Probabilistic programming languages (PPLs) are receiving widespread attention for performing Bayesian inference in complex generative models. However, applications to science remain limited because of the impracticability of rewriting complex scientific simulators in a PPL, the computational cost of inference, and the lack of scalable implementations. To address these, we present a novel PPL framework that couples directly to existing scientific simulators through a cross-platform probabilistic execution protocol and provides Markov chain Monte Carlo (MCMC) and deep-learning-based inference compilation (IC) engines for tractable inference. To guide IC inference, we perform distributed training of a dynamic 3DCNN--LSTM architecture with a PyTorch-MPI-based framework on 1,024 32-core CPU nodes of the Cori supercomputer with a global minibatch size of 128k: achieving a performance of 450 Tflop/s through enhancements to PyTorch. We demonstrate a Large Hadron Collider (LHC) use-case with the C++ Sherpa simulator and achieve the largest-scale posterior inference in a Turing-complete PPL.

We attempt to make two arguments in this essay. First, through a case study of a mobile phone based voice-media service we have been running in rural central India for more than six years, we describe several implementation complexities we had to navigate towards realizing our intended vision of bringing social development through technology. Most of these complexities arose in the interface of our technology with society, and we argue that even other technology providers can create similar processes to manage this socio-technological interface and ensure intended outcomes from their technology use. We then build our second argument about how to ensure that the organizations behind both market driven technologies and those technologies that are adopted by the state, pay due attention towards responsibly managing the socio-technological interface of their innovations. We advocate for the technology engineers and researchers who work within these organizations, to take up the responsibility and ensure that their labour leads to making the world a better place especially for the poor and marginalized. We outline possible governance structures that can give more voice to the technology developers to push their organizations towards ensuring that responsible outcomes emerge from their technology. We note that the examples we use to build our arguments are limited to contemporary information and communication technology (ICT) platforms used directly by end-users to share content with one another, and hence our argument may not generalize to other ICTs in a straightforward manner.

Values are things that are important to us. Actions activate values - they either go against our values or they promote our values. Values themselves can either be conforming or conflicting depending on the action that is taken. In this short paper, we argue that values may be classified as one of two types - conflicting and inherently conflicting values. They are distinguished by the fact that the latter in some sense can be thought of as being independent of actions. This allows us to do two things: i) check whether a set of values is consistent and ii) check whether it is in conflict with other sets of values.

Materials discovery is crucial for making scientific advances in many domains. Collections of data from experiments and first-principle computations have spurred interest in applying machine learning methods to create predictive models capable of mapping from composition and crystal structures to materials properties. Generally, these are regression problems with the input being a 1D vector composed of numerical attributes representing the material composition and/or crystal structure. While neural networks consisting of fully connected layers have been applied to such problems, their performance often suffers from the vanishing gradient problem when network depth is increased. In this paper, we study and propose design principles for building deep regression networks composed of fully connected layers with numerical vectors as input. We introduce a novel deep regression network with individual residual learning, IRNet, that places shortcut connections after each layer so that each layer learns the residual mapping between its output and input. We use the problem of learning properties of inorganic materials from numerical attributes derived from material composition and/or crystal structure to compare IRNet's performance against that of other machine learning techniques. Using multiple datasets from the Open Quantum Materials Database (OQMD) and Materials Project for training and evaluation, we show that IRNet provides significantly better prediction performance than the state-of-the-art machine learning approaches currently used by domain scientists. We also show that IRNet's use of individual residual learning leads to better convergence during the training phase than when shortcut connections are between multi-layer stacks while maintaining the same number of parameters.

As the size $n$ of datasets become massive, many commonly-used clustering algorithms (for example, $k$-means or hierarchical agglomerative clustering (HAC) require prohibitive computational cost and memory. In this paper, we propose a solution to these clustering problems by extending threshold clustering (TC) to problems of instance selection. TC is a recently developed clustering algorithm designed to partition data into many small clusters in linearithmic time (on average). Our proposed clustering method is as follows. First, TC is performed and clusters are reduced into single "prototype" points. Then, TC is applied repeatedly on these prototype points until sufficient data reduction has been obtained. Finally, a more sophisticated clustering algorithm is applied to the reduced prototype points, thereby obtaining a clustering on all $n$ data points. This entire procedure for clustering is called iterative hybridized threshold clustering (IHTC). Through simulation results and by applying our methodology on several real datasets, we show that IHTC combined with $k$-means or HAC substantially reduces the run time and memory usage of the original clustering algorithms while still preserving their performance. Additionally, IHTC helps prevent singular data points from being overfit by clustering algorithms.

