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.Comment: Paper at the International Conference of Machine Learning (2018), 2018-07-10 to 2018-07-15 in Stockholm, Swede

Leave Graphs Alone: Addressing Over-Squashing without Rewiring

Recent works have investigated the role of graph bottlenecks in preventing long-range information propagation in message-passing graph neural networks, causing the so-called `over-squashing' phenomenon. As a remedy, graph rewiring mechanisms have been proposed as preprocessing steps. Graph Echo State Networks (GESNs) are a reservoir computing model for graphs, where node embeddings are recursively computed by an untrained message-passing function. In this paper, we show that GESNs can achieve a significantly better accuracy on six heterophilic node classification tasks without altering the graph connectivity, thus suggesting a different route for addressing the over-squashing problem.Comment: Extended Abstract. Presented at the First Learning on Graphs Conference (LoG 2022), Virtual Event, December 9-12, 202

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.Comment: Pre-print of 'Fast and Deep Graph Neural Networks', accepted for AAAI 2020. This document includes the Supplementary Materia

Tree Echo State Networks

In this paper we present the Tree Echo State Network (TreeESN) model, generalizing the paradigm of Reservoir Computing to tree structured data. TreeESNs exploit an untrained generalized recursive reservoir, exhibiting extreme efficiency for learning in structured domains. In addition, we highlight through the paper other characteristics of the approach: First, we discuss the Markovian characterization of reservoir dynamics, extended to the case of tree domains, that is implied by the contractive setting of the TreeESN state transition function. Second, we study two types of state mapping functions to map the tree structured state of TreeESN into a fixed-size feature representation for classification or regression tasks. The critical role of the relation between the choice of the state mapping function and the Markovian characterization of the task is analyzed and experimentally investigated on both artificial and real-world tasks. Finally, experimental results on benchmark and real-world tasks show that the TreeESN approach, in spite of its efficiency, can achieve comparable results with state-of-the-art, although more complex, neural and kernel based models for tree structured data

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

Wild animals' biologging through machine learning models

In recent decades the biodiversity crisis has been characterised by a decline and extinction of many animal species worldwide. To aid in understanding the threats and causes of this demise, conservation scientists rely on remote assessments. Innovation in technology in the form of microelectromechanical systems (MEMs) has brought about great leaps forward in understanding of animal life. The MEMs are now readily available to ecologists for remotely monitoring the activities of wild animals. Since the advent of electronic tags, methods such as biologging are being increasingly applied to the study of animal ecology, providing information unattainable through other techniques. In this paper, we discuss a few relevant instances of biologging studies. We present an overview on biologging research area, describing the evolution of acquisition of behavioural information and the improvement provided by tags. In second part we will review some common data analysis techniques used to identify daily activity of animals

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.Comment: This is a pre-print of the paper submitted to the European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, ESANN 201