With the rapid increase of compound databases available in medicinal and material science, there is a growing need for learning representations of molecules in a semi-supervised manner. In this paper, we propose an unsupervised hierarchical feature extraction algorithm for molecules (or more generally, graph-structured objects with fixed number of types of nodes and edges), which is applicable to both unsupervised and semi-supervised tasks. Our method extends recently proposed Paragraph Vector algorithm[13] and incorporates neural message passing [7] to obtain hierarchical representations of subgraphs. We applied our method to an unsupervised task and demonstrated that it outperforms existing proposed methods in several benchmark datasets. We also experimentally showed that semi-supervised tasks enhanced predictive performance compared with supervised ones with labeled molecules only.

Labeling training data is increasingly the largest bottleneck in deploying machine learning systems. We present Snorkel, a first-of-its-kind system that enables users to train state-of-the-art models without hand labeling any training data. Instead, users write labeling functions that express arbitrary heuristics, which can have unknown accuracies and correlations. Snorkel denoises their outputs without access to ground truth by incorporating the first end-to-end implementation of our recently proposed machine learning paradigm, data programming. We present a flexible interface layer for writing labeling functions based on our experience over the past year collaborating with companies, agencies, and research labs. In a user study, subject matter experts build models 2.8x faster and increase predictive performance an average 45.5% versus seven hours of hand labeling. We study the modeling tradeoffs in this new setting and propose an optimizer for automating tradeoff decisions that gives up to 1.8x speedup per pipeline execution. In two collaborations, with the U.S. Department of Veterans Affairs and the U.S. Food and Drug Administration, and on four open-source text and image data sets representative of other deployments, Snorkel provides 132% average improvements to predictive performance over prior heuristic approaches and comes within an average 3.60% of the predictive performance of large hand-curated training sets.

HE number of diseases that can be treated by surgical operation has increased in recent years because of the development of medical technology. However, the complexity of treatment plans means that surgical navigation under treatment is a potentially valuable development. In surgical navigation, computer simulation of treatment plans is constructed before a surgery, and a virtual internal organ deformed following surgical treatment is presented to the surgeon during the surgery. It helps surgeons to operate as planned and provides an alert to prevent accidents, for example, they hurt important blood vessels. In surgical operations, laparoscopic surgery is considered less trauma for patients than laparotomy, and leads to faster recovery [1]. However, laparoscopic surgery is more difficult for doctors than laparotomy surgery, because it involves restricted vision and limited freedom of surgical instruments, making it difficult to move the instruments in the operating field [2].

The variability of the clusters generated by clustering techniques in the domain of latitude and longitude variables of fatal crash data are significantly unpredictable. This unpredictability, caused by the randomness of fatal crash incidents, reduces the accuracy of crash frequency (i.e., counts of fatal crashes per cluster) which is used to measure traffic safety in practice. In this paper, a quantitative measure of traffic safety that is not significantly affected by the aforementioned variability is proposed. It introduces a fatal point -- a segment with the highest frequency of fatality -- concept based on cluster characteristics and detects them by imposing rounding errors to the hundredth decimal place of the longitude. The frequencies of the cluster and the cluster's fatal point are combined to construct a low-sensitive quantitative measure of traffic safety for the cluster. The performance of the proposed measure of traffic safety is then studied by varying the parameter k of k-means clustering with the expectation that other clustering techniques can be adopted in a similar fashion. The 2015 North Carolina fatal crash dataset of Fatality Analysis Reporting System (FARS) is used to evaluate the proposed fatal point concept and perform experimental analysis to determine the effectiveness of the proposed measure. The empirical study shows that the average traffic safety, measured by the proposed quantitative measure over several clusters, is not significantly affected by the variability, compared to that of the standard crash frequency.

Analysis of flow cytometry data is an essential tool for clinical diagnosis of hematological and immunological conditions. Current clinical workflows rely on a manual process called gating to classify cells into their canonical types. This dependence on human annotation limits the rate, reproducibility, and complexity of flow cytometry analysis. In this paper, we propose using Mondrian processes to perform automated gating by incorporating prior information of the kind used by gating technicians. The method segments cells into types via Bayesian nonparametric trees. Examining the posterior over trees allows for interpretable visualizations and uncertainty quantification - two vital qualities for implementation in clinical practice.

We present a formalization of nested Monte Carlo (NMC) estimation, whereby terms in an outer estimator themselves involve calculation of separate, nested, Monte Carlo (MC) estimators. We demonstrate that, under mild conditions, NMC can provide consistent estimates of nested expectations, including cases involving arbitrary levels of nesting; establish corresponding rates of convergence; and provide empirical evidence that these rates are observed in practice. We further establish a number of pitfalls that can arise from naïve nesting of MC estimators, provide guidelines about how these can be avoided, and lay out novel methods for reformulating certain classes of nested expectation problems into single expectations, leading to improved convergence rates. Finally, we use one of these reformulations to derive a new estimator for use in discrete Bayesian experimental design problems which has a better convergence rate than existing methods. Our results have implications for a wide range of fields from probabilistic programming to deep generative models and serve both as an invitation for further inquiry and a caveat against careless use.

The adoption of automated, data-driven decision making in an ever expanding range of applications has raised concerns about its potential unfairness towards certain social groups. In this context, a number of recent studies have focused on defining, detecting, and removing unfairness from data-driven decision systems. However, the existing notions of fairness, based on parity (equality) in treatment or outcomes for different social groups, tend to be quite stringent, limiting the overall decision making accuracy. In this paper, we draw inspiration from the fair-division and envy-freeness literature in economics and game theory and propose preference-based notions of fairness -- given the choice between various sets of decision treatments or outcomes, any group of users would collectively prefer its treatment or outcomes, regardless of the (dis)parity as compared to the other groups. Then, we introduce tractable proxies to design margin-based classifiers that satisfy these preference-based notions of fairness. Finally, we experiment with a variety of synthetic and real-world datasets and show that preference-based fairness allows for greater decision accuracy than parity-based fairness.

Despite their popularity, the practical performance of asynchronous stochastic gradient descent methods (ASGD) for solving large scale machine learning problems are not as good as theoretical results indicate. We adopt and analyze a synchronous K-step averaging stochastic gradient descent algorithm which we call K-AVG. We establish the convergence results of K-AVG for nonconvex objectives and explain why the K-step delay is necessary and leads to better performance than traditional parallel stochastic gradient descent which is a special case of K-AVG with $K=1$. We also show that K-AVG scales better than ASGD. Another advantage of K-AVG over ASGD is that it allows larger stepsizes. On a cluster of $128$ GPUs, K-AVG is faster than ASGD implementations and achieves better accuracies and faster convergence for \cifar dataset.

Adaptive gradient methods have become recently very popular, in particular as they have been shown to be useful in the training of deep neural networks. In this paper we have analyzed RMSProp, originally proposed for the training of deep neural networks, in the context of online convex optimization and show $\sqrt{T}$-type regret bounds. Moreover, we propose two variants SC-Adagrad and SC-RMSProp for which we show logarithmic regret bounds for strongly convex functions. Finally, we demonstrate in the experiments that these new variants outperform other adaptive gradient techniques or stochastic gradient descent in the optimization of strongly convex functions as well as in training of deep neural networks.

Keras models follow Scikit-learn's interface of fit/predict with some notable extensions.