Collaborating Authors


Learning from Aggregate Observations Machine Learning

We study the problem of learning from aggregate observations where supervision signals are given to sets of instances instead of individual instances, while the goal is still to predict labels of unseen individuals. A well-known example is multiple instance learning (MIL). In this paper, we extend MIL beyond binary classification to other problems such as multiclass classification and regression. We present a probabilistic framework that is applicable to a variety of aggregate observations, e.g., pairwise similarity for classification and mean/difference/rank observation for regression. We propose a simple yet effective method based on the maximum likelihood principle, which can be simply implemented for various differentiable models such as deep neural networks and gradient boosting machines. Experiments on three novel problem settings -- classification via triplet comparison and regression via mean/rank observation indicate the effectiveness of the proposed method.

Scaling Bayesian inference of mixed multinomial logit models to very large datasets Machine Learning

Variational inference methods have been shown to lead to significant improvements in the computational efficiency of approximate Bayesian inference in mixed multinomial logit models when compared to standard Markov-chain Monte Carlo (MCMC) methods without compromising accuracy. However, despite their demonstrated efficiency gains, existing methods still suffer from important limitations that prevent them to scale to very large datasets, while providing the flexibility to allow for rich prior distributions and to capture complex posterior distributions. In this paper, we propose an Amortized Variational Inference approach that leverages stochastic backpropagation, automatic differentiation and GPU-accelerated computation, for effectively scaling Bayesian inference in Mixed Multinomial Logit models to very large datasets. Moreover, we show how normalizing flows can be used to increase the flexibility of the variational posterior approximations. Through an extensive simulation study, we empirically show that the proposed approach is able to achieve computational speedups of multiple orders of magnitude over traditional MSLE and MCMC approaches for large datasets without compromising estimation accuracy.

Supervised Autoencoders Learn Robust Joint Factor Models of Neural Activity Machine Learning

Factor models are routinely used for dimensionality reduction in modeling of correlated, high-dimensional data. We are particularly motivated by neuroscience applications collecting high-dimensional `predictors' corresponding to brain activity in different regions along with behavioral outcomes. Joint factor models for the predictors and outcomes are natural, but maximum likelihood estimates of these models can struggle in practice when there is model misspecification. We propose an alternative inference strategy based on supervised autoencoders; rather than placing a probability distribution on the latent factors, we define them as an unknown function of the high-dimensional predictors. This mapping function, along with the loadings, can be optimized to explain variance in brain activity while simultaneously being predictive of behavior. In practice, the mapping function can range in complexity from linear to more complex forms, such as splines or neural networks, with the usual tradeoff between bias and variance. This approach yields distinct solutions from a maximum likelihood inference strategy, as we demonstrate by deriving analytic solutions for a linear Gaussian factor model. Using synthetic data, we show that this function-based approach is robust against multiple types of misspecification. We then apply this technique to a neuroscience application resulting in substantial gains in predicting behavioral tasks from electrophysiological measurements in multiple factor models.

B-SCST: Bayesian Self-Critical Sequence Training for Image Captioning Machine Learning

Bayesian deep neural networks (DNN) provide a mathematically grounded framework to quantify uncertainty in their predictions. We propose a Bayesian variant of policy-gradient based reinforcement learning training technique for image captioning models to directly optimize non-differentiable image captioning quality metrics such as CIDEr-D. We extend the well-known Self-Critical Sequence Training (SCST) approach for image captioning models by incorporating Bayesian inference, and refer to it as B-SCST. The "baseline" reward for the policy-gradients in B-SCST is generated by averaging predictive quality metrics (CIDEr-D) of the captions drawn from the distribution obtained using a Bayesian DNN model. This predictive distribution is inferred using Monte Carlo (MC) dropout, which is one of the standard ways to approximate variational inference. We observe that B-SCST improves all the standard captioning quality scores on both Flickr30k and MS COCO datasets, compared to the SCST approach. We also provide a detailed study of uncertainty quantification for the predicted captions, and demonstrate that it correlates well with the CIDEr-D scores. To our knowledge, this is the first such analysis, and it can pave way to more practical image captioning solutions with interpretable models.

TRAMP: Compositional Inference with TRee Approximate Message Passing Machine Learning

We introduce tramp, standing for TRee Approximate Message Passing, a python package for compositional inference in high-dimensional tree-structured models. The package provides an unifying framework to study several approximate message passing algorithms previously derived for a variety of machine learning tasks such as generalized linear models, inference in multi-layer networks, matrix factorization, and reconstruction using non-separable penalties. For some models, the asymptotic performance of the algorithm can be theoretically predicted by the state evolution, and the measurements entropy estimated by the free entropy formalism. The implementation is modular by design: each module, which implements a factor, can be composed at will with other modules to solve complex inference tasks. The user only needs to declare the factor graph of the model: the inference algorithm, state evolution and entropy estimation are fully automated.

