arXiv subjects

Davide Bacciu

Publications and source records attributed to Davide Bacciu.

At least 109 records · Page 6Linked to original sources

arXiv2021

Catastrophic Forgetting in Deep Graph Networks: an Introductory Benchmark for Graph Classification

In this work, we study the phenomenon of catastrophic forgetting in the graph representation learning scenario. The primary objective of the analysis is to understand whether classical continual learning techniques for flat and sequential data have a tangible impact on performances when applied to graph data. To do so, we experiment with a structure-agnostic model and a deep graph network in a robust and controlled environment on three different datasets. The benchmark is complemented by an investigation on the effect of structure-preserving regularization techniques on catastrophic forgetting. We find that replay is the most effective strategy in so far, which also benefits the most from the use of regularization. Our findings suggest interesting future research at the intersection of the continual and graph representation learning fields. Finally, we provide researchers with a flexible software framework to reproduce our results and carry out further experiments.

cs.LG↗

arXiv2020

Generative Tomography Reconstruction

We propose an end-to-end differentiable architecture for tomography reconstruction that directly maps a noisy sinogram into a denoised reconstruction. Compared to existing approaches our end-to-end architecture produces more accurate reconstructions while using less parameters and time. We also propose a generative model that, given a noisy sinogram, can sample realistic reconstructions. This generative model can be used as prior inside an iterative process that, by taking into consideration the physical model, can reduce artifacts and errors in the reconstructions.

eess.IV↗

arXiv2020

Explaining Deep Graph Networks with Molecular Counterfactuals

We present a novel approach to tackle explainability of deep graph networks in the context of molecule property prediction tasks, named MEG (Molecular Explanation Generator). We generate informative counterfactual explanations for a specific prediction under the form of (valid) compounds with high structural similarity and different predicted properties. We discuss preliminary results showing how the model can convey non-ML experts with key insights into the learning model focus in the neighborhood of a molecule.

q-bio.QM↗

arXiv2020

Short-Term Memory Optimization in Recurrent Neural Networks by Autoencoder-based Initialization

Training RNNs to learn long-term dependencies is difficult due to vanishing gradients. We explore an alternative solution based on explicit memorization using linear autoencoders for sequences, which allows to maximize the short-term memory and that can be solved with a closed-form solution without backpropagation. We introduce an initialization schema that pretrains the weights of a recurrent neural network to approximate the linear autoencoder of the input sequences and we show how such pretraining can better support solving hard classification tasks with long sequences. We test our approach on sequential and permuted MNIST. We show that the proposed approach achieves a much lower reconstruction error for long sequences and a better gradient propagation during the finetuning phase.

cs.LG↗

arXiv2020

Learning from Non-Binary Constituency Trees via Tensor Decomposition

Processing sentence constituency trees in binarised form is a common and popular approach in literature. However, constituency trees are non-binary by nature. The binarisation procedure changes deeply the structure, furthering constituents that instead are close. In this work, we introduce a new approach to deal with non-binary constituency trees which leverages tensor-based models. In particular, we show how a powerful composition function based on the canonical tensor decomposition can exploit such a rich structure. A key point of our approach is the weight sharing constraint imposed on the factor matrices, which allows limiting the number of model parameters. Finally, we introduce a Tree-LSTM model which takes advantage of this composition function and we experimentally assess its performance on different NLP tasks.

cs.LG↗

arXiv2020

FADER: Fast Adversarial Example Rejection

Deep neural networks are vulnerable to adversarial examples, i.e., carefully-crafted inputs that mislead classification at test time. Recent defenses have been shown to improve adversarial robustness by detecting anomalous deviations from legitimate training samples at different layer representations - a behavior normally exhibited by adversarial attacks. Despite technical differences, all aforementioned methods share a common backbone structure that we formalize and highlight in this contribution, as it can help in identifying promising research directions and drawbacks of existing methods. The first main contribution of this work is the review of these detection methods in the form of a unifying framework designed to accommodate both existing defenses and newer ones to come. In terms of drawbacks, the overmentioned defenses require comparing input samples against an oversized number of reference prototypes, possibly at different representation layers, dramatically worsening the test-time efficiency. Besides, such defenses are typically based on ensembling classifiers with heuristic methods, rather than optimizing the whole architecture in an end-to-end manner to better perform detection. As a second main contribution of this work, we introduce FADER, a novel technique for speeding up detection-based methods. FADER overcome the issues above by employing RBF networks as detectors: by fixing the number of required prototypes, the runtime complexity of adversarial examples detectors can be controlled. Our experiments outline up to 73x prototypes reduction compared to analyzed detectors for MNIST dataset and up to 50x for CIFAR10 dataset respectively, without sacrificing classification accuracy on both clean and adversarial data.

