Bayesian inference is a way to get sharper predictions from your data. It's particularly useful when you don't have as much data as you would like and want to juice every last bit of predictive strength from it. Although it is sometimes described with reverence, Bayesian inference isn't magic or mystical. And even though the math under the hood can get dense, the concepts behind it are completely accessible. In brief, Bayesian inference lets you draw stronger conclusions from your data by folding in what you already know about the answer.

In the last few months, I have had several people contact me about their enthusiasm for venturing into the world of data science and using Machine Learning (ML) techniques to probe statistical regularities and build impeccable data-driven products. However, I have observed that some actually lack the necessary mathematical intuition and framework to get useful results. This is the main reason I decided to write this blog post. Recently, there has been an upsurge in the availability of many easy-to-use machine and deep learning packages such as scikit-learn, Weka, Tensorflow, R-caret etc. Machine Learning theory is a field that intersects statistical, probabilistic, computer science and algorithmic aspects arising from learning iteratively from data and finding hidden insights which can be used to build intelligent applications. Despite the immense possibilities of Machine and Deep Learning, a thorough mathematical understanding of many of these techniques is necessary for a good grasp of the inner workings of the algorithms and getting good results.

Tensor decomposition is an important technique for capturing the high-order interactions among multiway data. Multi-linear tensor composition methods, such as the Tucker decomposition and the CANDECOMP/PARAFAC (CP), assume that the complex interactions among objects are multi-linear, and are thus insufficient to represent nonlinear relationships in data. Another assumption of these methods is that a predefined rank should be known. However, the rank of tensors is hard to estimate, especially for cases with missing values. To address these issues, we design a Bayesian generative model for tensor decomposition. Different from the traditional Bayesian methods, the high-order interactions of tensor entries are modeled with variational auto-encoder. The proposed model takes advantages of Neural Networks and nonparametric Bayesian models, by replacing the multi-linear product in traditional Bayesian tensor decomposition with a complex nonlinear function (via Neural Networks) whose parameters can be learned from data. Experimental results on synthetic data and real-world chemometrics tensor data have demonstrated that our new model can achieve significantly higher prediction performance than the state-of-the-art tensor decomposition approaches.

We introduce a semi-parametric Bayesian model for survival analysis. The model is centred on a parametric baseline hazard, and uses a Gaussian process to model variations away from it nonparametrically, as well as dependence on covariates. As opposed to many other methods in survival analysis, our framework does not impose unnecessary constraints in the hazard rate or in the survival function. Furthermore, our model handles left, right and interval censoring mechanisms common in survival analysis. We propose a MCMC algorithm to perform inference and an approximation scheme based on random Fourier features to make computations faster. We report experimental results on synthetic and real data, showing that our model performs better than competing models such as Cox proportional hazards, ANOVA-DDP and random survival forests.

Genetic sequence data are well described by hidden Markov models (HMMs) in which latent states correspond to clusters of similar mutation patterns. Theory from statistical genetics suggests that these HMMs are nonhomogeneous (their transition probabilities vary along the chromosome) and have large support for self transitions. We develop a new nonparametric model of genetic sequence data, based on the hierarchical Dirichlet process, which supports these self transitions and nonhomogeneity. Our model provides a parameterization of the genetic process that is more parsimonious than other more general nonparametric models which have previously been applied to population genetics. We provide truncation-free MCMC inference for our model using a new auxiliary sampling scheme for Bayesian nonparametric HMMs. In a series of experiments on male X chromosome data from the Thousand Genomes Project and also on data simulated from a population bottleneck we show the benefits of our model over the popular finite model fastPHASE, which can itself be seen as a parametric truncation of our model. We find that the number of HMM states found by our model is correlated with the time to the most recent common ancestor in population bottlenecks. This work demonstrates the flexibility of Bayesian nonparametrics applied to large and complex genetic data.

Recent progress in artificial intelligence (AI) has renewed interest in building systems that learn and think like people. Many advances have come from using deep neural networks trained end-to-end in tasks such as object recognition, video games, and board games, achieving performance that equals or even beats humans in some respects. Despite their biological inspiration and performance achievements, these systems differ from human intelligence in crucial ways. We review progress in cognitive science suggesting that truly human-like learning and thinking machines will have to reach beyond current engineering trends in both what they learn, and how they learn it. Specifically, we argue that these machines should (a) build causal models of the world that support explanation and understanding, rather than merely solving pattern recognition problems; (b) ground learning in intuitive theories of physics and psychology, to support and enrich the knowledge that is learned; and (c) harness compositionality and learning-to-learn to rapidly acquire and generalize knowledge to new tasks and situations. We suggest concrete challenges and promising routes towards these goals that can combine the strengths of recent neural network advances with more structured cognitive models.

Reconstruction of the tridimensional geometry of a visual scene using the binocular disparity information is an important issue in computer vision and mobile robotics, which can be formulated as a Bayesian inference problem. However, computation of the full disparity distribution with an advanced Bayesian model is usually an intractable problem, and proves computationally challenging even with a simple model. In this paper, we show how probabilistic hardware using distributed memory and alternate representation of data as stochastic bitstreams can solve that problem with high performance and energy efficiency. We put forward a way to express discrete probability distributions using stochastic data representations and perform Bayesian fusion using those representations, and show how that approach can be applied to diparity computation. We evaluate the system using a simulated stochastic implementation and discuss possible hardware implementations of such architectures and their potential for sensorimotor processing and robotics.

One of the central themes in Sum-Product networks (SPNs) is the interpretation of sum nodes as marginalized latent variables (LVs). This interpretation yields an increased syntactic or semantic structure, allows the application of the EM algorithm and to efficiently perform MPE inference. In literature, the LV interpretation was justified by explicitly introducing the indicator variables corresponding to the LVs' states. However, as pointed out in this paper, this approach is in conflict with the completeness condition in SPNs and does not fully specify the probabilistic model. We propose a remedy for this problem by modifying the original approach for introducing the LVs, which we call SPN augmentation. We discuss conditional independencies in augmented SPNs, formally establish the probabilistic interpretation of the sum-weights and give an interpretation of augmented SPNs as Bayesian networks. Based on these results, we find a sound derivation of the EM algorithm for SPNs. Furthermore, the Viterbi-style algorithm for MPE proposed in literature was never proven to be correct. We show that this is indeed a correct algorithm, when applied to selective SPNs, and in particular when applied to augmented SPNs. Our theoretical results are confirmed in experiments on synthetic data and 103 real-world datasets.

We propose a geometric algorithm for topic learning and inference that is built on the convex geometry of topics arising from the Latent Dirichlet Allocation (LDA) model and its nonparametric extensions. To this end we study the optimization of a geometric loss function, which is a surrogate to the LDA's likelihood. Our method involves a fast optimization based weighted clustering procedure augmented with geometric corrections, which overcomes the computational and statistical inefficiencies encountered by other techniques based on Gibbs sampling and variational inference, while achieving the accuracy comparable to that of a Gibbs sampler. The topic estimates produced by our method are shown to be statistically consistent under some conditions. The algorithm is evaluated with extensive experiments on simulated and real data.

Non-negative Matrix Factorization (NMF) is a popular tool for data exploration. Bayesian NMF promises to also characterize uncertainty in the factorization. Unfortunately, current inference approaches such as MCMC mix slowly and tend to get stuck on single modes. We introduce a novel approach using rapidly-exploring random trees (RRTs) to asymptotically cover regions of high posterior density. These are placed in a principled Bayesian framework via an online extension to nonparametric variational inference. On experiments on real and synthetic data, we obtain greater coverage of the posterior and higher ELBO values than standard NMF inference approaches.