Real-world clinical problems are often characterized by multimodal data, usually associated with incomplete views and limited sample sizes in their cohorts, posing significant limitations for machine learning algorithms. In this work, we propose a Bayesian approach designed to efficiently handle these challenges while providing interpretable solutions. Our approach integrates (1) a generative formulation to capture cross-view relationships with a semi-supervised strategy, and (2) a discriminative task-oriented formulation to identify relevant information for specific downstream objectives. This dual generative-discriminative formulation offers both general understanding and task-specific insights; thus, it provides an automatic imputation of the missing views while enabling robust inference across different data sources. The potential of this approach becomes evident when applied to the multimodal clinical data, where our algorithm is able to capture and disentangle the complex interactions among biological, psychological, and sociodemographic modalities.

Mean field variational Bayes (MFVB) is a popular posterior approximation method due to its fast runtime on large-scale data sets. However, a well known failing of MFVB is that it underestimates the uncertainty of model variables (sometimes severely) and provides no information about model variable covariance. We generalize linear response methods from statistical physics to deliver accurate uncertainty estimates for model variables---both for individual variables and coherently across variables. We call our method linear response variational Bayes (LRVB). When the MFVB posterior approximation is in the exponential family, LRVB has a simple, analytic form, even for non-conjugate models. Indeed, we make no assumptions about the form of the true posterior. We demonstrate the accuracy and scalability of our method on a range of models for both simulated and real data.

Factor importance measures the impact of each feature on output prediction accuracy. Many existing works focus on the model-based importance, but an important feature in one learning algorithm may hold little significance in another model. Hence, a factor importance measure ought to characterize the feature's predictive potential without relying on a specific prediction algorithm. Such algorithm-agnostic importance is termed as intrinsic importance in Williamson et al. (2023), but their estimator again requires model fitting. To bypass the modeling step, we present the equivalence between predictiveness potential and total Sobol' indices from global sensitivity analysis, and introduce a novel consistent estimator that can be directly estimated from noisy data. Integrating with forward selection and backward elimination gives rise to FIRST, Factor Importance Ranking and Selection using Total (Sobol') indices. Extensive simulations are provided to demonstrate the effectiveness of FIRST on regression and binary classification problems, and a clear advantage over the state-of-the-art methods.

Mean field variational Bayes (MFVB) is a popular posterior approximation method due to its fast runtime on large-scale data sets. However, a well known failing of MFVB is that it underestimates the uncertainty of model variables (sometimes severely) and provides no information about model variable covariance. We generalize linear response methods from statistical physics to deliver accurate uncertainty estimates for model variables---both for individual variables and coherently across variables. We call our method linear response variational Bayes (LRVB). When the MFVB posterior approximation is in the exponential family, LRVB has a simple, analytic form, even for non-conjugate models.

Mathematical modeling with Ordinary Differential Equations (ODEs) has proven to be extremely successful in a variety of fields, including biology. However, these models are completely deterministic given a certain set of initial conditions. We convert mathematical ODE models of three benchmark biological systems to Dynamic Bayesian Networks (DBNs). The DBN model can handle model uncertainty and data uncertainty in a principled manner. They can be used for temporal data mining for noisy and missing variables. We apply Particle Filtering algorithm to infer the model variables by re-estimating the models parameters of various biological ODE models. The model parameters are automatically re-estimated using temporal evidence in the form of data streams. The results show that DBNs are capable of inferring the model variables of the ODE model with high accuracy in situations where data is missing, incomplete, sparse and irregular and true values of model parameters are not known.

PROFET: Construction and Inference of DBNs Based on Mathematical Models Hamda Ajmal, Michael Madden and Catherine Enright School of Computer Science, National University of Ireland Galway h.ajmal1@nuigalway.ie, Abstract This paper presents, evaluates, and discusses a new software tool to automatically build Dynamic Bayesian Networks (DBNs) from ordinary differential equations (ODEs) entered by the user. The DBNs generated from ODE models can handle both data uncertainty and model uncertainty in a principled manner. The application, named PROFET, can be used for temporal data mining with noisy or missing variables. It enables automatic re-estimation of model parameters using temporal evidence in the form of data streams. For temporal inference, PROFET includes both standard fixed time step particle filtering and its extension, adaptive-time particle filtering algorithms. Adaptive-time particle filtering enables the DBN to automatically adapt its time step length to match the dynamics of the model. We demonstrate PROFET's functionality by using it to infer the model variables by estimating the model parameters of four benchmark ODE systems. From the generation of the DBN model to temporal inference, the entire process is automated and is delivered as an open-source platform-independent software application with a comprehensive user interface. PROFET is released under the Apache License 2.0. Its source code, executable and documentation are available at http:://profet.

In this paper, we aim at providing an introduction to the gradient descent based optimization algorithms for learning deep neural network models. Deep learning models involving multiple nonlinear projection layers are very challenging to train. Nowadays, most of the deep learning model training still relies on the back propagation algorithm actually. In back propagation, the model variables will be updated iteratively until convergence with gradient descent based optimization algorithms. Besides the conventional vanilla gradient descent algorithm, many gradient descent variants have also been proposed in recent years to improve the learning performance, including Momentum, Adagrad, Adam, Gadam, etc., which will all be introduced in this paper respectively.

When training large machine learning models with many variables or parameters, a single machine is often inadequate since the model may be too large to fit in memory, while training can take a long time even with stochastic updates. A natural recourse is to turn to distributed cluster computing, in order to harness additional memory and processors. However, naive, unstructured parallelization of ML algorithms can make inefficient use of distributed memory, while failing to obtain proportional convergence speedups - or can even result in divergence. We develop a framework of primitives for dynamic model-parallelism, STRADS, in order to explore partitioning and update scheduling of model variables in distributed ML algorithms - thus improving their memory efficiency while presenting new opportunities to speed up convergence without compromising inference correctness. We demonstrate the efficacy of model-parallel algorithms implemented in STRADS versus popular implementations for Topic Modeling, Matrix Factorization and Lasso.