Jonathan Masci

Pietro Astolfi, Ruben Verhagen, Laurent Petit et al.

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.

Matthias Fey, Jan E. Lenssen, Christopher Morris et al.

This work presents a two-stage neural architecture for learning and refining structural correspondences between graphs. First, we use localized node embeddings computed by a graph neural network to obtain an initial ranking of soft correspondences between nodes. Secondly, we employ synchronous message passing networks to iteratively re-rank the soft correspondences to reach a matching consensus in local neighborhoods between graphs. We show, theoretically and empirically, that our message passing scheme computes a well-founded measure of consensus for corresponding neighborhoods, which is then used to guide the iterative re-ranking process. Our purely local and sparsity-aware architecture scales well to large, real-world inputs while still being able to recover global correspondences consistently. We demonstrate the practical effectiveness of our method on real-world tasks from the fields of computer vision and entity alignment between knowledge graphs, on which we improve upon the current state-of-the-art. Our source code is available under https://github.com/rusty1s/ deep-graph-matching-consensus.

Timothy Atkinson, Saeed Saremi, Faustino Gomez et al.

With the goal of designing novel inhibitors for SARS-CoV-1 and SARS-CoV-2, we propose the general molecule optimization framework, Molecular Neural Assay Search (MONAS), consisting of three components: a property predictor which identifies molecules with specific desirable properties, an energy model which approximates the statistical similarity of a given molecule to known training molecules, and a molecule search method. In this work, these components are instantiated with graph neural networks (GNNs), Deep Energy Estimator Networks (DEEN) and Monte Carlo tree search (MCTS), respectively. This implementation is used to identify 120K molecules (out of 40-million explored) which the GNN determined to be likely SARS-CoV-1 inhibitors, and, at the same time, are statistically close to the dataset used to train the GNN.

Etienne Perot, Pierre de Tournemire, Davide Nitti et al.

Event cameras encode visual information with high temporal precision, low data-rate, and high-dynamic range. Thanks to these characteristics, event cameras are particularly suited for scenarios with high motion, challenging lighting conditions and requiring low latency. However, due to the novelty of the field, the performance of event-based systems on many vision tasks is still lower compared to conventional frame-based solutions. The main reasons for this performance gap are: the lower spatial resolution of event sensors, compared to frame cameras; the lack of large-scale training datasets; the absence of well established deep learning architectures for event-based processing. In this paper, we address all these problems in the context of an event-based object detection task. First, we publicly release the first high-resolution large-scale dataset for object detection. The dataset contains more than 14 hours recordings of a 1 megapixel event camera, in automotive scenarios, together with 25M bounding boxes of cars, pedestrians, and two-wheelers, labeled at high frequency. Second, we introduce a novel recurrent architecture for event-based detection and a temporal consistency loss for better-behaved training. The ability to compactly represent the sequence of events into the internal memory of the model is essential to achieve high accuracy. Our model outperforms by a large margin feed-forward event-based architectures. Moreover, our method does not require any reconstruction of intensity images from events, showing that training directly from raw events is possible, more efficient, and more accurate than passing through an intermediate intensity image. Experiments on the dataset introduced in this work, for which events and gray level images are available, show performance on par with that of highly tuned and studied frame-based detectors.

Giorgio Giannone, Asha Anoosheh, Alessio Quaglino et al.

Event-based cameras are novel, efficient sensors inspired by the human vision system, generating an asynchronous, pixel-wise stream of data. Learning from such data is generally performed through heavy preprocessing and event integration into images. This requires buffering of possibly long sequences and can limit the response time of the inference system. In this work, we instead propose to directly use events from a DVS camera, a stream of intensity changes and their spatial coordinates. This sequence is used as the input for a novel \emph{asynchronous} RNN-like architecture, the Input-filtering Neural ODEs (INODE). This is inspired by the dynamical systems and filtering literature. INODE is an extension of Neural ODEs (NODE) that allows for input signals to be continuously fed to the network, like in filtering. The approach naturally handles batches of time series with irregular time-stamps by implementing a batch forward Euler solver. INODE is trained like a standard RNN, it learns to discriminate short event sequences and to perform event-by-event online inference. We demonstrate our approach on a series of classification tasks, comparing against a set of LSTM baselines. We show that, independently of the camera resolution, INODE can outperform the baselines by a large margin on the ASL task and it's on par with a much larger LSTM for the NCALTECH task. Finally, we show that INODE is accurate even when provided with very few events.

