The discovery of drug-target interactions (DTIs) is a very promising area of research with great potential. The accurate identification of reliable interactions among drugs and proteins via computational methods, which typically leverage heterogeneous information retrieved from diverse data sources, can boost the development of effective pharmaceuticals. Although random walk and matrix factorization techniques are widely used in DTI prediction, they have several limitations. Random walk-based embedding generation is usually conducted in an unsupervised manner, while the linear similarity combination in matrix factorization distorts individual insights offered by different views. To tackle these issues, we take a multi-layered network approach to handle diverse drug and target similarities, and propose a novel optimization framework, called Multiple similarity DeepWalk-based Matrix Factorization (MDMF), for DTI prediction. The framework unifies embedding generation and interaction prediction, learning vector representations of drugs and targets that not only retain higher-order proximity across all hyper-layers and layer-specific local invariance, but also approximate the interactions with their inner product. Furthermore, we develop an ensemble method (MDMF2A) that integrates two instantiations of the MDMF model, optimizing the area under the precision-recall curve (AUPR) and the area under the receiver operating characteristic curve (AUC) respectively. The empirical study on real-world DTI datasets shows that our method achieves statistically significant improvement over current state-of-the-art approaches in four different settings. Moreover, the validation of highly ranked non-interacting pairs also demonstrates the potential of MDMF2A to discover novel DTIs.

The pairwise objective paradigms are an important and essential aspect of machine learning. Examples of machine learning approaches that use pairwise objective functions include differential network in face recognition, metric learning, bipartite learning, multiple kernel learning, and maximizing of area under the curve (AUC). Compared to pointwise learning, pairwise learning's sample size grows quadratically with the number of samples and thus its complexity. Researchers mostly address this challenge by utilizing an online learning system. Recent research has, however, offered adaptive sample size training for smooth loss functions as a better strategy in terms of convergence and complexity, but without a comprehensive theoretical study. In a distinct line of research, importance sampling has sparked a considerable amount of interest in finite pointwise-sum minimization. This is because of the stochastic gradient variance, which causes the convergence to be slowed considerably. In this paper, we combine adaptive sample size and importance sampling techniques for pairwise learning, with convergence guarantees for nonsmooth convex pairwise loss functions. In particular, the model is trained stochastically using an expanded training set for a predefined number of iterations derived from the stability bounds. In addition, we demonstrate that sampling opposite instances at each iteration reduces the variance of the gradient, hence accelerating convergence. Experiments on a broad variety of datasets in AUC maximization confirm the theoretical results.

This paper presents an open-source Python toolbox called Ensemble Feature Importance (EFI) to provide machine learning (ML) researchers, domain experts, and decision makers with robust and accurate feature importance quantification and more reliable mechanistic interpretation of feature importance for prediction problems using fuzzy sets. The toolkit was developed to address uncertainties in feature importance quantification and lack of trustworthy feature importance interpretation due to the diverse availability of machine learning algorithms, feature importance calculation methods, and dataset dependencies. EFI merges results from multiple machine learning models with different feature importance calculation approaches using data bootstrapping and decision fusion techniques, such as mean, majority voting and fuzzy logic. The main attributes of the EFI toolbox are: (i) automatic optimisation of ML algorithms, (ii) automatic computation of a set of feature importance coefficients from optimised ML algorithms and feature importance calculation techniques, (iii) automatic aggregation of importance coefficients using multiple decision fusion techniques, and (iv) fuzzy membership functions that show the importance of each feature to the prediction task. The key modules and functions of the toolbox are described, and a simple example of their application is presented using the popular Iris dataset.

This paper narrows the gap between previous literature on quantum linear algebra and practical data analysis on a quantum computer, formalizing quantum procedures that speed-up the solution of eigenproblems for data representations in machine learning. The power and practical use of these subroutines is shown through new quantum algorithms, sublinear in the input matrix's size, for principal component analysis, correspondence analysis, and latent semantic analysis. We provide a theoretical analysis of the run-time and prove tight bounds on the randomized algorithms' error. We run experiments on multiple datasets, simulating PCA's dimensionality reduction for image classification with the novel routines. The results show that the run-time parameters that do not depend on the input's size are reasonable and that the error on the computed model is small, allowing for competitive classification performances.

This work considers the task of representation learning on the attributed relational graph (ARG). Both the nodes and edges in an ARG are associated with attributes/features allowing ARGs to encode rich structural information widely observed in real applications. Existing graph neural networks offer limited ability to capture complex interactions within local structural contexts, which hinders them from taking advantage of the expression power of ARGs. We propose Motif Convolution Module (MCM), a new motif-based graph representation learning technique to better utilize local structural information. The ability to handle continuous edge and node features is one of MCM's advantages over existing motif-based models. MCM builds a motif vocabulary in an unsupervised way and deploys a novel motif convolution operation to extract the local structural context of individual nodes, which is then used to learn higher-level node representations via multilayer perceptron and/or message passing in graph neural networks. When compared with other graph learning approaches to classifying synthetic graphs, our approach is substantially better in capturing structural context. We also demonstrate the performance and explainability advantages of our approach by applying it to several molecular benchmarks.

