Monitoring wildlife is essential for ecology and ethology, especially in light of the increasing human impact on ecosystems. Camera traps have emerged as habitat-centric sensors enabling the study of wildlife populations at scale with minimal disturbance. However, the lack of annotated video datasets limits the development of powerful video understanding models needed to process the vast amount of fieldwork data collected. To advance research in wild animal behavior monitoring we present MammAlps, a multi-modal and multi-view dataset of wildlife behavior monitoring from 9 camera-traps in the Swiss National Park. Mam-mAlps contains over 14 hours of video with audio, 2D segmentation maps and 8.5 hours of individual tracks densely labeled for species and behavior. Based on 6‘135 single animal clips, we propose the first hierarchical and multi-modal animal behavior recognition benchmark using audio, video and reference scene segmentation maps as inputs. Furthermore, we also propose a second ecology-oriented benchmark aiming at identifying activities, species, number of individuals and meteorological conditions from 397 multi-view and long-term ecological events, including false positive triggers. We advocate that both tasks are complementary and contribute to bridging the gap between machine learning and ecology. Code and data are available at https://github.com/eceo-epfl/MammAlps.

Sepideh Mamooler, Syrielle Montariol, Alexander Mathis, Antoine Bosselut. Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers). 2025.

Understanding behavior requires datasets that capture humans while carrying out complex tasks. The kitchen is an excellent environment for assessing human motor and cognitive function, as many complex actions are naturally exhibited in kitchens from chopping to cleaning. Here, we introduce the EPFL-Smart-Kitchen-30 dataset, collected in a noninvasive motion capture platform inside a kitchen environment. Nine static RGB-D cameras, inertial measurement units (IMUs) and one head-mounted HoloLens~2 headset were used to capture 3D hand, body, and eye movements. The EPFL-Smart-Kitchen-30 dataset is a multi-view action dataset with synchronized exocentric, egocentric, depth, IMUs, eye gaze, body and hand kinematics spanning 29.7 hours of 16 subjects cooking four different recipes. Action sequences were densely annotated with 33.78 action segments per minute. Leveraging this multi-modal dataset, we propose four benchmarks to advance behavior understanding and modeling through 1) a vision-language benchmark, 2) a semantic text-to-motion generation benchmark, 3) a multi-modal action recognition benchmark, 4) a pose-based action segmentation benchmark. We expect the EPFL-Smart-Kitchen-30 dataset to pave the way for better methods as well as insights to understand the nature of ecologically-valid human behavior. Code and data are available at https://amathislab.github.io/EPFL-Smart-Kitchen

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 in-troduce HOISDF, a Signed Distance Field (SDF) guided hand-object pose estimation network, which jointly exploits hand and object SDFs to provide a global, implicit repre-sentation over the complete reconstruction volume. Specif-ically, 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 esti-mation benchmarks (DexYCB and H03Dv2). Code is avail-able at https://github.com/amathislabIHOISDF.

Abstract Natural behavior is hierarchical. Yet, there is a paucity of benchmarks addressing this aspect. Recognizing the scarcity of large-scale hierarchical behavioral benchmarks, we create a novel synthetic basketball playing benchmark (Shot7M2). Beyond synthetic data, we extend BABEL into a hierarchical action segmentation benchmark (hBABEL). Then, we develop a masked autoencoder framework (hBehaveMAE) to elucidate the hierarchical nature of motion capture data in an unsupervised fashion. We find that hBehaveMAE learns interpretable latents on Shot7M2 and hBABEL, where lower encoder levels show a superior ability to represent fine-grained movements, while higher encoder levels capture complex actions and activities. Additionally, we evaluate hBehaveMAE on MABe22, a representation learning benchmark with short and long-term behavioral states. hBehaveMAE achieves state-of-the-art performance without domain-specific feature extraction. Together, these components synergistically contribute towards unveiling the hierarchical organization of natural behavior. Models and benchmarks are available at https://github.com/amathislab/BehaveMAE .

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 at https://github.com/sdascoli/odeformer.

Abstract Wildlife observation with camera traps has great potential for ethology and ecology, as it gathers data non-invasively in an automated way. However, camera traps produce large amounts of uncurated data, which is time-consuming to annotate. Existing methods to label these data automatically commonly use a fixed pre-defined set of distinctive classes and require many labeled examples per class to be trained. Moreover, the attributes of interest are sometimes rare and difficult to find in large data collections. Large pretrained vision-language models, such as contrastive language image pretraining (CLIP), offer great promises to facilitate the annotation process of camera-trap data. Images can be described with greater detail, the set of classes is not fixed and can be extensible on demand and pretrained models can help to retrieve rare samples. In this work, we explore the potential of CLIP to retrieve images according to environmental and ecological attributes. We create WildCLIP by fine-tuning CLIP on wildlife camera-trap images and to further increase its flexibility, we add an adapter module to better expand to novel attributes in a few-shot manner. We quantify WildCLIP’s performance and show that it can retrieve novel attributes in the Snapshot Serengeti dataset. Our findings outline new opportunities to facilitate annotation processes with complex and multi-attribute captions. The code is available at https://github.com/amathislab/wildclip .

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 bottomup 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

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.

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 used the MABe 2022 behavior challenge tasks to benchmark AmadeusGPT and show excellent performance. 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

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. The code is available at the following link: https://github.com/amathislab/dmap

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 wholebody 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. Code and data can be found at: https://github.com/African-Robotics-Unit/AcinoSet.

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.

Rodents use two distinct neuronal coordinate systems to estimate their position: place fields in the hippocampus and grid fields in the entorhinal cortex. Whereas place cells spike at only one particular spatial location, grid cells fire at multiple sites that correspond to the points of an imaginary hexagonal lattice. We study how to best construct place and grid codes, taking the probabilistic nature of neural spiking into account. Which spatial encoding properties of individual neurons confer the highest resolution when decoding the animal's position from the neuronal population response? A priori, estimating a spatial position from a grid code could be ambiguous, as regular periodic lattices possess translational symmetry. The solution to this problem requires lattices for grid cells with different spacings; the spatial resolution crucially depends on choosing the right ratios of these spacings across the population. We compute the expected error in estimating the position in both the asymptotic limit, using Fisher information, and for low spike counts, using maximum likelihood estimation. Achieving high spatial resolution and covering a large range of space in a grid code leads to a trade-off: the best grid code for spatial resolution is built of nested modules with different spatial periods, one inside the other, whereas maximizing the spatial range requires distinct spatial periods that are pairwisely incommensurate. Optimizing the spatial resolution predicts two grid cell properties that have been experimentally observed. First, short lattice spacings should outnumber long lattice spacings. Second, the grid code should be self-similar across different lattice spacings, so that the grid field always covers a fixed fraction of the lattice period. If these conditions are satisfied and the spatial "tuning curves" for each neuron span the same range of firing rates, then the resolution of the grid code easily exceeds that of the best possible place code with the same number of neurons.