Pietro Astolfi, Ruben Verhagen, Laurent Petit et al.

Tractograms are virtual representations of the white matter fibers of the brain. They are of primary interest for tasks like presurgical planning, and investigation of neuroplasticity or brain disorders. Each tractogram is composed of millions of fibers encoded as 3D polylines. Unfortunately, a large portion of those fibers are not anatomically plausible and can be considered artifacts of the tracking algorithms. Common methods for tractogram filtering are based on signal reconstruction, a principled approach, but unable to consider the knowledge of brain anatomy. In this work, we address the problem of tractogram filtering as a supervised learning problem by exploiting the ground truth annotations obtained with a recent heuristic method, which labels fibers as either anatomically plausible or non-plausible according to well-established anatomical properties. The intuitive idea is to model a fiber as a point cloud and the goal is to investigate whether and how a geometric deep learning model might capture its anatomical properties. Our contribution is an extension of the Dynamic Edge Convolution model that exploits the sequential relations of points in a fiber and discriminates with high accuracy plausible/non-plausible fibers.

Sebastian East, Marco Gallieri, Jonathan Masci et al.

This paper proposes a differentiable linear quadratic Model Predictive Control (MPC) framework for safe imitation learning. The infinite-horizon cost is enforced using a terminal cost function obtained from the discrete-time algebraic Riccati equation (DARE), so that the learned controller can be proven to be stabilizing in closed-loop. A central contribution is the derivation of the analytical derivative of the solution of the DARE, thereby allowing the use of differentiation-based learning methods. A further contribution is the structure of the MPC optimization problem: an augmented Lagrangian method ensures that the MPC optimization is feasible throughout training whilst enforcing hard constraints on state and input, and a pre-stabilizing controller ensures that the MPC solution and derivatives are accurate at each iteration. The learning capabilities of the framework are demonstrated in a set of numerical studies.

Giorgio Giannone, Saeed Saremi, Jonathan Masci et al.

We extend the framework of variational autoencoders to represent transformations explicitly in the latent space. In the family of hierarchical graphical models that emerges, the latent space is populated by higher order objects that are inferred jointly with the latent representations they act on. To explicitly demonstrate the effect of these higher order objects, we show that the inferred latent transformations reflect interpretable properties in the observation space. Furthermore, the model is structured in such a way that in the absence of transformations, we can run inference and obtain generative capabilities comparable with standard variational autoencoders. Finally, utilizing the trained encoder, we outperform the baselines by a wide margin on a challenging out-of-distribution classification task.

Marco Gallieri, Seyed Sina Mirrazavi Salehian, Nihat Engin Toklu et al.

Control applications present hard operational constraints. A violation of these can result in unsafe behavior. This paper introduces Safe Interactive Model Based Learning (SiMBL), a framework to refine an existing controller and a system model while operating on the real environment. SiMBL is composed of the following trainable components: a Lyapunov function, which determines a safe set; a safe control policy; and a Bayesian RNN forward model. A min-max control framework, based on alternate minimisation and backpropagation through the forward model, is used for the offline computation of the controller and the safe set. Safety is formally verified a-posteriori with a probabilistic method that utilizes the Noise Contrastive Priors (NPC) idea to build a Bayesian RNN forward model with an additive state uncertainty estimate which is large outside the training data distribution. Iterative refinement of the model and the safe set is achieved thanks to a novel loss that conditions the uncertainty estimates of the new model to be close to the current one. The learned safe set and model can also be used for safe exploration, i.e., to collect data within the safe invariant set, for which a simple one-step MPC is proposed. The single components are tested on the simulation of an inverted pendulum with limited torque and stability region, showing that iteratively adding more data can improve the model, the controller and the size of the safe region.

Alessio Quaglino, Marco Gallieri, Jonathan Masci et al.

