Background: Drug-drug interactions (DDIs) refer to processes triggered by the administration of two or more drugs leading to side effects beyond those observed when drugs are administered by themselves. Due to the massive number of possible drug pairs, it is nearly impossible to experimentally test all combinations and discover previously unobserved side effects. Therefore, machine learning based methods are being used to address this issue. Methods: We propose a Siamese self-attention multi-modal neural network for DDI prediction that integrates multiple drug similarity measures that have been derived from a comparison of drug characteristics including drug targets, pathways and gene expression profiles. Results: Our proposed DDI prediction model provides multiple advantages: 1) It is trained end-to-end, overcoming limitations of models composed of multiple separate steps, 2) it offers model explainability via an Attention mechanism for identifying salient input features and 3) it achieves similar or better prediction performance (AUPR scores ranging from 0.77 to 0.92) compared to state-of-the-art DDI models when tested on various benchmark datasets. Novel DDI predictions are further validated using independent data resources. Conclusions: We find that a Siamese multi-modal neural network is able to accurately predict DDIs and that an Attention mechanism, typically used in the Natural Language Processing domain, can be beneficially applied to aid in DDI model explainability.

As an important problem in modern data analytics, classification has witnessed varieties of applications from different domains. Different from conventional classification approaches, fair classification concerns the issues of unintentional biases against the sensitive features (e.g., gender, race). Due to high nonconvexity of fairness measures, existing methods are often unable to model exact fairness, which can cause inferior fair classification outcomes. This paper fills the gap by developing a novel unified framework to jointly optimize accuracy and fairness. The proposed framework is versatile and can incorporate different fairness measures studied in literature precisely as well as can be applicable to many classifiers including deep classification models. Specifically, in this paper, we first prove Fisher consistency of the proposed framework. We then show that many classification models within this framework can be recast as mixed-integer convex programs, which can be solved effectively by off-the-shelf solvers when the instance sizes are moderate and can be used as benchmarks to compare the efficiency of approximation algorithms. We prove that in the proposed framework, when the classification outcomes are known, the resulting problem, termed "unbiased subdata selection," is strongly polynomial-solvable and can be used to enhance the classification fairness by selecting more representative data points. This motivates us to develop an iterative refining strategy (IRS) to solve the large-scale instances, where we improve the classification accuracy and conduct the unbiased subdata selection in an alternating fashion. We study the convergence property of IRS and derive its approximation bound. More broadly, this framework can be leveraged to improve classification models with unbalanced data by taking F1 score into consideration.

Over the last decade, the long-running endeavour to automate high-level processes in machine learning (ML) has risen to mainstream prominence, stimulated by advances in optimisation techniques and their impact on selecting ML models/algorithms. Central to this drive is the appeal of engineering a computational system that both discovers and deploys high-performance solutions to arbitrary ML problems with minimal human interaction. Beyond this, an even loftier goal is the pursuit of autonomy, which describes the capability of the system to independently adjust an ML solution over a lifetime of changing contexts. However, these ambitions are unlikely to be achieved in a robust manner without the broader synthesis of various mechanisms and theoretical frameworks, which, at the present time, remain scattered across numerous research threads. Accordingly, this review seeks to motivate a more expansive perspective on what constitutes an automated/autonomous ML system, alongside consideration of how best to consolidate those elements. In doing so, we survey developments in the following research areas: hyperparameter optimisation, multi-component models, neural architecture search, automated feature engineering, meta-learning, multi-level ensembling, dynamic adaptation, multi-objective evaluation, resource constraints, flexible user involvement, and the principles of generalisation. We also develop a conceptual framework throughout the review, augmented by each topic, to illustrate one possible way of fusing high-level mechanisms into an autonomous ML system. Ultimately, we conclude that the notion of architectural integration deserves more discussion, without which the field of automated ML risks stifling both its technical advantages and general uptake.

Submitted to The Astrophysical Journal Letters ABSTRACT Sky surveys are the largest data generators in astronomy, making automated tools for extracting meaningful scientific information an absolute necessity. We show that, without the need for labels, self-supervised learning recovers representations of sky survey images that are semantically useful for a variety of scientific tasks. These representations can be directly used as features, or fine-tuned, to outperform supervised methods trained only on labeled data. We apply a contrastive learning framework on multi-band galaxy photometry from the Sloan Digital Sky Survey (SDSS), to learn image representations. We then use them for galaxy morphology classification, and fine-tune them for photometric redshift estimation, using labels from the Galaxy Zoo 2 dataset and SDSS spectroscopy. In both downstream tasks, using the same learned representations, we outperform the supervised stateof-the-art results, and we show that our approach can achieve the accuracy of supervised models while using 2-4 times fewer labels for training. INTRODUCTION the quantity and quality of (manually assigned) image labels. Observing and imaging objects in the sky has been Serendipitous discovery of an ionization echo from a the main driver of the scientific discovery process in astronomy, recently faded quasar (Lintott et al. 2009), and the cumbersome because doing controlled experiments is not a search for similar systems that followed (Keel viable option. It in the 1990s, spearheaded by SDSS (Gunn et al. 1998, demonstrates the need for methods which allow for the 2006), has rendered obsolete the approach of manual discovery of truly unusual and previously unseen objects, inspection of images by an expert.

