The multinomial probit Bayesian additive regression trees (MPBART) framework was proposed by Kindo et al. (KD), approximating the latent utilities in the multinomial probit (MNP) model with BART (Chipman et al. 2010). Compared to multinomial logistic models, MNP does not assume independent alternatives and the correlation structure among alternatives can be specified through multivariate Gaussian distributed latent utilities. We introduce two new algorithms for fitting the MPBART and show that the theoretical mixing rates of our proposals are equal or superior to the existing algorithm in KD. Through simulations, we explore the robustness of the methods to the choice of reference level, imbalance in outcome frequencies, and the specifications of prior hyperparameters for the utility error term. The work is motivated by the application of generating posterior predictive distributions for mortality and engagement in care among HIV-positive patients based on electronic health records (EHRs) from the Academic Model Providing Access to Healthcare (AMPATH) in Kenya. In both the application and simulations, we observe better performance using our proposals as compared to KD in terms of MCMC convergence rate and posterior predictive accuracy.

With the rapid development of biomedical software and hardware, a large amount of relational data interlinking genes, proteins, chemical components, drugs, diseases, and symptoms has been collected for modern biomedical research. Many graph-based learning methods have been proposed to analyze such type of data, giving a deeper insight into the topology and knowledge behind the biomedical data, which greatly benefit to both academic research and industrial application for human healthcare. However, the main difficulty is how to handle high dimensionality and sparsity of the biomedical graphs. Recently, graph embedding methods provide an effective and efficient way to address the above issues. It converts graph-based data into a low dimensional vector space where the graph structural properties and knowledge information are well preserved. In this survey, we conduct a literature review of recent developments and trends in applying graph embedding methods for biomedical data. We also introduce important applications and tasks in the biomedical domain as well as associated public biomedical datasets.

In recent years, deep neural networks have had great success in machine learning and pattern recognition. Architecture size for a neural network contributes significantly to the success of any neural network. In this study, we optimize the selection process by investigating different search algorithms to find a neural network architecture size that yields the highest accuracy. We apply binary search on a very well-defined binary classification network search space and compare the results to those of linear search. We also propose how to relax some of the assumptions regarding the dataset so that our solution can be generalized to any binary classification problem. We report a 100-fold running time improvement over the naive linear search when we apply the binary search method to our datasets in order to find the best architecture candidate. By finding the optimal architecture size for any binary classification problem quickly, we hope that our research contributes to discovering intelligent algorithms for optimizing architecture size selection in machine learning.

Conventional models for Visual Question Answering (VQA) explore deterministic approaches with various types of image features, question features, and attention mechanisms. However, there exist other modalities that can be explored in addition to image and question pairs to bring extra information to the models. In this work, we propose latent variable models for VQA where extra information (e.g. captions and answer categories) are incorporated as latent variables to improve inference, which in turn benefits question-answering performance. Experiments on the VQA v2.0 benchmarking dataset demonstrate the effectiveness of our proposed models in that they improve over strong baselines, especially those that do not rely on extensive language-vision pre-training.

Recent work on hyperparameters optimization (HPO) has shown the possibility of training certain hyperparameters together with regular parameters. However, these online HPO algorithms still require running evaluation on a set of validation examples at each training step, steeply increasing the training cost. To decide when to query the validation loss, we model online HPO as a time-varying Bayesian optimization problem, on top of which we propose a novel \textit{costly feedback} setting to capture the concept of the query cost. Under this setting, standard algorithms are cost-inefficient as they evaluate on the validation set at every round. In contrast, the cost-efficient GP-UCB algorithm proposed in this paper queries the unknown function only when the model is less confident about current decisions. We evaluate our proposed algorithm by tuning hyperparameters online for VGG and ResNet on CIFAR-10 and ImageNet100. Our proposed online HPO algorithm reaches human expert-level performance within a single run of the experiment, while incurring only modest computational overhead compared to regular training.

The right to be forgotten has been legislated in many countries but the enforcement in machine learning would cause unbearable costs: companies may need to delete whole models trained from massive resources because of single individual requests. Existing works propose to remove the influence of the requested datums on the learned models via its influence function which is no longer naturally well-defined in Bayesian inference. To address this problem, this paper proposes a {\it Bayesian inference forgetting} (BIF) framework to extend the applicable domain to Bayesian inference. In the BIF framework, we develop forgetting algorithms for variational inference and Markov chain Monte Carlo. We show that our algorithms can provably remove the influence of single datums on the learned models. Theoretical analysis demonstrates that our algorithms have guaranteed generalizability. Experiments of Gaussian mixture models on the synthetic dataset and Bayesian neural networks on the Fashion-MNIST dataset verify the feasibility of our methods. The source code package is available at \url{https://github.com/fshp971/BIF}.