This paper proposes the use of spectral element methods \citep{canuto_spectral_1988} for fast and accurate training of Neural Ordinary Differential Equations (ODE-Nets; \citealp{Chen2018NeuralOD}) for system identification. This is achieved by expressing their dynamics as a truncated series of Legendre polynomials. The series coefficients, as well as the network weights, are computed by minimizing the weighted sum of the loss function and the violation of the ODE-Net dynamics. The problem is solved by coordinate descent that alternately minimizes, with respect to the coefficients and the weights, two unconstrained sub-problems using standard backpropagation and gradient methods. The resulting optimization scheme is fully time-parallel and results in a low memory footprint. Experimental comparison to standard methods, such as backpropagation through explicit solvers and the adjoint technique \citep{Chen2018NeuralOD}, on training surrogate models of small and medium-scale dynamical systems shows that it is at least one order of magnitude faster at reaching a comparable value of the loss function. The corresponding testing MSE is one order of magnitude smaller as well, suggesting generalization capabilities increase.

Timon Willi, Jonathan Masci, Jürgen Schmidhuber et al.

We extend Neural Processes (NPs) to sequential data through Recurrent NPs or RNPs, a family of conditional state space models. RNPs model the state space with Neural Processes. Given time series observed on fast real-world time scales but containing slow long-term variabilities, RNPs may derive appropriate slow latent time scales. They do so in an efficient manner by establishing conditional independence among subsequences of the time series. Our theoretically grounded framework for stochastic processes expands the applicability of NPs while retaining their benefits of flexibility, uncertainty estimation, and favorable runtime with respect to Gaussian Processes (GPs). We demonstrate that state spaces learned by RNPs benefit predictive performance on real-world time-series data and nonlinear system identification, even in the case of limited data availability.

Jan Svoboda, Asha Anoosheh, Christian Osendorfer et al.

This paper introduces a neural style transfer model to generate a stylized image conditioning on a set of examples describing the desired style. The proposed solution produces high-quality images even in the zero-shot setting and allows for more freedom in changes to the content geometry. This is made possible by introducing a novel Two-Stage Peer-Regularization Layer that recombines style and content in latent space by means of a custom graph convolutional layer. Contrary to the vast majority of existing solutions, our model does not depend on any pre-trained networks for computing perceptual losses and can be trained fully end-to-end thanks to a new set of cyclic losses that operate directly in latent space and not on the RGB images. An extensive ablation study confirms the usefulness of the proposed losses and of the Two-Stage Peer-Regularization Layer, with qualitative results that are competitive with respect to the current state of the art using a single model for all presented styles. This opens the door to more abstract and artistic neural image generation scenarios, along with simpler deployment of the model.

Jan Eric Lenssen, Christian Osendorfer, Jonathan Masci

This paper presents an end-to-end differentiable algorithm for robust and detail-preserving surface normal estimation on unstructured point-clouds. We utilize graph neural networks to iteratively parameterize an adaptive anisotropic kernel that produces point weights for weighted least-squares plane fitting in local neighborhoods. The approach retains the interpretability and efficiency of traditional sequential plane fitting while benefiting from adaptation to data set statistics through deep learning. This results in a state-of-the-art surface normal estimator that is robust to noise, outliers and point density variation, preserves sharp features through anisotropic kernels and equivariance through a local quaternion-based spatial transformer. Contrary to previous deep learning methods, the proposed approach does not require any hand-crafted features or preprocessing. It improves on the state-of-the-art results while being more than two orders of magnitude faster and more parameter efficient.

Francesco Lattari, Marco Ciccone, Matteo Matteucci et al.

We introduce ReConvNet, a recurrent convolutional architecture for semi-supervised video object segmentation that is able to fast adapt its features to focus on any specific object of interest at inference time. Generalization to new objects never observed during training is known to be a hard task for supervised approaches that would need to be retrained. To tackle this problem, we propose a more efficient solution that learns spatio-temporal features self-adapting to the object of interest via conditional affine transformations. This approach is simple, can be trained end-to-end and does not necessarily require extra training steps at inference time. Our method shows competitive results on DAVIS2016 with respect to state-of-the art approaches that use online fine-tuning, and outperforms them on DAVIS2017. ReConvNet shows also promising results on the DAVIS-Challenge 2018 winning the $10$-th position.

Jan Svoboda, Jonathan Masci, Federico Monti et al.

