Alexander Mathis

Shaokai Ye, Jessy Lauer, Mu Zhou et al.

The process of quantifying and analyzing animal behavior involves translating the naturally occurring descriptive language of their actions into machine-readable code. Yet, codifying behavior analysis is often challenging without deep understanding of animal behavior and technical machine learning knowledge. To limit this gap, we introduce AmadeusGPT: a natural language interface that turns natural language descriptions of behaviors into machine-executable code. Large-language models (LLMs) such as GPT3.5 and GPT4 allow for interactive language-based queries that are potentially well suited for making interactive behavior analysis. However, the comprehension capability of these LLMs is limited by the context window size, which prevents it from remembering distant conversations. To overcome the context window limitation, we implement a novel dual-memory mechanism to allow communication between short-term and long-term memory using symbols as context pointers for retrieval and saving. Concretely, users directly use language-based definitions of behavior and our augmented GPT develops code based on the core AmadeusGPT API, which contains machine learning, computer vision, spatio-temporal reasoning, and visualization modules. Users then can interactively refine results, and seamlessly add new behavioral modules as needed. We benchmark AmadeusGPT and show we can produce state-of-the-art performance on the MABE 2022 behavior challenge tasks. Note, an end-user would not need to write any code to achieve this. Thus, collectively AmadeusGPT presents a novel way to merge deep biological knowledge, large-language models, and core computer vision modules into a more naturally intelligent system. Code and demos can be found at: https://github.com/AdaptiveMotorControlLab/AmadeusGPT.

Mu Zhou, Lucas Stoffl, Mackenzie Weygandt Mathis et al.

Frequent interactions between individuals are a fundamental challenge for pose estimation algorithms. Current pipelines either use an object detector together with a pose estimator (top-down approach), or localize all body parts first and then link them to predict the pose of individuals (bottom-up). Yet, when individuals closely interact, top-down methods are ill-defined due to overlapping individuals, and bottom-up methods often falsely infer connections to distant bodyparts. Thus, we propose a novel pipeline called bottom-up conditioned top-down pose estimation (BUCTD) that combines the strengths of bottom-up and top-down methods. Specifically, we propose to use a bottom-up model as the detector, which in addition to an estimated bounding box provides a pose proposal that is fed as condition to an attention-based top-down model. We demonstrate the performance and efficiency of our approach on animal and human pose estimation benchmarks. On CrowdPose and OCHuman, we outperform previous state-of-the-art models by a significant margin. We achieve 78.5 AP on CrowdPose and 48.5 AP on OCHuman, an improvement of 8.6% and 7.8% over the prior art, respectively. Furthermore, we show that our method strongly improves the performance on multi-animal benchmarks involving fish and monkeys. The code is available at https://github.com/amathislab/BUCTD

Cheryl Wang, Chun Kwang Tan, Balint K. Hodossy et al.

Athletic performance represents the pinnacle of human motor intelligence, demanding rapid choices, precise control, agility, and coordinated physical execution. Replicating this seamless combination of capabilities remains elusive in current artificial intelligence and robotic systems. Concurrently, understanding the biological mastery of these movements is hindered because complex muscle coordination is rarely measured in vivo due to the limitations of physical equipment. To bridge this fundamental gap in understanding, MyoChallenge at NeurIPS 2025 established a pioneering benchmark for motor control intelligence in sports, leveraging high-fidelity musculoskeletal models within physics simulation combined with machine learning-driven algorithms. The competition introduces two distinct tracks emphasizing either upper or lower limbs control: a table tennis rally task utilizing a biomechanic upper limb composed of an arm with a hand and a trunk; and a soccer penalty kick using a biomechanic model of legs and a trunk. Marking the fourth iteration of the MyoChallenge series, this event attracted almost 70 teams and over 560 submissions globally, uniting a diverse community ranging from physicians and neuroscientists to machine learning experts. The competition facilitated the development of several state-of-the-art control algorithms for a musculoskeletal system capable of sports agility, leveraging techniques such as physics-based motion planners, on-policy behaviour cloning, hierarchical planning, and muscle synergies. By integrating standardized tasks and physiologically realistic models into the open-source framework of MyoSuite, MyoChallenge'25 serves as a reproducible and reusable testbed to accelerate interdisciplinary research across machine learning, biomechanics, sports science, and neuroscience. Project page: https://www.myosuite.org//myochallenge/myochallenge-2025.

