Jun 12, 2019

Exploiting Worker Correlation for Label Aggregation in Crowdsourcing Crowdsourcing has emerged as a core component of data science pipelines. From collected noisy worker labels, aggregation models that incorporate worker reliability parameters aim to infer a latent true annotation. In this paper, we argue that existing crowdsourcing approaches do not sufficiently model worker correlations observed in practical settings; we propose in response an enhanced Bayesian classifier combination (EBCC) model, with inference based on a mean-field variational approach. An introduced mixture of intra-class reliabilities---connected to tensor decomposition and item clustering---induces inter-worker correlation. EBCC does not suffer the limitations of existing correlation models: intractable marginalisation of missing labels and poor scaling to large worker cohorts. Extensive empirical comparison on 17 real-world datasets sees EBCC achieving the highest mean accuracy across 10 benchmark crowdsourcing methods. Efficient Amortised Bayesian Inference for Hierarchical and Nonlinear Dynamical Systems We introduce a flexible, scalable Bayesian inference framework for nonlinear dynamical systems characterised by distinct and hierarchical variability at the individual, group, and population levels. Our model class is a generalisation of nonlinear mixed-effects (NLME) dynamical systems, the statistical workhorse for many experimental sciences. We cast parameter inference as stochastic optimisation of an end-to-end differentiable, block-conditional variational autoencoder. We specify the dynamics of the data-generating process as an ordinary differential equation (ODE) such that both the ODE and its solver are fully differentiable. This model class is highly flexible: the ODE right-hand sides can be a mixture of user-prescribed or white-box" sub-components and neural network orblack-box" sub-components. Using stochastic optimisation, our amortised inference algorithm could seamlessly scale up to massive data collection pipelines (common in labs with robotic automation). Finally, our framework supports interpretability with respect to the underlying dynamics, as well as predictive generalization to unseen combinations of group components (also called zero-shot" learning). We empirically validate our method by predicting the dynamic behaviour of bacteria that were genetically engineered to function as biosensors. A Multitask Multiple Kernel Learning Algorithm for Survival Analysis with Application to Cancer Biology Predictive performance of machine learning algorithms on related problems can be improved using multitask learning approaches. Rather than performing survival analysis on each data set to predict survival times of cancer patients, we developed a novel multitask approach based on multiple kernel learning (MKL). Our multitask MKL algorithm both works on multiple cancer data sets and integrates cancer-related pathways/gene sets into survival analysis. We tested our algorithm, which is named as Path2MSurv, on the Cancer Genome Atlas data sets analyzing gene expression profiles of 7,655 patients from 20 cancer types together with cancer-specific pathway/gene set collections. Path2MSurv obtained better or comparable predictive performance when compared against random survival forest, survival support vector machine, and single-task variant of our algorithm. Path2MSurv has the ability to identify key pathways/gene sets in predicting survival times of patients from different cancer types. Fast and Flexible Inference of Joint Distributions from their Marginals Across the social sciences and elsewhere, practitioners frequently have to reason about relationships between random variables, despite lacking joint observations of the variables. This is sometimes called an ecological'' inference; given samples from the marginal distributions of the variables, one attempts to infer their joint distribution. The problem is inherently ill-posed, yet only a few models have been proposed for bringing prior information into the problem, often relying on restrictive or unrealistic assumptions and lacking a unified approach. In this paper, we treat the inference problem generally and propose a unified class of models that encompasses some of those previously proposed while including many new ones. Previous work has relied on either relaxation or approximate inference via MCMC, with the latter known to mix prohibitively slowly for this type of problem. Here we instead give a single exact inference algorithm that works for the entire model class via an efficient fixed point iteration called Dykstra's method. We investigate empirically both the computational cost of our algorithm and the accuracy of the new models on real datasets, showing favorable performance in both cases and illustrating the impact of increased flexibility in modeling enabled by this work. Cognitive model priors for predicting human decisions Human decision-making underlies all economic behavior. For the past four decades, human decision-making under uncertainty has continued to be explained by theoretical models based on prospect theory, a framework that was awarded the Nobel Prize in Economic Sciences. However, theoretical models of this kind have developed slowly, and robust, high-precision predictive models of human decisions remain a challenge. While machine learning is a natural candidate for solving these problems, it is currently unclear to what extent it can improve predictions obtained by current theories. We argue that this is mainly due to data scarcity, since noisy human behavior requires massive sample sizes to be accurately captured by off-the-shelf machine learning methods. To solve this problem, what is needed are machine learning models with appropriate inductive biases for capturing human behavior, and larger datasets. We offer two contributions towards this end: first, we construct “cognitive model priors” by pretraining neural networks with synthetic data generated by cognitive models (i.e., theoretical models developed by cognitive psychologists). We find that fine-tuning these networks on small datasets of real human decisions results in unprecedented state-of-the-art improvements on two benchmark datasets. Second, we present the first large-scale dataset for human decision-making, containing over 240,000 human judgments across over 13,000 decision problems. This dataset reveals the circumstances where cognitive model priors are useful, and provides a new standard for benchmarking prediction of human decisions under uncertainty. Conditioning by adaptive sampling for robust design We consider design problems wherein the goal is to maximize or specify the value of one or more properties of interest. For example, in protein design, one may wish to find the protein sequence which maximizes its fluorescence. We assume access to one or more black box stochastic "oracle" predictive functions, each