Jiri Sedlar

Jiri Sedlar, Karla Stepanova, Radoslav Skoviera et al.

This paper introduces a dataset for training and evaluating methods for 6D pose estimation of hand-held tools in task demonstrations captured by a standard RGB camera. Despite the significant progress of 6D pose estimation methods, their performance is usually limited for heavily occluded objects, which is a common case in imitation learning, where the object is typically partially occluded by the manipulating hand. Currently, there is a lack of datasets that would enable the development of robust 6D pose estimation methods for these conditions. To overcome this problem, we collect a new dataset (Imitrob) aimed at 6D pose estimation in imitation learning and other applications where a human holds a tool and performs a task. The dataset contains image sequences of nine different tools and twelve manipulation tasks with two camera viewpoints, four human subjects, and left/right hand. Each image is accompanied by an accurate ground truth measurement of the 6D object pose obtained by the HTC Vive motion tracking device. The use of the dataset is demonstrated by training and evaluating a recent 6D object pose estimation method (DOPE) in various setups.

Anton Bushuiev, Roman Bushuiev, Petr Kouba et al.

Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning approaches have substantially advanced the field, they often struggle to generalize beyond training data in practical scenarios. The contributions of this work are three-fold. First, we construct PPIRef, the largest and non-redundant dataset of 3D protein-protein interactions, enabling effective large-scale learning. Second, we leverage the PPIRef dataset to pre-train PPIformer, a new SE(3)-equivariant model generalizing across diverse protein-binder variants. We fine-tune PPIformer to predict effects of mutations on protein-protein interactions via a thermodynamically motivated adjustment of the pre-training loss function. Finally, we demonstrate the enhanced generalization of our new PPIformer approach by outperforming other state-of-the-art methods on new, non-leaking splits of standard labeled PPI mutational data and independent case studies optimizing a human antibody against SARS-CoV-2 and increasing the thrombolytic activity of staphylokinase.

Anton Bushuiev, Roman Bushuiev, Jiri Sedlar et al.

In recent years, there has been remarkable progress in machine learning for protein-protein interactions. However, prior work has predominantly focused on improving learning algorithms, with less attention paid to evaluation strategies and data preparation. Here, we demonstrate that further development of machine learning methods may be hindered by the quality of existing train-test splits. Specifically, we find that commonly used splitting strategies for protein complexes, based on protein sequence or metadata similarity, introduce major data leakage. This may result in overoptimistic evaluation of generalization, as well as unfair benchmarking of the models, biased towards assessing their overfitting capacity rather than practical utility. To overcome the data leakage, we recommend constructing data splits based on 3D structural similarity of protein-protein interfaces and suggest corresponding algorithms. We believe that addressing the data leakage problem is critical for further progress in this research area.

Jakub Kopko, David Graber, Saltuk Mustafa Eyrilmez et al.

As machine learning becomes increasingly central to molecular design, it is vital to ensure the reliability of learnable protein-ligand scoring functions on novel protein targets. While many scoring functions perform well on standard benchmarks, their ability to generalize beyond training data remains a significant challenge. In this work, we evaluate the generalization capability of state-of-the-art scoring functions on dataset splits that simulate evaluation on targets with a limited number of known structures and experimental affinity measurements. Our analysis reveals that the commonly used benchmarks do not reflect the true challenge of generalizing to novel targets. We also investigate whether large-scale self-supervised pretraining can bridge this generalization gap and we provide preliminary evidence of its potential. Furthermore, we probe the efficacy of simple methods that leverage limited test-target data to improve scoring function performance. Our findings underscore the need for more rigorous evaluation protocols and offer practical guidance for designing scoring functions with predictive power extending to novel protein targets.

Anton Bushuiev, Roman Bushuiev, Olga Pimenova et al.

Generalization beyond training data remains a central challenge in machine learning for biology. A common way to enhance generalization is self-supervised pre-training on large datasets. However, aiming to perform well on all possible proteins can limit a model's capacity to excel on any specific one, whereas experimentalists typically need accurate predictions for individual proteins they study, often not covered in training data. To address this limitation, we propose a method that enables self-supervised customization of protein language models to one target protein at a time, on the fly, and without assuming any additional data. We show that our Protein Test-Time Training (ProteinTTT) method consistently enhances generalization across different models, their sizes, and datasets. ProteinTTT improves structure prediction for challenging targets, achieves new state-of-the-art results on protein fitness prediction, and enhances function prediction on two tasks. Through two challenging case studies, we also show that customization via ProteinTTT achieves more accurate antibody-antigen loop modeling and enhances 19% of structures in the Big Fantastic Virus Database, delivering improved predictions where general-purpose AlphaFold2 and ESMFold struggle.