Chengkun Li, Cheryl Wang, Bianca Ziliotto et al.

Learning motor control for muscle-driven musculoskeletal models is hindered by the computational cost of biomechanically accurate simulation and the scarcity of validated, open full-body models. Here we present MuscleMimic, an open-source framework for scalable motion imitation learning with physiologically realistic, muscle-actuated humanoids. MuscleMimic provides two validated musculoskeletal embodiments - a fixed-root upper-body model (126 muscles) for bimanual manipulation and a full-body model (416 muscles) for locomotion - together with a retargeting pipeline that maps SMPL-format motion capture data onto musculoskeletal structures while preserving kinematic and dynamic consistency. Leveraging massively parallel GPU simulation, the framework achieves order-of-magnitude training speedups over prior CPU-based approaches while maintaining comprehensive collision handling, enabling a single generalist policy to be trained on hundreds of diverse motions within days. The resulting policy faithfully reproduces a broad repertoire of human movements under full muscular control and can be fine-tuned to novel motions within hours. Biomechanical validation against experimental walking and running data demonstrates strong agreement in joint kinematics (mean correlation r = 0.90), while muscle activation analysis reveals both the promise and fundamental challenges of achieving physiological fidelity through kinematic imitation alone. By lowering the computational and data barriers to musculoskeletal simulation, MuscleMimic enables systematic model validation across diverse dynamic movements and broader participation in neuromuscular control research. Code, models, checkpoints, and retargeted datasets are available at: https://github.com/amathislab/musclemimic

Alberto Silvio Chiappa, Alessandro Marin Vargas, Alexander Mathis

Biological and artificial agents need to deal with constant changes in the real world. We study this problem in four classical continuous control environments, augmented with morphological perturbations. Learning to locomote when the length and the thickness of different body parts vary is challenging, as the control policy is required to adapt to the morphology to successfully balance and advance the agent. We show that a control policy based on the proprioceptive state performs poorly with highly variable body configurations, while an (oracle) agent with access to a learned encoding of the perturbation performs significantly better. We introduce DMAP, a biologically-inspired, attention-based policy network architecture. DMAP combines independent proprioceptive processing, a distributed policy with individual controllers for each joint, and an attention mechanism, to dynamically gate sensory information from different body parts to different controllers. Despite not having access to the (hidden) morphology information, DMAP can be trained end-to-end in all the considered environments, overall matching or surpassing the performance of an oracle agent. Thus DMAP, implementing principles from biological motor control, provides a strong inductive bias for learning challenging sensorimotor tasks. Overall, our work corroborates the power of these principles in challenging locomotion tasks.

Stéphane d'Ascoli, Sören Becker, Alexander Mathis et al.

We introduce ODEFormer, the first transformer able to infer multidimensional ordinary differential equation (ODE) systems in symbolic form from the observation of a single solution trajectory. We perform extensive evaluations on two datasets: (i) the existing "Strogatz" dataset featuring two-dimensional systems; (ii) ODEBench, a collection of one- to four-dimensional systems that we carefully curated from the literature to provide a more holistic benchmark. ODEFormer consistently outperforms existing methods while displaying substantially improved robustness to noisy and irregularly sampled observations, as well as faster inference. We release our code, model and benchmark dataset publicly.

Haozhe Qi, Kevin Qu, Mahdi Rad et al.

