagnosis, scoring clinical outcomes, and measuring walking. BiomechGPT provides an important step towards a foundation model for rehabilitation movement data.

Eric Zhan, Jennifer J. Sun, Ann Kennedy et al.

We present a framework for the unsupervised learning of neurosymbolic encoders, which are encoders obtained by composing neural networks with symbolic programs from a domain-specific language. Our framework naturally incorporates symbolic expert knowledge into the learning process, which leads to more interpretable and factorized latent representations compared to fully neural encoders. We integrate modern program synthesis techniques with the variational autoencoding (VAE) framework, in order to learn a neurosymbolic encoder in conjunction with a standard decoder. The programmatic descriptions from our encoders can benefit many analysis workflows, such as in behavior modeling where interpreting agent actions and movements is important. We evaluate our method on learning latent representations for real-world trajectory data from animal biology and sports analytics. We show that our approach offers significantly better separation of meaningful categories than standard VAEs and leads to practical gains on downstream analysis tasks, such as for behavior classification.

Megan Tjandrasuwita, Jennifer J. Sun, Ann Kennedy et al.

Hand-annotated data can vary due to factors such as subjective differences, intra-rater variability, and differing annotator expertise. We study annotations from different experts who labelled the same behavior classes on a set of animal behavior videos, and observe a variation in annotation styles. We propose a new method using program synthesis to help interpret annotation differences for behavior analysis. Our model selects relevant trajectory features and learns a temporal filter as part of a program, which corresponds to estimated importance an annotator places on that feature at each timestamp. Our experiments on a dataset from behavioral neuroscience demonstrate that compared to baseline approaches, our method is more accurate at capturing annotator labels and learns interpretable temporal filters. We believe that our method can lead to greater reproducibility of behavior annotations used in scientific studies. We plan to release our code.

Jennifer J. Sun, Tomomi Karigo, Dipam Chakraborty et al.

Multi-agent behavior modeling aims to understand the interactions that occur between agents. We present a multi-agent dataset from behavioral neuroscience, the Caltech Mouse Social Interactions (CalMS21) Dataset. Our dataset consists of trajectory data of social interactions, recorded from videos of freely behaving mice in a standard resident-intruder assay. To help accelerate behavioral studies, the CalMS21 dataset provides benchmarks to evaluate the performance of automated behavior classification methods in three settings: (1) for training on large behavioral datasets all annotated by a single annotator, (2) for style transfer to learn inter-annotator differences in behavior definitions, and (3) for learning of new behaviors of interest given limited training data. The dataset consists of 6 million frames of unlabeled tracked poses of interacting mice, as well as over 1 million frames with tracked poses and corresponding frame-level behavior annotations. The challenge of our dataset is to be able to classify behaviors accurately using both labeled and unlabeled tracking data, as well as being able to generalize to new settings.

Jennifer J. Sun, Ann Kennedy, Eric Zhan et al.

Specialized domain knowledge is often necessary to accurately annotate training sets for in-depth analysis, but can be burdensome and time-consuming to acquire from domain experts. This issue arises prominently in automated behavior analysis, in which agent movements or actions of interest are detected from video tracking data. To reduce annotation effort, we present TREBA: a method to learn annotation-sample efficient trajectory embedding for behavior analysis, based on multi-task self-supervised learning. The tasks in our method can be efficiently engineered by domain experts through a process we call "task programming", which uses programs to explicitly encode structured knowledge from domain experts. Total domain expert effort can be reduced by exchanging data annotation time for the construction of a small number of programmed tasks. We evaluate this trade-off using data from behavioral neuroscience, in which specialized domain knowledge is used to identify behaviors. We present experimental results in three datasets across two domains: mice and fruit flies. Using embeddings from TREBA, we reduce annotation burden by up to a factor of 10 without compromising accuracy compared to state-of-the-art features. Our results thus suggest that task programming and self-supervision can be an effective way to reduce annotation effort for domain experts.