We consider the problem of maximum likelihood classification of a high dimensional data point y to billions of classes $x_1,...,x_N$, where the conditional probability p(y|x) is known. In the most general case, the complexity of the brute-force method for this classification grows linearly, O(N), with the number of classes N. Efficient multiclass classification methods have been introduced to solve this problem with logarithmic complexity. However, these methods suffer from the curse of dimensionality, i.e., in large dimensions their complexity approaches $O(N)$ per query data point. In the special case where the conditional probability distribution $p(y|x)$ is a Gaussian centered at x, i.e., $p(y|x) \propto N (x,\sigma)$, the maximum likelihood classification reduces to the nearest neighbor search with the Euclidean norm. Sublinear methods based on locality sensitive hashing (LSH) have been introduced to solve an approximate version of the nearest neighbor search for high dimensional data. Inspired by these advances, here we introduce distribution sensitive hashing (DSH) to solve an approximate version of the maximum likelihood classification problem through joint dimensionality reduction. In the case of discrete probability distributions, we design TreeDSH, a universal family of distribution sensitive hashes based on the decision trees, and show that their complexity grow sub-linearly. Theory and simulation presented in this paper demonstrate that TreeDSH is more efficient than LSH-hamming and Min-Hashing schemes. Finally, we apply TreeDSH to the problem of peptide identification from mass spectrometry data.

We study the extent to which we can infer users' geographical locations from social media. Location inference from social media can benefit many applications, such as disaster management, targeted advertising, and news content tailoring. The challenges, however, lie in the limited amount of labeled data and the large scale of social networks. In this paper, we formalize the problem of inferring location from social media into a semi-supervised factor graph model (SSFGM). The model provides a probabilistic framework in which various sources of information (e.g., content and social network) can be combined together. We design a two-layer neural network to learn feature representations, and incorporate the learned latent features into SSFGM. To deal with the large-scale problem, we propose a Two-Chain Sampling (TCS) algorithm to learn SSFGM. The algorithm achieves a good trade-off between accuracy and efficiency. Experiments on Twitter and Weibo show that the proposed TCS algorithm for SSFGM can substantially improve the inference accuracy over several state-of-the-art methods. More importantly, TCS achieves over 100x speedup comparing with traditional propagation-based methods (e.g., loopy belief propagation).

Separable Non-negative Matrix Factorization (SNMF) is an important method for topic modeling, where "separable" assumes every topic contains at least one anchor word, defined as a word that has non-zero probability only on that topic. SNMF focuses on the word co-occurrence patterns to reveal topics by two steps: anchor word selection and topic recovery. The quality of the anchor words strongly influences the quality of the extracted topics. Existing anchor word selection algorithm is to greedily find an approximate convex hull in a high-dimensional word co-occurrence space. In this work, we propose a new method for the anchor word selection by associating the word co-occurrence probability with the words similarity and assuming that the most different words on semantic are potential candidates for the anchor words. Therefore, if the similarity of a word-pair is very low, then the two words are very likely to be the anchor words. According to the statistical information of text corpora, we can get the similarity of all word-pairs. We build the word similarity graph where the nodes correspond to words and weights on edges stand for the word-pair similarity. Following this way, we design a greedy method to find a minimum edge-weight anchor clique of a given size in the graph for the anchor word selection. Extensive experiments on real-world corpus demonstrate the effectiveness of the proposed anchor word selection method that outperforms the common convex hull-based methods on the revealed topic quality. Meanwhile, our method is much faster than typical SNMF based method.

Finite mixture model is an important branch of clustering methods and can be applied on data sets with mixed types of variables. However, challenges exist in its applications. First, it typically relies on the EM algorithm which could be sensitive to the choice of initial values. Second, biomarkers subject to limits of detection (LOD) are common to encounter in clinical data, which brings censored variables into finite mixture model. Additionally, researchers are recently getting more interest in variable importance due to the increasing number of variables that become available for clustering. To address these challenges, we propose a Bayesian finite mixture model to simultaneously conduct variable selection, account for biomarker LOD and obtain clustering results. We took a Bayesian approach to obtain parameter estimates and the cluster membership to bypass the limitation of the EM algorithm. To account for LOD, we added one more step in Gibbs sampling to iteratively fill in biomarker values below or above LODs. In addition, we put a spike-and-slab type of prior on each variable to obtain variable importance. Simulations across various scenarios were conducted to examine the performance of this method. Real data application on electronic health records was also conducted.

Modern neural network training relies on piece-wise (sub-)differentiable functions in order to use backpropation for efficient calculation of gradients. In this work, we introduce a novel method to allow for non-differentiable functions at intermediary layers of deep neural networks. We do so through the introduction of a differentiable approximation bridge (DAB) neural network which provides smooth approximations to the gradient of the non-differentiable function. We present strong empirical results (performing over 600 experiments) in three different domains: unsupervised (image) representation learning, image classification, and sequence sorting to demonstrate that our proposed method improves state of the art performance. We demonstrate that utilizing non-differentiable functions in unsupervised (image) representation learning improves reconstruction quality and posterior linear separability by 10%. We also observe an accuracy improvement of 77% in neural sequence sorting and a 25% improvement against the straight-through estimator [3] in an image classification setting with the sort non-linearity. This work enables the usage of functions that were previously not usable in neural networks.