Long video understanding remains challenging for Multi-modal Large Language Models (MLLMs) due to high memory costs and context-length limits. Prior approaches mitigate this by scoring and selecting frames/tokens within short clips, but they lack a principled mechanism to (i) compare relevance across distant video clips and (ii) stop processing once sufficient evidence has been gathered. We propose AdaptToken, a training-free framework that turns an MLLM's self-uncertainty into a global control signal for long-video token selection. AdaptToken splits a video into groups, extracts cross-modal attention to rank tokens within each group, and uses the model's response entropy to estimate each group's prompt relevance. This entropy signal enables a global token budget allocation across groups and further supports early stopping (AdaptToken-Lite), skipping the remaining groups when the model becomes sufficiently certain. Across four long-video benchmarks (VideoMME, LongVideoBench, LVBench, and MLVU) and multiple base MLLMs (7B-72B), AdaptToken consistently improves accuracy (e.g., +6.7 on average over Qwen2.5-VL 7B) and continues to benefit from extremely long inputs (up to 10K frames), while AdaptToken-Lite reduces inference time by about half with comparable performance. Project page: https://haozheqi.github.io/adapt-token

Haozhe Qi, Chen Zhao, Mathieu Salzmann et al.

Human hands are highly articulated and versatile at handling objects. Jointly estimating the 3D poses of a hand and the object it manipulates from a monocular camera is challenging due to frequent occlusions. Thus, existing methods often rely on intermediate 3D shape representations to increase performance. These representations are typically explicit, such as 3D point clouds or meshes, and thus provide information in the direct surroundings of the intermediate hand pose estimate. To address this, we introduce HOISDF, a Signed Distance Field (SDF) guided hand-object pose estimation network, which jointly exploits hand and object SDFs to provide a global, implicit representation over the complete reconstruction volume. Specifically, the role of the SDFs is threefold: equip the visual encoder with implicit shape information, help to encode hand-object interactions, and guide the hand and object pose regression via SDF-based sampling and by augmenting the feature representations. We show that HOISDF achieves state-of-the-art results on hand-object pose estimation benchmarks (DexYCB and HO3Dv2). Code is available at https://github.com/amathislab/HOISDF

Merkourios Simos, Alberto Silvio Chiappa, Alexander Mathis

How do humans move? The quest to understand human motion has broad applications in numerous fields, ranging from computer animation and motion synthesis to neuroscience, human prosthetics and rehabilitation. Although advances in reinforcement learning (RL) have produced impressive results in capturing human motion using simplified humanoids, controlling physiologically accurate models of the body remains an open challenge. In this work, we present a model-free motion imitation framework (KINESIS) to advance the understanding of muscle-based motor control. Using a musculoskeletal model of the lower body with 80 muscle actuators and 20 DoF, we demonstrate that KINESIS achieves strong imitation performance on 1.9 hours of motion capture data, is controllable by natural language through pre-trained text-to-motion generative models, and can be fine-tuned to carry out high-level tasks such as target goal reaching. Importantly, KINESIS generates muscle activity patterns that correlate well with human EMG activity. The physiological plausibility makes KINESIS a promising model for tackling challenging problems in human motor control theory, which we highlight by investigating Bernstein's redundancy problem in the context of locomotion. Code, videos and benchmarks will be available at https://github.com/amathislab/Kinesis.

Alberto Silvio Chiappa, Alessandro Marin Vargas, Ann Zixiang Huang et al.

In Reinforcement Learning, agents learn policies by exploring and interacting with the environment. Due to the curse of dimensionality, learning policies that map high-dimensional sensory input to motor output is particularly challenging. During training, state of the art methods (SAC, PPO, etc.) explore the environment by perturbing the actuation with independent Gaussian noise. While this unstructured exploration has proven successful in numerous tasks, it can be suboptimal for overactuated systems. When multiple actuators, such as motors or muscles, drive behavior, uncorrelated perturbations risk diminishing each other's effect, or modifying the behavior in a task-irrelevant way. While solutions to introduce time correlation across action perturbations exist, introducing correlation across actuators has been largely ignored. Here, we propose LATent TIme-Correlated Exploration (Lattice), a method to inject temporally-correlated noise into the latent state of the policy network, which can be seamlessly integrated with on- and off-policy algorithms. We demonstrate that the noisy actions generated by perturbing the network's activations can be modeled as a multivariate Gaussian distribution with a full covariance matrix. In the PyBullet locomotion tasks, Lattice-SAC achieves state of the art results, and reaches 18% higher reward than unstructured exploration in the Humanoid environment. In the musculoskeletal control environments of MyoSuite, Lattice-PPO achieves higher reward in most reaching and object manipulation tasks, while also finding more energy-efficient policies with reductions of 20-60%. Overall, we demonstrate the effectiveness of structured action noise in time and actuator space for complex motor control tasks. The code is available at: https://github.com/amathislab/lattice.