cs.LG↗

arXiv2020

Perplexity-free Parametric t-SNE

The t-distributed Stochastic Neighbor Embedding (t-SNE) algorithm is a ubiquitously employed dimensionality reduction (DR) method. Its non-parametric nature and impressive efficacy motivated its parametric extension. It is however bounded to a user-defined perplexity parameter, restricting its DR quality compared to recently developed multi-scale perplexity-free approaches. This paper hence proposes a multi-scale parametric t-SNE scheme, relieved from the perplexity tuning and with a deep neural network implementing the mapping. It produces reliable embeddings with out-of-sample extensions, competitive with the best perplexity adjustments in terms of neighborhood preservation on multiple data sets.

cs.LG↗

arXiv2020

ROS-Neuro Integration of Deep Convolutional Autoencoders for EEG Signal Compression in Real-time BCIs

Typical EEG-based BCI applications require the computation of complex functions over the noisy EEG channels to be carried out in an efficient way. Deep learning algorithms are capable of learning flexible nonlinear functions directly from data, and their constant processing latency is perfect for their deployment into online BCI systems. However, it is crucial for the jitter of the processing system to be as low as possible, in order to avoid unpredictable behaviour that can ruin the system's overall usability. In this paper, we present a novel encoding method, based on on deep convolutional autoencoders, that is able to perform efficient compression of the raw EEG inputs. We deploy our model in a ROS-Neuro node, thus making it suitable for the integration in ROS-based BCI and robotic systems in real world scenarios. The experimental results show that our system is capable to generate meaningful compressed encoding preserving to original information contained in the raw input. They also show that the ROS-Neuro node is able to produce such encodings at a steady rate, with minimal jitter. We believe that our system can represent an important step towards the development of an effective BCI processing pipeline fully standardized in ROS-Neuro framework.

cs.LG↗

arXiv2020

Tensor Decompositions in Recursive Neural Networks for Tree-Structured Data

The paper introduces two new aggregation functions to encode structural knowledge from tree-structured data. They leverage the Canonical and Tensor-Train decompositions to yield expressive context aggregation while limiting the number of model parameters. Finally, we define two novel neural recursive models for trees leveraging such aggregation functions, and we test them on two tree classification tasks, showing the advantage of proposed models when tree outdegree increases.

cs.LG↗

arXiv2020

Accelerating the identification of informative reduced representations of proteins with deep learning for graphs

The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD trajectories induces the need of automated and transferable methods to rationalise the raw data and make quantitative sense out of them. Recently, an algorithmic approach was developed by some of us to identify the subset of a protein's atoms, or mapping, that enables the most informative description of it. This method relies on the computation, for a given reduced representation, of the associated mapping entropy, that is, a measure of the information loss due to the simplification. Albeit relatively straightforward, this calculation can be time consuming. Here, we describe the implementation of a deep learning approach aimed at accelerating the calculation of the mapping entropy. The method relies on deep graph networks, which provide extreme flexibility in the input format. We show that deep graph networks are accurate and remarkably efficient, with a speedup factor as large as $10^5$ with respect to the algorithmic computation of the mapping entropy. Applications of this method, which entails a great potential in the study of biomolecules when used to reconstruct its mapping entropy landscape, reach much farther than this, being the scheme easily transferable to the computation of arbitrary functions of a molecule's structure.

physics.comp-ph↗

arXiv2020

Incremental Training of a Recurrent Neural Network Exploiting a Multi-Scale Dynamic Memory

The effectiveness of recurrent neural networks can be largely influenced by their ability to store into their dynamical memory information extracted from input sequences at different frequencies and timescales. Such a feature can be introduced into a neural architecture by an appropriate modularization of the dynamic memory. In this paper we propose a novel incrementally trained recurrent architecture targeting explicitly multi-scale learning. First, we show how to extend the architecture of a simple RNN by separating its hidden state into different modules, each subsampling the network hidden activations at different frequencies. Then, we discuss a training algorithm where new modules are iteratively added to the model to learn progressively longer dependencies. Each new module works at a slower frequency than the previous ones and it is initialized to encode the subsampled sequence of hidden activations. Experimental results on synthetic and real-world datasets on speech recognition and handwritten characters show that the modular architecture and the incremental training algorithm improve the ability of recurrent neural networks to capture long-term dependencies.

cs.LG↗

arXiv2020

Generalising Recursive Neural Models by Tensor Decomposition

Most machine learning models for structured data encode the structural knowledge of a node by leveraging simple aggregation functions (in neural models, typically a weighted sum) of the information in the node's neighbourhood. Nevertheless, the choice of simple context aggregation functions, such as the sum, can be widely sub-optimal. In this work we introduce a general approach to model aggregation of structural context leveraging a tensor-based formulation. We show how the exponential growth in the size of the parameter space can be controlled through an approximation based on the Tucker tensor decomposition. This approximation allows limiting the parameters space size, decoupling it from its strict relation with the size of the hidden encoding space. By this means, we can effectively regulate the trade-off between expressivity of the encoding, controlled by the hidden size, computational complexity and model generalisation, influenced by parameterisation. Finally, we introduce a new Tensorial Tree-LSTM derived as an instance of our framework and we use it to experimentally assess our working hypotheses on tree classification scenarios.