Stacked Generalizations in Imbalanced Fraud Data Sets using Resampling Methods Machine Learning

This study uses stacked generalization, which is a two-step process of combining machine learning methods, called meta or super learners, for improving the performance of algorithms in step one (by minimizing the error rate of each individual algorithm to reduce its bias in the learning set) and then in step two inputting the results into the meta learner with its stacked blended output (demonstrating improved performance with the weakest algorithms learning better). The method is essentially an enhanced cross-validation strategy. Although the process uses great computational resources, the resulting performance metrics on resampled fraud data show that increased system cost can be justified. A fundamental key to fraud data is that it is inherently not systematic and, as of yet, the optimal resampling methodology has not been identified. Building a test harness that accounts for all permutations of algorithm sample set pairs demonstrates that the complex, intrinsic data structures are all thoroughly tested. Using a comparative analysis on fraud data that applies stacked generalizations provides useful insight needed to find the optimal mathematical formula to be used for imbalanced fraud data sets.

Sum-product networks: A survey Artificial Intelligence

A sum-product network (SPN) is a probabilistic model, based on a rooted acyclic directed graph, in which terminal nodes represent univariate probability distributions and non-terminal nodes represent convex combinations (weighted sums) and products of probability functions. They are closely related to probabilistic graphical models, in particular to Bayesian networks with multiple context-specific independencies. Their main advantage is the possibility of building tractable models from data, i.e., models that can perform several inference tasks in time proportional to the number of links in the graph. They are somewhat similar to neural networks and can address the same kinds of problems, such as image processing and natural language understanding. This paper offers a survey of SPNs, including their definition, the main algorithms for inference and learning from data, the main applications, a brief review of software libraries, and a comparison with related models

Flows for simultaneous manifold learning and density estimation Machine Learning

We introduce manifold-modeling flows (MFMFs), a new class of generative models that simultaneously learn the data manifold as well as a tractable probability density on that manifold. Combining aspects of normalizing flows, GANs, autoencoders, and energy-based models, they have the potential to represent data sets with a manifold structure more faithfully and provide handles on dimensionality reduction, denoising, and out-of-distribution detection. We argue why such models should not be trained by maximum likelihood alone and present a new training algorithm that separates manifold and density updates. With two pedagogical examples we demonstrate how manifold-modeling flows let us learn the data manifold and allow for better inference than standard flows in the ambient data space.

BayesFlow: Learning complex stochastic models with invertible neural networks Machine Learning

Estimating the parameters of mathematical models is a common problem in almost all branches of science. However, this problem can prove notably difficult when processes and model descriptions become increasingly complex and an explicit likelihood function is not available. With this work, we propose a novel method for globally amortized Bayesian inference based on invertible neural networks which we call BayesFlow. The method uses simulation to learn a global estimator for the probabilistic mapping from observed data to underlying model parameters. A neural network pre-trained in this way can then, without additional training or optimization, infer full posteriors on arbitrary many real data sets involving the same model family. In addition, our method incorporates a summary network trained to embed the observed data into maximally informative summary statistics. Learning summary statistics from data makes the method applicable to modeling scenarios where standard inference techniques with hand-crafted summary statistics fail. We demonstrate the utility of BayesFlow on challenging intractable models from population dynamics, epidemiology, cognitive science and ecology. We argue that BayesFlow provides a general framework for building reusable Bayesian parameter estimation machines for any process model from which data can be simulated.

Uncertainty Estimation in Cancer Survival Prediction Machine Learning

Survival models are used in various fields, such as the development of cancer treatment protocols. Although many statistical and machine learning models have been proposed to achieve accurate survival predictions, little attention has been paid to obtain well-calibrated uncertainty estimates associated with each prediction. The currently popular models are opaque and untrustworthy in that they often express high confidence even on those test cases that are not similar to the training samples, and even when their predictions are wrong. We propose a Bayesian framework for survival models that not only gives more accurate survival predictions but also quantifies the survival uncertainty better. Our approach is a novel combination of variational inference for uncertainty estimation, neural multi-task logistic regression for estimating nonlinear and time-varying risk models, and an additional sparsity-inducing prior to work with high dimensional data.