Machine learning techniques typically rely on large datasets to create accurate classifiers. However, there are situations when data is scarce and expensive to acquire. This is the case of studies that rely on state-of-the-art computational models which typically take days to run, thus hindering the potential of machine learning tools. In this work, we present a novel classifier that takes advantage of lower fidelity models and inexpensive approximations to predict the binary output of expensive computer simulations. We postulate an autoregressive model between the different levels of fidelity with Gaussian process priors. We adopt a fully Bayesian treatment for the hyper-parameters and use Markov Chain Mont Carlo samplers. We take advantage of the probabilistic nature of the classifier to implement active learning strategies. We also introduce a sparse approximation to enhance the ability of themulti-fidelity classifier to handle large datasets. We test these multi-fidelity classifiers against their single-fidelity counterpart with synthetic data, showing a median computational cost reduction of 23% for a target accuracy of 90%. In an application to cardiac electrophysiology, the multi-fidelity classifier achieves an F1 score, the harmonic mean of precision and recall, of 99.6% compared to 74.1% of a single-fidelity classifier when both are trained with 50 samples. In general, our results show that the multi-fidelity classifiers outperform their single-fidelity counterpart in terms of accuracy in all cases. We envision that this new tool will enable researchers to study classification problems that would otherwise be prohibitively expensive. Source code is available at https://github.com/fsahli/MFclass.

Variational Inference is a powerful tool in the Bayesian modeling toolkit, however, its effectiveness is determined by the expressivity of the utilized variational distributions in terms of their ability to match the true posterior distribution. In turn, the expressivity of the variational family is largely limited by the requirement of having a tractable density function. To overcome this roadblock, we introduce a new family of variational upper bounds on a marginal log density in the case of hierarchical models (also known as latent variable models). We then give an upper bound on the Kullback-Leibler divergence and derive a family of increasingly tighter variational lower bounds on the otherwise intractable standard evidence lower bound for hierarchical variational distributions, enabling the use of more expressive approximate posteriors. We show that previously known methods, such as Hierarchical Variational Models, Semi-Implicit Variational Inference and Doubly Semi-Implicit Variational Inference can be seen as special cases of the proposed approach, and empirically demonstrate superior performance of the proposed method in a set of experiments.

In this report we review memory-based meta-learning as a tool for building sample-efficient strategies that learn from past experience to adapt to any task within a target class. Our goal is to equip the reader with the conceptual foundations of this tool for building new, scalable agents that operate on broad domains. To do so, we present basic algorithmic templates for building near-optimal predictors and reinforcement learners which behave as if they had a probabilistic model that allowed them to efficiently exploit task structure. Furthermore, we recast memory-based meta-learning within a Bayesian framework, showing that the meta-learned strategies are near-optimal because they amortize Bayes-filtered data, where the adaptation is implemented in the memory dynamics as a state-machine of sufficient statistics. Essentially, memory-based meta-learning translates the hard problem of probabilistic sequential inference into a regression problem.

Clinical decision making is challenging because of pathological complexity, as well as large amounts of heterogeneous data generated as part of routine clinical care. In recent years, machine learning tools have been developed to aid this process. Intensive care unit (ICU) admissions represent the most data dense and time-critical patient care episodes. In this context, prediction models may help clinicians determine which patients are most at risk and prioritize care. However, flexible tools such as artificial neural networks (ANNs) suffer from a lack of interpretability limiting their acceptability to clinicians. In this work, we propose a novel interpretable Bayesian neural network architecture which offers both the flexibility of ANNs and interpretability in terms of feature selection. In particular, we employ a sparsity inducing prior distribution in a tied manner to learn which features are important for outcome prediction. We evaluate our approach on the task of mortality prediction using two real-world ICU cohorts. In collaboration with clinicians we found that, in addition to the predicted outcome results, our approach can provide novel insights into the importance of different clinical measurements. This suggests that our model can support medical experts in their decision making process.

We propose a topological learning algorithm for the estimation of the conditional dependency structure of large sets of random variables from sparse and noisy data. The algorithm, named Maximally Filtered Clique Forest (MFCF), produces a clique forest and an associated Markov Random Field (MRF) by generalising Prim's minimum spanning tree algorithm. To the best of our knowledge, the MFCF presents three elements of novelty with respect to existing structure learning approaches. The first is the repeated application of a local topological move, the clique expansion, that preserves the decomposability of the underlying graph. Through this move the decomposability and calculation of scores is performed incrementally at the variable (rather than edge) level, and this provides better computational performance and an intuitive application of multivariate statistical tests. The second is the capability to accommodate a variety of score functions and, while this paper is focused on multivariate normal distributions, it can be directly generalised to different types of statistics. Finally, the third is the variable range of allowed clique sizes which is an adjustable topological constraint that acts as a topological penalizer providing a way to tackle sparsity at $l_0$ semi-norm level; this allows a clean decoupling of structure learning and parameter estimation. The MFCF produces a representation of the clique forest, together with a perfect ordering of the cliques and a perfect elimination ordering for the vertices. As an example we propose an application to covariance selection models and we show that the MCFC outperforms the Graphical Lasso for a number of classes of matrices.