583 research outputs found

    Graph Laplacian for Semi-Supervised Learning

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    Semi-supervised learning is highly useful in common scenarios where labeled data is scarce but unlabeled data is abundant. The graph (or nonlocal) Laplacian is a fundamental smoothing operator for solving various learning tasks. For unsupervised clustering, a spectral embedding is often used, based on graph-Laplacian eigenvectors. For semi-supervised problems, the common approach is to solve a constrained optimization problem, regularized by a Dirichlet energy, based on the graph-Laplacian. However, as supervision decreases, Dirichlet optimization becomes suboptimal. We therefore would like to obtain a smooth transition between unsupervised clustering and low-supervised graph-based classification. In this paper, we propose a new type of graph-Laplacian which is adapted for Semi-Supervised Learning (SSL) problems. It is based on both density and contrastive measures and allows the encoding of the labeled data directly in the operator. Thus, we can perform successfully semi-supervised learning using spectral clustering. The benefits of our approach are illustrated for several SSL problems.Comment: 12 pages, 6 figure

    A Quasi-Wasserstein Loss for Learning Graph Neural Networks

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    When learning graph neural networks (GNNs) in node-level prediction tasks, most existing loss functions are applied for each node independently, even if node embeddings and their labels are non-i.i.d. because of their graph structures. To eliminate such inconsistency, in this study we propose a novel Quasi-Wasserstein (QW) loss with the help of the optimal transport defined on graphs, leading to new learning and prediction paradigms of GNNs. In particular, we design a "Quasi-Wasserstein" distance between the observed multi-dimensional node labels and their estimations, optimizing the label transport defined on graph edges. The estimations are parameterized by a GNN in which the optimal label transport may determine the graph edge weights optionally. By reformulating the strict constraint of the label transport to a Bregman divergence-based regularizer, we obtain the proposed Quasi-Wasserstein loss associated with two efficient solvers learning the GNN together with optimal label transport. When predicting node labels, our model combines the output of the GNN with the residual component provided by the optimal label transport, leading to a new transductive prediction paradigm. Experiments show that the proposed QW loss applies to various GNNs and helps to improve their performance in node-level classification and regression tasks

    Computational Approaches to Drug Profiling and Drug-Protein Interactions

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    Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a long period of stagnation in drug approvals. Due to the extreme costs associated with introducing a drug to the market, locating and understanding the reasons for clinical failure is key to future productivity. As part of this PhD, three main contributions were made in this respect. First, the web platform, LigNFam enables users to interactively explore similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly, two deep-learning-based binding site comparison tools were developed, competing with the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold relationships and has already been used in multiple projects, including integration into a virtual screening pipeline to increase the tractability of ultra-large screening experiments. Together, and with existing tools, the contributions made will aid in the understanding of drug-protein relationships, particularly in the fields of off-target prediction and drug repurposing, helping to design better drugs faster

    A review of technical factors to consider when designing neural networks for semantic segmentation of Earth Observation imagery

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    Semantic segmentation (classification) of Earth Observation imagery is a crucial task in remote sensing. This paper presents a comprehensive review of technical factors to consider when designing neural networks for this purpose. The review focuses on Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Generative Adversarial Networks (GANs), and transformer models, discussing prominent design patterns for these ANN families and their implications for semantic segmentation. Common pre-processing techniques for ensuring optimal data preparation are also covered. These include methods for image normalization and chipping, as well as strategies for addressing data imbalance in training samples, and techniques for overcoming limited data, including augmentation techniques, transfer learning, and domain adaptation. By encompassing both the technical aspects of neural network design and the data-related considerations, this review provides researchers and practitioners with a comprehensive and up-to-date understanding of the factors involved in designing effective neural networks for semantic segmentation of Earth Observation imagery.Comment: 145 pages with 32 figure

    An Analytical Performance Evaluation on Multiview Clustering Approaches

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    The concept of machine learning encompasses a wide variety of different approaches, one of which is called clustering. The data points are grouped together in this approach to the problem. Using a clustering method, it is feasible, given a collection of data points, to classify each data point as belonging to a specific group. This can be done if the algorithm is given the collection of data points. In theory, data points that constitute the same group ought to have attributes and characteristics that are equivalent to one another, however data points that belong to other groups ought to have properties and characteristics that are very different from one another. The generation of multiview data is made possible by recent developments in information collecting technologies. The data were collected from à variety of sources and were analysed using a variety of perspectives. The data in question are what are known as multiview data. On a single view, the conventional clustering algorithms are applied. In spite of this, real-world data are complicated and can be clustered in a variety of different ways, depending on how the data are interpreted. In practise, the real-world data are messy. In recent years, Multiview Clustering, often known as MVC, has garnered an increasing amount of attention due to its goal of utilising complimentary and consensus information derived from different points of view. On the other hand, the vast majority of the systems that are currently available only enable the single-clustering scenario, whereby only makes utilization of a single cluster to split the data. This is the case since there is only one cluster accessible. In light of this, it is absolutely necessary to carry out investigation on the multiview data format. The study work is centred on multiview clustering and how well it performs compared to these other strategies

