arXiv subjects

Alessio Micheli

Publications and source records attributed to Alessio Micheli.

31 records · Page 2Linked to original sources

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.

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arXiv2020

Machine learning approaches for identifying prey handling activity in otariid pinnipeds

Systems developed in wearable devices with sensors onboard are widely used to collect data of humans and animals activities with the perspective of an on-board automatic classification of data. An interesting application of these systems is to support animals' behaviour monitoring gathered by sensors' data analysis. This is a challenging area and in particular with fixed memories capabilities because the devices should be able to operate autonomously for long periods before being retrieved by human operators, and being able to classify activities onboard can significantly improve their autonomy. In this paper, we focus on the identification of prey handling activity in seals (when the animal start attaching and biting the prey), which is one of the main movement that identifies a successful foraging activity. Data taken into consideration are streams of 3D accelerometers and depth sensors values collected by devices attached directly on seals. To analyse these data, we propose an automatic model based on Machine Learning (ML) algorithms. In particular, we compare the performance (in terms of accuracy and F1score) of three ML algorithms: Input Delay Neural Networks, Support Vector Machines, and Echo State Networks. We attend to the final aim of developing an automatic classifier on-board. For this purpose, in this paper, the comparison is performed concerning the performance obtained by each ML approach developed and its memory footprint. In the end, we highlight the advantage of using an ML algorithm, in terms of feasibility in wild animals' monitoring.

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arXiv2020

Edge-based sequential graph generation with recurrent neural networks

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

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arXiv2020

Theoretically Expressive and Edge-aware Graph Learning

We propose a new Graph Neural Network that combines recent advancements in the field. We give theoretical contributions by proving that the model is strictly more general than the Graph Isomorphism Network and the Gated Graph Neural Network, as it can approximate the same functions and deal with arbitrary edge values. Then, we show how a single node information can flow through the graph unchanged.

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arXiv2019

Contextual Graph Markov Model: A Deep and Generative Approach to Graph Processing

We introduce the Contextual Graph Markov Model, an approach combining ideas from generative models and neural networks for the processing of graph data. It founds on a constructive methodology to build a deep architecture comprising layers of probabilistic models that learn to encode the structured information in an incremental fashion. Context is diffused in an efficient and scalable way across the graph vertexes and edges. The resulting graph encoding is used in combination with discriminative models to address structure classification benchmarks.

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arXiv2019

Comparison between DeepESNs and gated RNNs on multivariate time-series prediction

We propose an experimental comparison between Deep Echo State Networks (DeepESNs) and gated Recurrent Neural Networks (RNNs) on multivariate time-series prediction tasks. In particular, we compare reservoir and fully-trained RNNs able to represent signals featured by multiple time-scales dynamics. The analysis is performed in terms of efficiency and prediction accuracy on 4 polyphonic music tasks. Our results show that DeepESN is able to outperform ESN in terms of prediction accuracy and efficiency. Whereas, between fully-trained approaches, Gated Recurrent Units (GRU) outperforms Long Short-Term Memory (LSTM) and simple RNN models in most cases. Overall, DeepESN turned out to be extremely more efficient than others RNN approaches and the best solution in terms of prediction accuracy on 3 out of 4 tasks.

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arXiv2019

Fast and Deep Graph Neural Networks

We address the efficiency issue for the construction of a deep graph neural network (GNN). The approach exploits the idea of representing each input graph as a fixed point of a dynamical system (implemented through a recurrent neural network), and leverages a deep architectural organization of the recurrent units. Efficiency is gained by many aspects, including the use of small and very sparse networks, where the weights of the recurrent units are left untrained under the stability condition introduced in this work. This can be viewed as a way to study the intrinsic power of the architecture of a deep GNN, and also to provide insights for the set-up of more complex fully-trained models. Through experimental results, we show that even without training of the recurrent connections, the architecture of small deep GNN is surprisingly able to achieve or improve the state-of-the-art performance on a significant set of tasks in the field of graphs classification.