Deep learning systems have become ubiquitous in many aspects of our lives. Unfortunately, it has been shown that such systems are vulnerable to adversarial attacks, making them prone to potential unlawful uses. Designing deep neural networks that are robust to adversarial attacks is a fundamental step in making such systems safer and deployable in a broader variety of applications (e.g. autonomous driving), but more importantly is a necessary step to design novel and more advanced architectures built on new computational paradigms rather than marginally building on the existing ones. In this paper we introduce PeerNets, a novel family of convolutional networks alternating classical Euclidean convolutions with graph convolutions to harness information from a graph of peer samples. This results in a form of non-local forward propagation in the model, where latent features are conditioned on the global structure induced by the graph, that is up to 3 times more robust to a variety of white- and black-box adversarial attacks compared to conventional architectures with almost no drop in accuracy.

Marco Ciccone, Marco Gallieri, Jonathan Masci et al.

This paper introduces Non-Autonomous Input-Output Stable Network(NAIS-Net), a very deep architecture where each stacked processing block is derived from a time-invariant non-autonomous dynamical system. Non-autonomy is implemented by skip connections from the block input to each of the unrolled processing stages and allows stability to be enforced so that blocks can be unrolled adaptively to a pattern-dependent processing depth. NAIS-Net induces non-trivial, Lipschitz input-output maps, even for an infinite unroll length. We prove that the network is globally asymptotically stable so that for every initial condition there is exactly one input-dependent equilibrium assuming $tanh$ units, and incrementally stable for ReL units. An efficient implementation that enforces the stability under derived conditions for both fully-connected and convolutional layers is also presented. Experimental results show how NAIS-Net exhibits stability in practice, yielding a significant reduction in generalization gap compared to ResNets.

Federico Monti, Davide Boscaini, Jonathan Masci et al.

Deep learning has achieved a remarkable performance breakthrough in several fields, most notably in speech recognition, natural language processing, and computer vision. In particular, convolutional neural network (CNN) architectures currently produce state-of-the-art performance on a variety of image analysis tasks such as object detection and recognition. Most of deep learning research has so far focused on dealing with 1D, 2D, or 3D Euclidean-structured data such as acoustic signals, images, or videos. Recently, there has been an increasing interest in geometric deep learning, attempting to generalize deep learning methods to non-Euclidean structured data such as graphs and manifolds, with a variety of applications from the domains of network analysis, computational social science, or computer graphics. In this paper, we propose a unified framework allowing to generalize CNN architectures to non-Euclidean domains (graphs and manifolds) and learn local, stationary, and compositional task-specific features. We show that various non-Euclidean CNN methods previously proposed in the literature can be considered as particular instances of our framework. We test the proposed method on standard tasks from the realms of image-, graph- and 3D shape analysis and show that it consistently outperforms previous approaches.

Davide Boscaini, Jonathan Masci, Emanuele Rodolà et al.

Establishing correspondence between shapes is a fundamental problem in geometry processing, arising in a wide variety of applications. The problem is especially difficult in the setting of non-isometric deformations, as well as in the presence of topological noise and missing parts, mainly due to the limited capability to model such deformations axiomatically. Several recent works showed that invariance to complex shape transformations can be learned from examples. In this paper, we introduce an intrinsic convolutional neural network architecture based on anisotropic diffusion kernels, which we term Anisotropic Convolutional Neural Network (ACNN). In our construction, we generalize convolutions to non-Euclidean domains by constructing a set of oriented anisotropic diffusion kernels, creating in this way a local intrinsic polar representation of the data (`patch'), which is then correlated with a filter. Several cascades of such filters, linear, and non-linear operators are stacked to form a deep neural network whose parameters are learned by minimizing a task-specific cost. We use ACNNs to effectively learn intrinsic dense correspondences between deformable shapes in very challenging settings, achieving state-of-the-art results on some of the most difficult recent correspondence benchmarks.

Jonathan Masci, Davide Boscaini, Michael M. Bronstein et al.

Feature descriptors play a crucial role in a wide range of geometry analysis and processing applications, including shape correspondence, retrieval, and segmentation. In this paper, we introduce Geodesic Convolutional Neural Networks (GCNN), a generalization of the convolutional networks (CNN) paradigm to non-Euclidean manifolds. Our construction is based on a local geodesic system of polar coordinates to extract "patches", which are then passed through a cascade of filters and linear and non-linear operators. The coefficients of the filters and linear combination weights are optimization variables that are learned to minimize a task-specific cost function. We use GCNN to learn invariant shape features, allowing to achieve state-of-the-art performance in problems such as shape description, retrieval, and correspondence.