Recent years have witnessed a fast-growing interest in computing explanations for Machine Learning (ML) models predictions. For non-interpretable ML models, the most commonly used approaches for computing explanations are heuristic in nature. In contrast, recent work proposed rigorous approaches for computing explanations, which hold for a given ML model and prediction over the entire instance space. This paper extends earlier work to the case of boosted trees and assesses the quality of explanations obtained with state-of-the-art heuristic approaches. On most of the datasets considered, and for the vast majority of instances, the explanations obtained with heuristic approaches are shown to be inadequate when the entire instance space is (implicitly) considered.

Preventing organizations from Cyber exploits needs timely intelligence about Cyber vulnerabilities and attacks, referred as threats. Cyber threat intelligence can be extracted from various sources including social media platforms where users publish the threat information in real time. Gathering Cyber threat intelligence from social media sites is a time consuming task for security analysts that can delay timely response to emerging Cyber threats. We propose a framework for automatically gathering Cyber threat intelligence from Twitter by using a novelty detection model. Our model learns the features of Cyber threat intelligence from the threat descriptions published in public repositories such as Common Vulnerabilities and Exposures (CVE) and classifies a new unseen tweet as either normal or anomalous to Cyber threat intelligence. We evaluate our framework using a purpose-built data set of tweets from 50 influential Cyber security related accounts over twelve months (in 2018). Our classifier achieves the F1-score of 0.643 for classifying Cyber threat tweets and outperforms several baselines including binary classification models. Our analysis of the classification results suggests that Cyber threat relevant tweets on Twitter do not often include the CVE identifier of the related threats. Hence, it would be valuable to collect these tweets and associate them with the related CVE identifier for cyber security applications.

Information-theoretic quantities, such as mutual information and conditional entropy, are useful statistics for measuring the dependence between two random variables. However, estimating these quantities in a non-parametric fashion is difficult, especially when the variables are high-dimensional, a mixture of continuous and discrete values, or both. In this paper, we propose a decision forest method, Conditional Forests (CF), to estimate these quantities. By combining quantile regression forests with honest sampling, and introducing a finite sample correction, CF improves finite sample bias in a range of settings. We demonstrate through simulations that CF achieves smaller bias and variance in both low- and high-dimensional settings for estimating posteriors, conditional entropy, and mutual information. We then use CF to estimate the amount of information between neuron class and other ceulluar feautres.

Many Machine Learning algorithms, such as deep neural networks, have long been criticized for being "black-boxes"-a kind of models unable to provide how it arrive at a decision without further efforts to interpret. This problem has raised concerns on model applications' trust, safety, nondiscrimination, and other ethical issues. In this paper, we discuss the machine learning interpretability of a real-world application, eXtreme Multi-label Learning (XML), which involves learning models from annotated data with many pre-defined labels. We propose a two-step XML approach that combines deep non-negative autoencoder with other multi-label classifiers to tackle different data applications with a large number of labels. Our experimental result shows that the proposed approach is able to cope with many-label problems as well as to provide interpretable label hierarchies and dependencies that helps us understand how the model recognizes the existences of objects in an image.

Machine learning algorithms designed to characterize, monitor, and intervene on human health (ML4H) are expected to perform safely and reliably when operating at scale, potentially outside strict human supervision. This requirement warrants a stricter attention to issues of reproducibility than other fields of machine learning. In this work, we conduct a systematic evaluation of over 100 recently published ML4H research papers along several dimensions related to reproducibility. We find that the field of ML4H compares poorly to more established machine learning fields, particularly concerning data and code accessibility. Finally, drawing from success in other fields of science, we propose recommendations to data providers, academic publishers, and the ML4H research community in order to promote reproducible research moving forward.