We explore the merits of training of support vector machines for binary classification by means of solving systems of ordinary differential equations. We thus assume a continuous time perspective on a machine learning problem which may be of interest for implementations on (re)emerging hardware platforms such as analog- or quantum computers.

Stochastic approximation algorithms are iterative procedures which are used to approximate a target value in an environment where the target is unknown and direct observations are corrupted by noise. These algorithms are useful, for instance, for root-finding and function minimization when the target function or model is not directly known. Originally introduced in a 1951 paper by Robbins and Monro, the field of Stochastic approximation has grown enormously and has come to influence application domains from adaptive signal processing to artificial intelligence. As an example, the Stochastic Gradient Descent algorithm which is ubiquitous in various subdomains of Machine Learning is based on stochastic approximation theory. In this paper, we give a formal proof (in the Coq proof assistant) of a general convergence theorem due to Aryeh Dvoretzky [21] (proven in 1956) which implies the convergence of important classical methods such as the Robbins-Monro and the Kiefer-Wolfowitz algorithms. In the process, we build a comprehensive Coq library of measure-theoretic probability theory and stochastic processes.

Parameter tuning for robotic systems is a time-consuming and challenging task that often relies on domain expertise of the human operator. Moreover, existing learning methods are not well suited for parameter tuning for many reasons including: the absence of a clear numerical metric for `good robotic behavior'; limited data due to the reliance on real-world experimental data; and the large search space of parameter combinations. In this work, we present an open-source MATLAB Preference Optimization and Learning Algorithms for Robotics toolbox (POLAR) for systematically exploring high-dimensional parameter spaces using human-in-the-loop preference-based learning. This aim of this toolbox is to systematically and efficiently accomplish one of two objectives: 1) to optimize robotic behaviors for human operator preference; 2) to learn the operator's underlying preference landscape to better understand the relationship between adjustable parameters and operator preference. The POLAR toolbox achieves these objectives using only subjective feedback mechanisms (pairwise preferences, coactive feedback, and ordinal labels) to infer a Bayesian posterior over the underlying reward function dictating the user's preferences. We demonstrate the performance of the toolbox in simulation and present various applications of human-in-the-loop preference-based learning.

The automated machine learning (AutoML) process can require searching through complex configuration spaces of not only machine learning (ML) components and their hyperparameters but also ways of composing them together, i.e. forming ML pipelines. Optimisation efficiency and the model accuracy attainable for a fixed time budget suffer if this pipeline configuration space is excessively large. A key research question is whether it is both possible and practical to preemptively avoid costly evaluations of poorly performing ML pipelines by leveraging their historical performance for various ML tasks, i.e. meta-knowledge. The previous experience comes in the form of classifier/regressor accuracy rankings derived from either (1) a substantial but non-exhaustive number of pipeline evaluations made during historical AutoML runs, i.e. 'opportunistic' meta-knowledge, or (2) comprehensive cross-validated evaluations of classifiers/regressors with default hyperparameters, i.e. 'systematic' meta-knowledge. Numerous experiments with the AutoWeka4MCPS package suggest that (1) opportunistic/systematic meta-knowledge can improve ML outcomes, typically in line with how relevant that meta-knowledge is, and (2) configuration-space culling is optimal when it is neither too conservative nor too radical. However, the utility and impact of meta-knowledge depend critically on numerous facets of its generation and exploitation, warranting extensive analysis; these are often overlooked/underappreciated within AutoML and meta-learning literature. In particular, we observe strong sensitivity to the `challenge' of a dataset, i.e. whether specificity in choosing a predictor leads to significantly better performance. Ultimately, identifying `difficult' datasets, thus defined, is crucial to both generating informative meta-knowledge bases and understanding optimal search-space reduction strategies.

Understanding human behavior is an important task and has applications in many domains such as targeted advertisement, health analytics, security, and entertainment, etc. For this purpose, designing a system for activity recognition (AR) is important. However, since every human can have different behaviors, understanding and analyzing common patterns become a challenging task. Since smartphones are easily available to every human being in the modern world, using them to track the human activities becomes possible. In this paper, we extracted different human activities using accelerometer, magnetometer, and gyroscope sensors of android smartphones by building an android mobile applications. Using different social media applications, such as Facebook, Instagram, Whatsapp, and Twitter, we extracted the raw sensor values along with the attributes of $29$ subjects along with their attributes (class labels) such as age, gender, and left/right/both hands application usage. We extract features from the raw signals and use them to perform classification using different machine learning (ML) algorithms. Using statistical analysis, we show the importance of different features towards the prediction of class labels. In the end, we use the trained ML model on our data to extract unknown features from a well known activity recognition data from UCI repository, which highlights the potential of privacy breach using ML models. This security analysis could help researchers in future to take appropriate steps to preserve the privacy of human subjects.