Rupesh Kumar Srivastava, Jonathan Masci, Faustino Gomez et al.

Recently proposed neural network activation functions such as rectified linear, maxout, and local winner-take-all have allowed for faster and more effective training of deep neural architectures on large and complex datasets. The common trait among these functions is that they implement local competition between small groups of computational units within a layer, so that only part of the network is activated for any given input pattern. In this paper, we attempt to visualize and understand this self-modularization, and suggest a unified explanation for the beneficial properties of such networks. We also show how our insights can be directly useful for efficiently performing retrieval over large datasets using neural networks.

Marijn Stollenga, Jonathan Masci, Faustino Gomez et al.

Traditional convolutional neural networks (CNN) are stationary and feedforward. They neither change their parameters during evaluation nor use feedback from higher to lower layers. Real brains, however, do. So does our Deep Attention Selective Network (dasNet) architecture. DasNets feedback structure can dynamically alter its convolutional filter sensitivities during classification. It harnesses the power of sequential processing to improve classification performance, by allowing the network to iteratively focus its internal attention on some of its convolutional filters. Feedback is trained through direct policy search in a huge million-dimensional parameter space, through scalable natural evolution strategies (SNES). On the CIFAR-10 and CIFAR-100 datasets, dasNet outperforms the previous state-of-the-art model.

Jonathan Masci, Alex M. Bronstein, Michael M. Bronstein et al.

In recent years, a lot of attention has been devoted to efficient nearest neighbor search by means of similarity-preserving hashing. One of the plights of existing hashing techniques is the intrinsic trade-off between performance and computational complexity: while longer hash codes allow for lower false positive rates, it is very difficult to increase the embedding dimensionality without incurring in very high false negatives rates or prohibiting computational costs. In this paper, we propose a way to overcome this limitation by enforcing the hash codes to be sparse. Sparse high-dimensional codes enjoy from the low false positive rates typical of long hashes, while keeping the false negative rates similar to those of a shorter dense hashing scheme with equal number of degrees of freedom. We use a tailored feed-forward neural network for the hashing function. Extensive experimental evaluation involving visual and multi-modal data shows the benefits of the proposed method.

Alessandro Giusti, Dan C. Cireşan, Jonathan Masci et al.

Deep Neural Networks now excel at image classification, detection and segmentation. When used to scan images by means of a sliding window, however, their high computational complexity can bring even the most powerful hardware to its knees. We show how dynamic programming can speedup the process by orders of magnitude, even when max-pooling layers are present.

Jonathan Masci, Alessandro Giusti, Dan Cireşan et al.

We present a fast algorithm for training MaxPooling Convolutional Networks to segment images. This type of network yields record-breaking performance in a variety of tasks, but is normally trained on a computationally expensive patch-by-patch basis. Our new method processes each training image in a single pass, which is vastly more efficient. We validate the approach in different scenarios and report a 1500-fold speed-up. In an application to automated steel defect detection and segmentation, we obtain excellent performance with short training times.

Jonathan Masci, Ueli Meier, Gabriel Fricout et al.

We present a Multi-Scale Pyramidal Pooling Network, featuring a novel pyramidal pooling layer at multiple scales and a novel encoding layer. Thanks to the former the network does not require all images of a given classification task to be of equal size. The encoding layer improves generalisation performance in comparison to similar neural network architectures, especially when training data is scarce. We evaluate and compare our system to convolutional neural networks and state-of-the-art computer vision methods on various benchmark datasets. We also present results on industrial steel defect classification, where existing architectures are not applicable because of the constraint on equally sized input images. The proposed architecture can be seen as a fully supervised hierarchical bag-of-features extension that is trained online and can be fine-tuned for any given task.

Jonathan Masci, Michael M. Bronstein, Alexander A. Bronstein et al.

We introduce an efficient computational framework for hashing data belonging to multiple modalities into a single representation space where they become mutually comparable. The proposed approach is based on a novel coupled siamese neural network architecture and allows unified treatment of intra- and inter-modality similarity learning. Unlike existing cross-modality similarity learning approaches, our hashing functions are not limited to binarized linear projections and can assume arbitrarily complex forms. We show experimentally that our method significantly outperforms state-of-the-art hashing approaches on multimedia retrieval tasks.