The prevalence of state-sponsored propaganda on the Internet has become a cause for concern in the recent years. While much effort has been made to identify state-sponsored Internet propaganda, the problem remains far from being solved because the ambiguous definition of propaganda leads to unreliable data labelling, and the huge amount of potential predictive features causes the models to be inexplicable. This paper is the first attempt to build a balanced dataset for this task. The dataset is comprised of propaganda by three different organizations across two time periods. A multi-model framework for detecting propaganda messages solely based on the visual and textual content is proposed which achieves a promising performance on detecting propaganda by the three organizations both for the same time period (training and testing on data from the same time period) (F1=0.869) and for different time periods (training on past, testing on future) (F1=0.697). To reduce the influence of false positive predictions, we change the threshold to test the relationship between the false positive and true positive rates and provide explanations for the predictions made by our models with visualization tools to enhance the interpretability of our framework. Our new dataset and general framework provide a strong benchmark for the task of identifying state-sponsored Internet propaganda and point out a potential path for future work on this task.

Partially Observable Monte-Carlo Planning (POMCP) is a powerful online algorithm able to generate approximate policies for large Partially Observable Markov Decision Processes. The online nature of this method supports scalability by avoiding complete policy representation. The lack of an explicit representation however hinders interpretability. In this work, we propose a methodology based on Satisfiability Modulo Theory (SMT) for analyzing POMCP policies by inspecting their traces, namely sequences of belief-action-observation triplets generated by the algorithm. The proposed method explores local properties of policy behavior to identify unexpected decisions. We propose an iterative process of trace analysis consisting of three main steps, i) the definition of a question by means of a parametric logical formula describing (probabilistic) relationships between beliefs and actions, ii) the generation of an answer by computing the parameters of the logical formula that maximize the number of satisfied clauses (solving a MAX-SMT problem), iii) the analysis of the generated logical formula and the related decision boundaries for identifying unexpected decisions made by POMCP with respect to the original question. We evaluate our approach on Tiger, a standard benchmark for POMDPs, and a real-world problem related to mobile robot navigation. Results show that the approach can exploit human knowledge on the domain, outperforming state-of-the-art anomaly detection methods in identifying unexpected decisions. An improvement of the Area Under Curve up to 47\% has been achieved in our tests.

Chromosome karyotype analysis is of great clinical importance in the diagnosis and treatment of diseases, especially for genetic diseases. Since manual analysis is highly time and effort consuming, computer-assisted automatic chromosome karyotype analysis based on images is routinely used to improve the efficiency and accuracy of the analysis. Due to the strip shape of the chromosomes, they easily get overlapped with each other when imaged, significantly affecting the accuracy of the analysis afterward. Conventional overlapping chromosome segmentation methods are usually based on manually tagged features, hence, the performance of which is easily affected by the quality, such as resolution and brightness, of the images. To address the problem, in this paper, we present an adversarial multiscale feature learning framework to improve the accuracy and adaptability of overlapping chromosome segmentation. Specifically, we first adopt the nested U-shape network with dense skip connections as the generator to explore the optimal representation of the chromosome images by exploiting multiscale features. Then we use the conditional generative adversarial network (cGAN) to generate images similar to the original ones, the training stability of which is enhanced by applying the least-square GAN objective. Finally, we employ Lovasz-Softmax to help the model converge in a continuous optimization setting. Comparing with the established algorithms, the performance of our framework is proven superior by using public datasets in eight evaluation criteria, showing its great potential in overlapping chromosome segmentation

Disadvantaged groups around the world have suffered and endured higher mortality during the current COVID-19 pandemic. This contrast disparity suggests that socioeconomic and health-related factors may drive inequality in disease outcome. To identify these factors correlated with COVID-19 outcome, country aggregate data provided by the Lancet COVID-19 Commission subjected to correlation analysis. Socioeconomic and health-related variables were used to predict mortality in the top 5 most affected countries using ridge regression and extreme gradient boosting (XGBoost) models. Our data reveal that predictors related to demographics and social disadvantage correlate with COVID-19 mortality per million and that XGBoost performed better than ridge regression. Taken together, our findings suggest that the health consequence of the current pandemic is not just confined to indiscriminate impact of a viral infection but that these preventable effects are amplified based on pre-existing health and socioeconomic inequalities.

Training datasets for machine learning often have some form of missingness. For example, to learn a model for deciding whom to give a loan, the available training data includes individuals who were given a loan in the past, but not those who were not. This missingness, if ignored, nullifies any fairness guarantee of the training procedure when the model is deployed. Using causal graphs, we characterize the missingness mechanisms in different real-world scenarios. We show conditions under which various distributions, used in popular fairness algorithms, can or can not be recovered from the training data. Our theoretical results imply that many of these algorithms can not guarantee fairness in practice. Modeling missingness also helps to identify correct design principles for fair algorithms. For example, in multi-stage settings where decisions are made in multiple screening rounds, we use our framework to derive the minimal distributions required to design a fair algorithm. Our proposed algorithm decentralizes the decision-making process and still achieves similar performance to the optimal algorithm that requires centralization and non-recoverable distributions.

Popularity of social networks has rapidly increased over the past few years, and daily lives interrupt without their proper functioning. Social networking platform provide multiple interaction types between individuals, such as creating and joining groups, sending and receiving messages, sharing interests and creating friendship relationships. This paper addresses an important problem in social networks analysis and mining that is how to predict link initiation feedback in two-way networks. Relationships between two individuals in a two-way network include a link invitation from one of the individuals, which will be an established link if it is accepted by the invitee. We consider a sport gaming social networking platform and construct a multilayer social network between a number of users. The network formed by the link initiation process is on one of the layers, while the other two layers include a messaging relationships and interactions between the users. We propose a methodology to solve the link initiation feedback prediction problem in this multilayer fashion. The proposed method is based on features extracted from meta-paths, i.e. paths defined between different individuals from multiples layers in multilayer networks. We proposed a cluster-based approach to handle the sparsity issue in the dataset. Experimental results show that the proposed method can provide accurate prediction that outperforms state-of-the-art methods.