of which maps from an input (e.g., protein sequences or images) design space to a distribution over a property of interest (e.g., protein fluorescence or image content). Given such stochastic oracles, our problem is to find an input that best achieves our goal. At first glance, this problem can be framed as one of optimizing the oracle with respect to the input. However, in most real world settings, the oracle will not exactly capture the ground truth, and critically, may catastrophically fail to do so in extrapolation space. Thus, we frame the goal as one modelling the density of some original set of training data (e.g., a set of real protein sequences), and then conditioning this distribution on the desired properties, which yields an annealed adaptive sampling method which is also well-suited to rare conditioning events. We demonstrate experimentally that our approach outperforms other recently presented methods for tackling similar problems. Direct Uncertainty Prediction for Medical Second Opinions The issue of disagreements amongst human experts is a ubiquitous one in both machine learning and medicine. In medicine, this often corresponds to doctor disagreements on a patient diagnosis. In this work, we show that machine learning models can be successfully trained to give uncertainty scores to data instances that result in high expert disagreements. In particular, they can identify patient cases that would benefit most from a medical second opinion. Our central methodological finding is that Direct Uncertainty Prediction (DUP), training a model to predict an uncertainty score directly from the raw patient features, works better than Uncertainty Via Classification, the two step process of training a classifier and postprocessing the output distribution to give an uncertainty score. We show this both with a theoretical result, and on extensive evaluations on a large scale medical imaging application. Dynamic Measurement Scheduling for Event Forecasting using Deep RL Current clinical practice for monitoring patients' health follows either regular or heuristic-based lab test (e.g. blood test) scheduling. Such practice not only gives rise to redundant measurements accruing cost, but may even lead to unnecessary patient discomfort. From the computational perspective, heuristic-based test scheduling might lead to reduced accuracy of clinical forecasting models. A data-driven measurement scheduling is likely to lead to both more accurate predictions and less measurement costs. We address the scheduling problem using deep reinforcement learning (RL) and propose a general and scalable framework to achieve high predictive gain and low measurement cost, by scheduling fewer, but strategically timed tests. Using simulations we show that our policy outperforms heuristic-based measurement scheduling having higher predictive gain and lower cost. We then learn a scheduling policy for mortality forecasting in the real-world clinical dataset (MIMIC3). Our policy decreases the total number of measurements by 31% without reducing the predictive performance, or improves 3 times more predictive gain with the same number of measurements. Parameter efficient training of deep convolutional neural networks by dynamic sparse reparameterization Deep neural networks are typically highly over-parameterized with pruning techniques able to remove a significant fraction of network parameters with little loss in accuracy. Recently, techniques based on dynamic re-allocation of non-zero parameters have emerged for training sparse networks directly without having to train a large dense model beforehand. We present a parameter re-allocation scheme that addresses the limitations of previous methods such as their high computational cost and the fixed number of parameters they allocate to each layer. We investigate the performance of these dynamic re-allocation methods in deep convolutional networks and show that our method outperforms previous static and dynamic parameterization methods, yielding the best accuracy for a given number of training parameters, and performing on par with networks obtained by iteratively pruning a trained dense model. We further investigated the mechanisms underlying the superior performance of the resulting sparse networks. We found that neither the structure, nor the initialization of the sparse networks discovered by our parameter reallocation scheme are sufficient to explain their superior generalization performance. Rather, it is the continuous exploration of different sparse network structures during training that is critical to effective learning. We show that it is more fruitful to explore these structural degrees of freedom than to add extra parameters to the network. Code used to run all experiments is available under the anonymous repository: https://gitlab.com/anonymous.icml.2019/dynamic-parameterization-icml19. DeepNose: Using artificial neural networks to represent the space of odorants The olfactory system employs an ensemble of odorant receptors (ORs) to sense odorants and to derive olfactory percepts. We trained artificial neural networks to represent the chemical space of odorants and used that representation to predict human olfactory percepts. We hypothesized that ORs may be considered 3D convolutional filters that extract molecular features and can be trained using machine learning methods. First, we trained a convolutional autoencoder, called DeepNose, to deduce a low-dimensional representation of odorant molecules which were represented by their 3D spatial structure. Next, we tested the ability of DeepNose features in predicting physical properties and odorant percepts based on 3D molecular structure alone. We found that despite the lack of human expertise, DeepNose features led to predictions of both physical properties and perceptions of comparable accuracy to molecular descriptors often used in computational chemistry, such as Dragon descriptors. We propose that DeepNose network can extract de novo chemical features predictive of various bioactivities and can help understand the factors influencing the composition of ORs ensemble.

The International Conference on Machine Learning (ICML) is the premier gathering of professionals dedicated to the advancement of the branch of artificial intelligence known as machine learning. ICML is globally renowned for presenting and publishing cutting-edge research on all aspects of machine learning used in closely related areas like artificial intelligence, statistics and data science, as well as important application areas such as machine vision, computational biology, speech recognition, and robotics. ICML is one of the fastest growing artificial intelligence conferences in the world. Participants at ICML span a wide range of backgrounds, from academic and industrial researchers, to entrepreneurs and engineers, to graduate students and postdocs.

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