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arXiv2019

Richness of Deep Echo State Network Dynamics

Reservoir Computing (RC) is a popular methodology for the efficient design of Recurrent Neural Networks (RNNs). Recently, the advantages of the RC approach have been extended to the context of multi-layered RNNs, with the introduction of the Deep Echo State Network (DeepESN) model. In this paper, we study the quality of state dynamics in progressively higher layers of DeepESNs, using tools from the areas of information theory and numerical analysis. Our experimental results on RC benchmark datasets reveal the fundamental role played by the strength of inter-reservoir connections to increasingly enrich the representations developed in higher layers. Our analysis also gives interesting insights into the possibility of effective exploitation of training algorithms based on stochastic gradient descent in the RC field.

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arXiv2019

Reservoir Topology in Deep Echo State Networks

Deep Echo State Networks (DeepESNs) recently extended the applicability of Reservoir Computing (RC) methods towards the field of deep learning. In this paper we study the impact of constrained reservoir topologies in the architectural design of deep reservoirs, through numerical experiments on several RC benchmarks. The major outcome of our investigation is to show the remarkable effect, in terms of predictive performance gain, achieved by the synergy between a deep reservoir construction and a structured organization of the recurrent units in each layer. Our results also indicate that a particularly advantageous architectural setting is obtained in correspondence of DeepESNs where reservoir units are structured according to a permutation recurrent matrix.

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arXiv2019

Embeddings and Representation Learning for Structured Data

Performing machine learning on structured data is complicated by the fact that such data does not have vectorial form. Therefore, multiple approaches have emerged to construct vectorial representations of structured data, from kernel and distance approaches to recurrent, recursive, and convolutional neural networks. Recent years have seen heightened attention in this demanding field of research and several new approaches have emerged, such as metric learning on structured data, graph convolutional neural networks, and recurrent decoder networks for structured data. In this contribution, we provide an high-level overview of the state-of-the-art in representation learning and embeddings for structured data across a wide range of machine learning fields.

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arXiv2018

Tree Edit Distance Learning via Adaptive Symbol Embeddings

Metric learning has the aim to improve classification accuracy by learning a distance measure which brings data points from the same class closer together and pushes data points from different classes further apart. Recent research has demonstrated that metric learning approaches can also be applied to trees, such as molecular structures, abstract syntax trees of computer programs, or syntax trees of natural language, by learning the cost function of an edit distance, i.e. the costs of replacing, deleting, or inserting nodes in a tree. However, learning such costs directly may yield an edit distance which violates metric axioms, is challenging to interpret, and may not generalize well. In this contribution, we propose a novel metric learning approach for trees which we call embedding edit distance learning (BEDL) and which learns an edit distance indirectly by embedding the tree nodes as vectors, such that the Euclidean distance between those vectors supports class discrimination. We learn such embeddings by reducing the distance to prototypical trees from the same class and increasing the distance to prototypical trees from different classes. In our experiments, we show that BEDL improves upon the state-of-the-art in metric learning for trees on six benchmark data sets, ranging from computer science over biomedical data to a natural-language processing data set containing over 300,000 nodes.

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arXiv2018

Deep Echo State Networks for Diagnosis of Parkinson's Disease

In this paper, we introduce a novel approach for diagnosis of Parkinson's Disease (PD) based on deep Echo State Networks (ESNs). The identification of PD is performed by analyzing the whole time-series collected from a tablet device during the sketching of spiral tests, without the need for feature extraction and data preprocessing. We evaluated the proposed approach on a public dataset of spiral tests. The results of experimental analysis show that DeepESNs perform significantly better than shallow ESN model. Overall, the proposed approach obtains state-of-the-art results in the identification of PD on this kind of temporal data.

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arXiv2017

Hierarchical Temporal Representation in Linear Reservoir Computing

Recently, studies on deep Reservoir Computing (RC) highlighted the role of layering in deep recurrent neural networks (RNNs). In this paper, the use of linear recurrent units allows us to bring more evidence on the intrinsic hierarchical temporal representation in deep RNNs through frequency analysis applied to the state signals. The potentiality of our approach is assessed on the class of Multiple Superimposed Oscillator tasks. Furthermore, our investigation provides useful insights to open a discussion on the main aspects that characterize the deep learning framework in the temporal domain.

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