Devis Tuia, Benjamin Kellenberger, Sara Beery et al.

Data acquisition in animal ecology is rapidly accelerating due to inexpensive and accessible sensors such as smartphones, drones, satellites, audio recorders and bio-logging devices. These new technologies and the data they generate hold great potential for large-scale environmental monitoring and understanding, but are limited by current data processing approaches which are inefficient in how they ingest, digest, and distill data into relevant information. We argue that machine learning, and especially deep learning approaches, can meet this analytic challenge to enhance our understanding, monitoring capacity, and conservation of wildlife species. Incorporating machine learning into ecological workflows could improve inputs for population and behavior models and eventually lead to integrated hybrid modeling tools, with ecological models acting as constraints for machine learning models and the latter providing data-supported insights. In essence, by combining new machine learning approaches with ecological domain knowledge, animal ecologists can capitalize on the abundance of data generated by modern sensor technologies in order to reliably estimate population abundances, study animal behavior and mitigate human/wildlife conflicts. To succeed, this approach will require close collaboration and cross-disciplinary education between the computer science and animal ecology communities in order to ensure the quality of machine learning approaches and train a new generation of data scientists in ecology and conservation.

Daniel Joska, Liam Clark, Naoya Muramatsu et al.

Animals are capable of extreme agility, yet understanding their complex dynamics, which have ecological, biomechanical and evolutionary implications, remains challenging. Being able to study this incredible agility will be critical for the development of next-generation autonomous legged robots. In particular, the cheetah (acinonyx jubatus) is supremely fast and maneuverable, yet quantifying its whole-body 3D kinematic data during locomotion in the wild remains a challenge, even with new deep learning-based methods. In this work we present an extensive dataset of free-running cheetahs in the wild, called AcinoSet, that contains 119,490 frames of multi-view synchronized high-speed video footage, camera calibration files and 7,588 human-annotated frames. We utilize markerless animal pose estimation to provide 2D keypoints. Then, we use three methods that serve as strong baselines for 3D pose estimation tool development: traditional sparse bundle adjustment, an Extended Kalman Filter, and a trajectory optimization-based method we call Full Trajectory Estimation. The resulting 3D trajectories, human-checked 3D ground truth, and an interactive tool to inspect the data is also provided. We believe this dataset will be useful for a diverse range of fields such as ecology, neuroscience, robotics, biomechanics as well as computer vision.

Lucas Stoffl, Maxime Vidal, Alexander Mathis

We propose an end-to-end trainable approach for multi-instance pose estimation, called POET (POse Estimation Transformer). Combining a convolutional neural network with a transformer encoder-decoder architecture, we formulate multiinstance pose estimation from images as a direct set prediction problem. Our model is able to directly regress the pose of all individuals, utilizing a bipartite matching scheme. POET is trained using a novel set-based global loss that consists of a keypoint loss, a visibility loss and a class loss. POET reasons about the relations between multiple detected individuals and the full image context to directly predict their poses in parallel. We show that POET achieves high accuracy on the COCO keypoint detection task while having less parameters and higher inference speed than other bottom-up and top-down approaches. Moreover, we show successful transfer learning when applying POET to animal pose estimation. To the best of our knowledge, this model is the first end-to-end trainable multi-instance pose estimation method and we hope it will serve as a simple and promising alternative.