cs.LG↗

arXiv2020

A Gentle Introduction to Deep Learning for Graphs

The adaptive processing of graph data is a long-standing research topic which has been lately consolidated as a theme of major interest in the deep learning community. The snap increase in the amount and breadth of related research has come at the price of little systematization of knowledge and attention to earlier literature. This work is designed as a tutorial introduction to the field of deep learning for graphs. It favours a consistent and progressive introduction of the main concepts and architectural aspects over an exposition of the most recent literature, for which the reader is referred to available surveys. The paper takes a top-down view to the problem, introducing a generalized formulation of graph representation learning based on a local and iterative approach to structured information processing. It introduces the basic building blocks that can be combined to design novel and effective neural models for graphs. The methodological exposition is complemented by a discussion of interesting research challenges and applications in the field.

cs.LG↗

arXiv2020

Continual Learning with Gated Incremental Memories for sequential data processing

The ability to learn in dynamic, nonstationary environments without forgetting previous knowledge, also known as Continual Learning (CL), is a key enabler for scalable and trustworthy deployments of adaptive solutions. While the importance of continual learning is largely acknowledged in machine vision and reinforcement learning problems, this is mostly under-documented for sequence processing tasks. This work proposes a Recurrent Neural Network (RNN) model for CL that is able to deal with concept drift in input distribution without forgetting previously acquired knowledge. We also implement and test a popular CL approach, Elastic Weight Consolidation (EWC), on top of two different types of RNNs. Finally, we compare the performances of our enhanced architecture against EWC and RNNs on a set of standard CL benchmarks, adapted to the sequential data processing scenario. Results show the superior performance of our architecture and highlight the need for special solutions designed to address CL in RNNs.

cs.LG↗

arXiv2020

A Deep Generative Model for Fragment-Based Molecule Generation

Molecule generation is a challenging open problem in cheminformatics. Currently, deep generative approaches addressing the challenge belong to two broad categories, differing in how molecules are represented. One approach encodes molecular graphs as strings of text, and learns their corresponding character-based language model. Another, more expressive, approach operates directly on the molecular graph. In this work, we address two limitations of the former: generation of invalid and duplicate molecules. To improve validity rates, we develop a language model for small molecular substructures called fragments, loosely inspired by the well-known paradigm of Fragment-Based Drug Design. In other words, we generate molecules fragment by fragment, instead of atom by atom. To improve uniqueness rates, we present a frequency-based masking strategy that helps generate molecules with infrequent fragments. We show experimentally that our model largely outperforms other language model-based competitors, reaching state-of-the-art performances typical of graph-based approaches. Moreover, generated molecules display molecular properties similar to those in the training sample, even in absence of explicit task-specific supervision.

stat.ML↗

arXiv2020

Tensor Decompositions in Deep Learning

The paper surveys the topic of tensor decompositions in modern machine learning applications. It focuses on three active research topics of significant relevance for the community. After a brief review of consolidated works on multi-way data analysis, we consider the use of tensor decompositions in compressing the parameter space of deep learning models. Lastly, we discuss how tensor methods can be leveraged to yield richer adaptive representations of complex data, including structured information. The paper concludes with a discussion on interesting open research challenges.

cs.LG↗

arXiv2020

Learning Style-Aware Symbolic Music Representations by Adversarial Autoencoders

We address the challenging open problem of learning an effective latent space for symbolic music data in generative music modeling. We focus on leveraging adversarial regularization as a flexible and natural mean to imbue variational autoencoders with context information concerning music genre and style. Through the paper, we show how Gaussian mixtures taking into account music metadata information can be used as an effective prior for the autoencoder latent space, introducing the first Music Adversarial Autoencoder (MusAE). The empirical analysis on a large scale benchmark shows that our model has a higher reconstruction accuracy than state-of-the-art models based on standard variational autoencoders. It is also able to create realistic interpolations between two musical sequences, smoothly changing the dynamics of the different tracks. Experiments show that the model can organise its latent space accordingly to low-level properties of the musical pieces, as well as to embed into the latent variables the high-level genre information injected from the prior distribution to increase its overall performance. This allows us to perform changes to the generated pieces in a principled way.

cs.SD↗

arXiv2020

Measuring the effects of confounders in medical supervised classification problems: the Confounding Index (CI)

Over the years, there has been growing interest in using Machine Learning techniques for biomedical data processing. When tackling these tasks, one needs to bear in mind that biomedical data depends on a variety of characteristics, such as demographic aspects (age, gender, etc) or the acquisition technology, which might be unrelated with the target of the analysis. In supervised tasks, failing to match the ground truth targets with respect to such characteristics, called confounders, may lead to very misleading estimates of the predictive performance. Many strategies have been proposed to handle confounders, ranging from data selection, to normalization techniques, up to the use of training algorithm for learning with imbalanced data. However, all these solutions require the confounders to be known a priori. To this aim, we introduce a novel index that is able to measure the confounding effect of a data attribute in a bias-agnostic way. This index can be used to quantitatively compare the confounding effects of different variables and to inform correction methods such as normalization procedures or ad-hoc-prepared learning algorithms. The effectiveness of this index is validated on both simulated data and real-world neuroimaging data.

cs.LG↗