Is deep learning over-hyped? Where are the case studies that compare state-of-the-art deep learners with simpler options? In response to this gap in the literature, this paper offers one case study on using deep learning to predict issue close time in Bugzilla. We report here that a SIMPLE extension to a decades-old feedforward neural network works better than the more recent, and more elaborate, "long-short term memory" deep learning (which are currently popular in the SE literature). SIMPLE is a combination of a fast feedforward network and a hyper-parameter optimizer. SIMPLE runs in 3 seconds while the newer algorithms take 6 hours to terminate. Since it runs so fast, it is more amenable to being tuned by our optimizer. This paper reports results seen after running SIMPLE on issue close time data from 45,364 issues raised in Chromium, Eclipse, and Firefox projects from January 2010 to March 2016. In our experiments, this SIMPLEr tuning approach achieves significantly better predictors for issue close time than the more complex deep learner. These better and SIMPLEr results can be generated 2,700 times faster than if using a state-of-the-art deep learner. From this result, we make two conclusions. Firstly, for predicting issue close time, we would recommend SIMPLE over complex deep learners. Secondly, before analysts try very sophisticated (but very slow) algorithms, they might achieve better results, much sooner, by applying hyper-parameter optimization to simple (but very fast) algorithms.

Federated learning brings potential benefits of faster learning, better solutions, and a greater propensity to transfer when heterogeneous data from different parties increases diversity. However, because federated learning tasks tend to be large and complex, and training times non-negligible, it is important for the aggregation algorithm to be robust to non-IID data and corrupted parties. This robustness relies on the ability to identify, and appropriately weight, incompatible parties. Recent work assumes that a \textit{reference dataset} is available through which to perform the identification. We consider settings where no such reference dataset is available; rather, the quality and suitability of the parties needs to be \textit{inferred}. We do so by bringing ideas from crowdsourced predictions and collaborative filtering, where one must infer an unknown ground truth given proposals from participants with unknown quality. We propose novel federated learning aggregation algorithms based on Bayesian inference that adapt to the quality of the parties. Empirically, we show that the algorithms outperform standard and robust aggregation in federated learning on both synthetic and real data.

To perform Bayesian inference for stochastic simulator models for which the likelihood is not accessible, Likelihood-Free Inference (LFI) relies on simulations from the model. Standard LFI methods can be split according to how these simulations are used: to build an explicit Surrogate Likelihood, or to accept/reject parameter values according to a measure of distance from the observations (Approximate Bayesian Computation (ABC)). In both cases, simulations are adaptively tailored to the value of the observation. Here, we generate parameter-simulation pairs from the model independently on the observation, and use them to learn a conditional exponential family likelihood approximation; to parametrize it, we use Neural Networks whose weights are tuned with Score Matching. With our likelihood approximation, we can employ MCMC for doubly intractable distributions to draw samples from the posterior for any number of observations without additional model simulations, with performance competitive to comparable approaches. Further, the sufficient statistics of the exponential family can be used as summaries in ABC, outperforming the state-of-the-art method in five different models with known likelihood. Finally, we apply our method to a challenging model from meteorology.

Given (small amounts of) time-series' data from a high-dimensional, fine-grained, multiscale dynamical system, we propose a generative framework for learning an effective, lower-dimensional, coarse-grained dynamical model that is predictive of the fine-grained system's long-term evolution but also of its behavior under different initial conditions. We target fine-grained models as they arise in physical applications (e.g. molecular dynamics, agent-based models), the dynamics of which are strongly non-stationary but their transition to equilibrium is governed by unknown slow processes which are largely inaccessible by brute-force simulations. Approaches based on domain knowledge heavily rely on physical insight in identifying temporally slow features and fail to enforce the long-term stability of the learned dynamics. On the other hand, purely statistical frameworks lack interpretability and rely on large amounts of expensive simulation data (long and multiple trajectories) as they cannot infuse domain knowledge. The generative framework proposed achieves the aforementioned desiderata by employing a flexible prior on the complex plane for the latent, slow processes, and an intermediate layer of physics-motivated latent variables that reduces reliance on data and imbues inductive bias. In contrast to existing schemes, it does not require the a priori definition of projection operators from the fine-grained description and addresses simultaneously the tasks of dimensionality reduction and model estimation. We demonstrate its efficacy and accuracy in multiscale physical systems of particle dynamics where probabilistic, long-term predictions of phenomena not contained in the training data are produced.