A tractogram is a virtual representation of the brain white matter. It is composed of millions of virtual fibers, encoded as 3D polylines, which approximate the white matter axonal pathways. To date, tractograms are the most accurate white matter representation and thus are used for tasks like presurgical planning and investigations of neuroplasticity, brain disorders, or brain networks. However, it is a well-known issue that a large portion of tractogram fibers is not anatomically plausible and can be considered artifacts of the tracking procedure. With Verifyber, we tackle the problem of filtering out such non-plausible fibers using a novel fully-supervised learning approach. Differently from other approaches based on signal reconstruction and/or brain topology regularization, we guide our method with the existing anatomical knowledge of the white matter. Using tractograms annotated according to anatomical principles, we train our model, Verifyber, to classify fibers as either anatomically plausible or non-plausible. The proposed Verifyber model is an original Geometric Deep Learning method that can deal with variable size fibers, while being invariant to fiber orientation. Our model considers each fiber as a graph of points, and by learning features of the edges between consecutive points via the proposed sequence Edge Convolution, it can capture the underlying anatomical properties. The output filtering results highly accurate and robust across an extensive set of experiments, and fast; with a 12GB GPU, filtering a tractogram of 1M fibers requires less than a minute. Verifyber implementation and trained models are available at https://github.com/FBK-NILab/verifyber.

Real-world robotic grasping can be done robustly if a complete 3D Point Cloud Data (PCD) of an object is available. However, in practice, PCDs are often incomplete when objects are viewed from few and sparse viewpoints before the grasping action, leading to the generation of wrong or inaccurate grasp poses. We propose a novel grasping strategy, named 3DSGrasp, that predicts the missing geometry from the partial PCD to produce reliable grasp poses. Our proposed PCD completion network is a Transformer-based encoder-decoder network with an Offset-Attention layer. Our network is inherently invariant to the object pose and point's permutation, which generates PCDs that are geometrically consistent and completed properly. Experiments on a wide range of partial PCD show that 3DSGrasp outperforms the best state-of-the-art method on PCD completion tasks and largely improves the grasping success rate in real-world scenarios. The code and dataset will be made available upon acceptance.

Artificial neural networks can learn complex, salient data features to achieve a given task. On the opposite end of the spectrum, mathematically grounded methods such as topological data analysis allow users to design analysis pipelines fully aware of data constraints and symmetries. We introduce a class of persistence-based neural network layers. Persistence-based layers allow the users to easily inject knowledge about symmetries (equivariance) respected by the data, are equipped with learnable weights, and can be composed with state-of-the-art neural architectures.

Quantifying motion in 3D is important for studying the behavior of humans and other animals, but manual pose annotations are expensive and time-consuming to obtain. Self-supervised keypoint discovery is a promising strategy for estimating 3D poses without annotations. However, current keypoint discovery approaches commonly process single 2D views and do not operate in the 3D space. We propose a new method to perform self-supervised keypoint discovery in 3D from multi-view videos of behaving agents, without any keypoint or bounding box supervision in 2D or 3D. Our method uses an encoder-decoder architecture with a 3D volumetric heatmap, trained to reconstruct spatiotemporal differences across multiple views, in addition to joint length constraints on a learned 3D skeleton of the subject. In this way, we discover keypoints without requiring manual supervision in videos of humans and rats, demonstrating the potential of 3D keypoint discovery for studying behavior.

Artificial intelligence is set to be deployed in operating rooms to improve surgical care. This early-stage clinical evaluation shows the feasibility of concurrently attaining real-time, high-quality predictions from several deep neural networks for endoscopic video analysis deployed for assistance during three laparoscopic cholecystectomies.

AI-based code generators are an emerging solution for automatically writing programs starting from descriptions in natural language, by using deep neural networks (Neural Machine Translation, NMT). In particular, code generators have been used for ethical hacking and offensive security testing by generating proof-of-concept attacks. Unfortunately, the evaluation of code generators still faces several issues. The current practice uses automatic metrics, which compute the textual similarity of generated code with ground-truth references. However, it is not clear what metric to use, and which metric is most suitable for specific contexts. This practical experience report analyzes a large set of output similarity metrics on offensive code generators. We apply the metrics on two state-of-the-art NMT models using two datasets containing offensive assembly and Python code with their descriptions in the English language. We compare the estimates from the automatic metrics with human evaluation and provide practical insights into their strengths and limitations.

Assessing the critical view of safety in laparoscopic cholecystectomy requires accurate identification and localization of key anatomical structures, reasoning about their geometric relationships to one another, and determining the quality of their exposure. In this work, we propose to capture each of these aspects by modeling the surgical scene with a disentangled latent scene graph representation, which we can then process using a graph neural network. Unlike previous approaches using graph representations, we explicitly encode in our graphs semantic information such as object locations and shapes, class probabilities and visual features. We also incorporate an auxiliary image reconstruction objective to help train the latent graph representations. We demonstrate the value of these components through comprehensive ablation studies and achieve state-of-the-art results for critical view of safety prediction across multiple experimental settings.

Searching for a path between two nodes in a graph is one of the most well-studied and fundamental problems in computer science. In numerous domains such as robotics, AI, or biology, practitioners develop search heuristics to accelerate their pathfinding algorithms. However, it is a laborious and complex process to hand-design heuristics based on the problem and the structure of a given use case. Here we present PHIL (Path Heuristic with Imitation Learning), a novel neural architecture and a training algorithm for discovering graph search and navigation heuristics from data by leveraging recent advances in imitation learning and graph representation learning. At training time, we aggregate datasets of search trajectories and ground-truth shortest path distances, which we use to train a specialized graph neural network-based heuristic function using backpropagation through steps of the pathfinding process. Our heuristic function learns graph embeddings useful for inferring node distances, runs in constant time independent of graph sizes, and can be easily incorporated in an algorithm such as A* at test time. Experiments show that PHIL reduces the number of explored nodes compared to state-of-the-art methods on benchmark datasets by 58.5\% on average, can be directly applied in diverse graphs ranging from biological networks to road networks, and allows for fast planning in time-critical robotics domains.

Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the structure of the drug, resulting in a loss of information. Graph neural networks have seen great success in recent years, thanks to their ability of exploiting the information conveyed by the graph structure and labels. These models have been used in a wide variety of biological applications, among which the prediction of drug side-effects on a large knowledge graph. Exploiting the molecular graph encoding the structure of the drug represents a novel approach, in which the problem is formulated as a multi-class multi-label graph-focused classification. We developed a methodology to carry out this task, using recurrent Graph Neural Networks, and building a dataset from freely accessible and well established data sources. The results show that our method has an improved classification capability, under many parameters and metrics, with respect to previously available predictors.

Neural algorithmic reasoning studies the problem of learning algorithms with neural networks, especially with graph architectures. A recent proposal, XLVIN, reaps the benefits of using a graph neural network that simulates the value iteration algorithm in deep reinforcement learning agents. It allows model-free planning without access to privileged information about the environment, which is usually unavailable. However, XLVIN only supports discrete action spaces, and is hence nontrivially applicable to most tasks of real-world interest. We expand XLVIN to continuous action spaces by discretization, and evaluate several selective expansion policies to deal with the large planning graphs. Our proposal, CNAP, demonstrates how neural algorithmic reasoning can make a measurable impact in higher-dimensional continuous control settings, such as MuJoCo, bringing gains in low-data settings and outperforming model-free baselines.