Sébastien B. Hausmann, Alessandro Marin Vargas, Alexander Mathis et al.

The utility of machine learning in understanding the motor system is promising a revolution in how to collect, measure, and analyze data. The field of movement science already elegantly incorporates theory and engineering principles to guide experimental work, and in this review we discuss the growing use of machine learning: from pose estimation, kinematic analyses, dimensionality reduction, and closed-loop feedback, to its use in understanding neural correlates and untangling sensorimotor systems. We also give our perspective on new avenues where markerless motion capture combined with biomechanical modeling and neural networks could be a new platform for hypothesis-driven research.

Maxime Vidal, Nathan Wolf, Beth Rosenberg et al.

Identifying individual animals is crucial for many biological investigations. In response to some of the limitations of current identification methods, new automated computer vision approaches have emerged with strong performance. Here, we review current advances of computer vision identification techniques to provide both computer scientists and biologists with an overview of the available tools and discuss their applications. We conclude by offering recommendations for starting an animal identification project, illustrate current limitations and propose how they might be addressed in the future.

Alexander Mathis, Steffen Schneider, Jessy Lauer et al.

Extracting behavioral measurements non-invasively from video is stymied by the fact that it is a hard computational problem. Recent advances in deep learning have tremendously advanced predicting posture from videos directly, which quickly impacted neuroscience and biology more broadly. In this primer we review the budding field of motion capture with deep learning. In particular, we will discuss the principles of those novel algorithms, highlight their potential as well as pitfalls for experimentalists, and provide a glimpse into the future.

Mackenzie W. Mathis, Alexander Mathis

Recent advances in computer vision have made accurate, fast and robust measurement of animal behavior a reality. In the past years powerful tools specifically designed to aid the measurement of behavior have come to fruition. Here we discuss how capturing the postures of animals - pose estimation - has been rapidly advancing with new deep learning methods. While challenges still remain, we envision that the fast-paced development of new deep learning tools will rapidly change the landscape of realizable real-world neuroscience.

Alexander Mathis, Thomas Biasi, Steffen Schneider et al.

Neural networks are highly effective tools for pose estimation. However, as in other computer vision tasks, robustness to out-of-domain data remains a challenge, especially for small training sets that are common for real-world applications. Here, we probe the generalization ability with three architecture classes (MobileNetV2s, ResNets, and EfficientNets) for pose estimation. We developed a dataset of 30 horses that allowed for both "within-domain" and "out-of-domain" (unseen horse) benchmarking - this is a crucial test for robustness that current human pose estimation benchmarks do not directly address. We show that better ImageNet-performing architectures perform better on both within- and out-of-domain data if they are first pretrained on ImageNet. We additionally show that better ImageNet models generalize better across animal species. Furthermore, we introduce Horse-C, a new benchmark for common corruptions for pose estimation, and confirm that pretraining increases performance in this domain shift context as well. Overall, our results demonstrate that transfer learning is beneficial for out-of-domain robustness.

Alexander Mathis, Pranav Mamidanna, Taiga Abe et al.

Quantifying behavior is crucial for many applications in neuroscience. Videography provides easy methods for the observation and recording of animal behavior in diverse settings, yet extracting particular aspects of a behavior for further analysis can be highly time consuming. In motor control studies, humans or other animals are often marked with reflective markers to assist with computer-based tracking, yet markers are intrusive (especially for smaller animals), and the number and location of the markers must be determined a priori. Here, we present a highly efficient method for markerless tracking based on transfer learning with deep neural networks that achieves excellent results with minimal training data. We demonstrate the versatility of this framework by tracking various body parts in a broad collection of experimental settings: mice odor trail-tracking, egg-laying behavior in drosophila, and mouse hand articulation in a skilled forelimb task. For example, during the skilled reaching behavior, individual joints can be automatically tracked (and a confidence score is reported). Remarkably, even when a small number of frames are labeled ($\approx 200$), the algorithm achieves excellent tracking performance on test frames that is comparable to human accuracy.