    Inhomogeneous graph trend filtering via a l2,0 cardinality penalty

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    We study estimation of piecewise smooth signals over a graph. We propose a â„“2,0\ell_{2,0}-norm penalized Graph Trend Filtering (GTF) model to estimate piecewise smooth graph signals that exhibits inhomogeneous levels of smoothness across the nodes. We prove that the proposed GTF model is simultaneously a k-means clustering on the signal over the nodes and a minimum graph cut on the edges of the graph, where the clustering and the cut share the same assignment matrix. We propose two methods to solve the proposed GTF model: a spectral decomposition method and a method based on simulated annealing. In the experiment on synthetic and real-world datasets, we show that the proposed GTF model has a better performances compared with existing approaches on the tasks of denoising, support recovery and semi-supervised classification. We also show that the proposed GTF model can be solved more efficiently than existing models for the dataset with a large edge set.Comment: 21 pages, 3 figures, 4 table

    The Role of Synthetic Data in Improving Supervised Learning Methods: The Case of Land Use/Land Cover Classification

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    A thesis submitted in partial fulfillment of the requirements for the degree of Doctor in Information ManagementIn remote sensing, Land Use/Land Cover (LULC) maps constitute important assets for various applications, promoting environmental sustainability and good resource management. Although, their production continues to be a challenging task. There are various factors that contribute towards the difficulty of generating accurate, timely updated LULC maps, both via automatic or photo-interpreted LULC mapping. Data preprocessing, being a crucial step for any Machine Learning task, is particularly important in the remote sensing domain due to the overwhelming amount of raw, unlabeled data continuously gathered from multiple remote sensing missions. However a significant part of the state-of-the-art focuses on scenarios with full access to labeled training data with relatively balanced class distributions. This thesis focuses on the challenges found in automatic LULC classification tasks, specifically in data preprocessing tasks. We focus on the development of novel Active Learning (AL) and imbalanced learning techniques, to improve ML performance in situations with limited training data and/or the existence of rare classes. We also show that much of the contributions presented are not only successful in remote sensing problems, but also in various other multidisciplinary classification problems. The work presented in this thesis used open access datasets to test the contributions made in imbalanced learning and AL. All the data pulling, preprocessing and experiments are made available at https://github.com/joaopfonseca/publications. The algorithmic implementations are made available in the Python package ml-research at https://github.com/joaopfonseca/ml-research

    BitGNN: Unleashing the Performance Potential of Binary Graph Neural Networks on GPUs

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    Recent studies have shown that Binary Graph Neural Networks (GNNs) are promising for saving computations of GNNs through binarized tensors. Prior work, however, mainly focused on algorithm designs or training techniques, leaving it open to how to materialize the performance potential on accelerator hardware fully. This work redesigns the binary GNN inference backend from the efficiency perspective. It fills the gap by proposing a series of abstractions and techniques to map binary GNNs and their computations best to fit the nature of bit manipulations on GPUs. Results on real-world graphs with GCNs, GraphSAGE, and GraphSAINT show that the proposed techniques outperform state-of-the-art binary GNN implementations by 8-22X with the same accuracy maintained. BitGNN code is publicly available.Comment: To appear in the International Conference on Supercomputing (ICS'23

    Proceedings of the 8th Workshop on Detection and Classification of Acoustic Scenes and Events (DCASE 2023)

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    This volume gathers the papers presented at the Detection and Classification of Acoustic Scenes and Events 2023 Workshop (DCASE2023), Tampere, Finland, during 21–22 September 2023

    Transformers for Capturing Multi-level Graph Structure using Hierarchical Distances

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    Graph transformers need strong inductive biases to derive meaningful attention scores. Yet, current proposals rarely address methods capturing longer ranges, hierarchical structures, or community structures, as they appear in various graphs such as molecules, social networks, and citation networks. In this paper, we propose a hierarchy-distance structural encoding (HDSE), which models a hierarchical distance between the nodes in a graph focusing on its multi-level, hierarchical nature. In particular, this yields a framework which can be flexibly integrated with existing graph transformers, allowing for simultaneous application with other positional representations. Through extensive experiments on 12 real-world datasets, we demonstrate that our HDSE method successfully enhances various types of baseline transformers, achieving state-of-the-art empirical performances on 10 benchmark datasets
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