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Below you will find a list of our publications in chronological order

Selected Publications


Contact-implicit Trajectory Optimization Using Orthogonal Collocation

A. Patel, S. Shield, S. Kazi, A. Johnson & L. Biegler

In this letter, we propose a method to improve the accuracy of trajectory optimization for dynamic robots with intermittent contact by using orthogonal collocation. Until recently, most trajectory optimization methods for systems with contacts employ mode-scheduling, which requires an a priori knowledge of the contact order and thus cannot produce complex or non-intuitive behaviors. Contact-implicit trajectory optimization methods offer a solution to this by allowing the optimization to make or break contacts as needed, but thus far have suffered from poor accuracy. Here, we combine methods from direct collocation using higher order orthogonal polynomials with contact-implicit optimization to generate trajectories with significantly improved accuracy. The key insight is to increase the order of the polynomial representation while maintaining the assumption that impact occurs over the duration of one finite element.


Using DeepLabCut for 3D Markerless Pose Estimation Across Species and Behaviors

T. Nath, A. Mathis, A.C. Chen, A. Patel, M. Bethge & M.W. Mathis

Noninvasive behavioral tracking of animals during experiments is crucial to many scientific pursuits. Extracting the poses of animals without using markers is often essential for measuring behavioral effects in biomechanics, genetics, ethology & neuroscience. Yet, extracting detailed poses without markers in dynamically changing backgrounds has been challenging. We recently introduced an open source toolbox called DeepLabCut that builds on a state-of-the-art human pose estimation algorithm to allow a user to train a deep neural network using limited training data to precisely track user-defined features that matches human labeling accuracy. Here, with this paper we provide an updated toolbox that is self contained within a Python package that includes new features such as graphical user interfaces and active-learning based network refinement. Lastly, we provide a step-by-step guide for using DeepLabCut.


AcinoSet: a 3D Pose Estimation Dataset and Baseline Models for Cheetahs in the Wild

D. Joska, L. Clark, N. Muramatsu, R Jericevich, F. Nicolls, A. Mathis, M. W. Mathis & A. Patel

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. Markerless animal pose estimation is used to provide 2D keypoints. Three methods are employed for 3D pose estimation: 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:


Project Name

Conference Papers

N. Muramatsu, Z. da Silva, D. Joska, F. Nicolls and A. Patel. 2022, October. Improving 3D Markerless Pose Estimation of Animals in the Wild using Low-Cost Cameras. 2022 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS) (pp. 3770-3776). IEEE.

S. Shield and A. Patel, 2022, October. Minor Change, Major Gains II: Are Maximal Coordinates the Fastest Choice for Trajectory Optimization?. In 2022 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS) (pp. 12963-12970). IEEE.

J. Pilbrough, P. Amayo, 2022 International Conference on Robotics and Automation (ICRA), (pp. 10898-10904). IEEE.

C.C. Francis, J. Mwangama, 5th International Conference on Energy, Electrical and Power Engineering (CEEPE), (pp. 199-204).

Z. Martin, S. Hendricks and A. Patel in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops, 2021, (pp. 4594-4603).

D. Joska, L. Clark, N. Muramatsu, R. Jericevich, F. Nicolls, A. Mathis, M.W. Mathis and A. Patel, 2021 IEEE International Conference on Robotics and Automation (ICRA), (pp. 13901-13908).

C. Fisher, J. Van Zyl, R. Govender, A. Patel, 2021 IEEE International Conference on Robotics and Automation (ICRA), (pp. 8345-8351).

J. Pilbrough, P. Amayo, 2021 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), (pp. 6617-6624).

M. R. M. Anfar and J. Mwangama in 2021 International Conference on Artificial Intelligence in Information and Communication (ICAIIC), 2021, (pp. 144-149).

L. Mamushiane, L.S. Mboweni, H.I. Kobo, J. Mwangama, A.A. Lysko, 2021.

A.B.D. Kinabo, J. Mwangama, A.A. Lysko, 2021 7th International Conference on Advanced Computing and Communication Systems (ICACCS) (Vol. 1, pp 715-722). IEEE.

A.B.D. Kinabo, J. Mwangama, A.A. Lysko, 2021 IST-Africa Conference (IST-Africa), (pp. 1-9). IEEE.

Journal Articles

S. Shield and A. Patel. 2023. From Dima to Kemba: Ten Years of Cheetah-Inspired Research at the African Robotics Unit. Scientific African, p.e01640.

L. Paul, M. Naughton, B. Jones, D. Davidow, A. Patel, M. Lambert, S. Hendricks. 2022, Sports medicine-open 8 (1), (pp. 1-38).

S. Shield, A.M. Johnson, A. Patel, IEEE Robotics and Automation Letters 7 (2), (pp. 5779-5786).

J. Norby, J.Y. Li, C. Selby, A. Patel and A.M. Johnson in IEEE Transactions on Robotics.

M.J. Schwaner, S.T. Hsieh, I. Braasch, S. Bradley, C.B. Campos, C.E. Collins, C.M. Donatelli, F.E. Fish, O.E. Fitch, B.E. Flammang, B.E. Jackson, A. Jusufi, P.J. Mekdara, A. Patel, B.J. Swalla, M. Vickaryous and C.P. McGowan in Integrative and Comparative Biology, 2021.

S. Shield, R. Jericevich, A. Patel and A. Jusufi in Integrative and Comparative Biology, 2021.

C. Fisher and A. Patel in SAIEE Africa Research Journal 112 (3), (pp. 126-133).

U. Uyoata, J. Mwangama, R. Adeogun, IEEE Access 9, (pp. 132675-132704).

C. Fisher, A. Blom and A. Patel in Frontiers in Mechanical Engineering 6 (2020): 54.

A. Knemeyer, S. Shield and A. Patel, 2020, in IEEE Robotics and Automation Letters.


J. Norby, J.Y. Li, C. Selby, A. Patel and A.M. Johnson in Bulletin of the American Physical Society, 2021.

A. Patel, R. Jericevich, A. Knemeyer and A. Jusufi in Integrative and Comparitive Biology 61, E687-E688.

A. Patel, P.Suhrcke, A. Zeloof, P. Li, C. Selby, A. Johnson, 2018.


A. Patel, C. Fisher, B. Stocks, F. Nicolls, E. Boje, INTEGRATIVE AND COMPARATIVE BIOLOGY 57, E373-E373.


S.E. Nwachukwu, M. Chepkoech, A.A. Lysko, K. Awodele, J. Mwangama, C.R. Burger, 2022 IEEE 7th Forum on Research and Technologies for Society and Industry Innovation (RTSI), (pp. 154-160).


N. Mukudu, R. Steinke, G. Carella, J. Mwangama, A. Corici, N. Ventura, A. Willner, T. Magedanz, M. Barros, and A. Gavras, 2017.

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