Zongmian Li, Jiri Sedlar, Justin Carpentier et al.

In this paper, we introduce a method to automatically reconstruct the 3D motion of a person interacting with an object from a single RGB video. Our method estimates the 3D poses of the person together with the object pose, the contact positions and the contact forces exerted on the human body. The main contributions of this work are three-fold. First, we introduce an approach to jointly estimate the motion and the actuation forces of the person on the manipulated object by modeling contacts and the dynamics of the interactions. This is cast as a large-scale trajectory optimization problem. Second, we develop a method to automatically recognize from the input video the 2D position and timing of contacts between the person and the object or the ground, thereby significantly simplifying the complexity of the optimization. Third, we validate our approach on a recent video+MoCap dataset capturing typical parkour actions, and demonstrate its performance on a new dataset of Internet videos showing people manipulating a variety of tools in unconstrained environments.

Hajime Taira, Ignacio Rocco, Jiri Sedlar et al.

Visual localization in large and complex indoor scenes, dominated by weakly textured rooms and repeating geometric patterns, is a challenging problem with high practical relevance for applications such as Augmented Reality and robotics. To handle the ambiguities arising in this scenario, a common strategy is, first, to generate multiple estimates for the camera pose from which a given query image was taken. The pose with the largest geometric consistency with the query image, e.g., in the form of an inlier count, is then selected in a second stage. While a significant amount of research has concentrated on the first stage, there is considerably less work on the second stage. In this paper, we thus focus on pose verification. We show that combining different modalities, namely appearance, geometry, and semantics, considerably boosts pose verification and consequently pose accuracy. We develop multiple hand-crafted as well as a trainable approach to join into the geometric-semantic verification and show significant improvements over state-of-the-art on a very challenging indoor dataset.

Zongmian Li, Jiri Sedlar, Justin Carpentier et al.

In this paper, we introduce a method to automatically reconstruct the 3D motion of a person interacting with an object from a single RGB video. Our method estimates the 3D poses of the person and the object, contact positions, and forces and torques actuated by the human limbs. The main contributions of this work are three-fold. First, we introduce an approach to jointly estimate the motion and the actuation forces of the person on the manipulated object by modeling contacts and the dynamics of their interactions. This is cast as a large-scale trajectory optimization problem. Second, we develop a method to automatically recognize from the input video the position and timing of contacts between the person and the object or the ground, thereby significantly simplifying the complexity of the optimization. Third, we validate our approach on a recent MoCap dataset with ground truth contact forces and demonstrate its performance on a new dataset of Internet videos showing people manipulating a variety of tools in unconstrained environments.

Radoslav Skoviera, Karla Stepanova, Michael Tesar et al.

In this paper, we consider the problem of learning object manipulation tasks from human demonstration using RGB or RGB-D cameras. We highlight the key challenges in capturing sufficiently good data with no tracking devices - starting from sensor selection and accurate 6DoF pose estimation to natural language processing. In particular, we focus on two showcases: gluing task with a glue gun and simple block-stacking with variable blocks. Furthermore, we discuss how a linguistic description of the task could help to improve the accuracy of task description. We also present the whole architecture of our transfer of the imitated task to the simulated and real robot environment.

Zeynettin Akkus, Issa Ali, Jiri Sedlar et al.

Objective: Several studies have associated codeletion of chromosome arms 1p/19q in low-grade gliomas (LGG) with positive response to treatment and longer progression free survival. Therefore, predicting 1p/19q status is crucial for effective treatment planning of LGG. In this study, we predict the 1p/19q status from MR images using convolutional neural networks (CNN), which could be a noninvasive alternative to surgical biopsy and histopathological analysis. Method: Our method consists of three main steps: image registration, tumor segmentation, and classification of 1p/19q status using CNN. We included a total of 159 LGG with 3 image slices each who had biopsy-proven 1p/19q status (57 nondeleted and 102 codeleted) and preoperative postcontrast-T1 (T1C) and T2 images. We divided our data into training, validation, and test sets. The training data was balanced for equal class probability and then augmented with iterations of random translational shift, rotation, and horizontal and vertical flips to increase the size of the training set. We shuffled and augmented the training data to counter overfitting in each epoch. Finally, we evaluated several configurations of a multi-scale CNN architecture until training and validation accuracies became consistent. Results: The results of the best performing configuration on the unseen test set were 93.3% (sensitivity), 82.22% (specificity), and 87.7% (accuracy). Conclusion: Multi-scale CNN with their self-learning capability provides promising results for predicting 1p/19q status noninvasively based on T1C and T2 images. Significance: Predicting 1p/19q status noninvasively from MR images would allow selecting effective treatment strategies for LGG patients without the need for surgical biopsy.