Predictive Collective Variable Discovery with Deep Bayesian Models

Extending spatio-temporal scale limitations of models for complex atomistic systems considered in biochemistry and materials science necessitates the development of enhanced sampling methods. The potential acceleration in exploring the configurational space by enhanced sampling methods depends on the choice of collective variables (CVs). In this work, we formulate the discovery of CVs as a Bayesian inference problem and consider the CVs as hidden generators of the full-atomistic trajectory. The ability to generate samples of the fine-scale atomistic configurations using limited training data allows us to compute estimates of observables as well as our probabilistic confidence on them. The methodology is based on emerging methodological advances in machine learning and variational inference. The discovered CVs are related to physicochemical properties which are essential for understanding mechanisms especially in unexplored complex systems. We provide a quantitative assessment of the CVs in terms of their predictive ability for alanine dipeptide (ALA-2) and ALA-15 peptide

Incorporating physical constraints in a deep probabilistic machine learning framework for coarse-graining dynamical systems

Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a data-based, probablistic perspective that enables the quantification of predictive uncertainties. One of the outstanding problems has been the introduction of physical constraints in the probabilistic machine learning objectives. The primary utility of such constraints stems from the undisputed physical laws such as conservation of mass, energy etc. that they represent. Furthermore and apart from leading to physically realistic predictions, they can significantly reduce the requisite amount of training data which for high-dimensional, multiscale systems are expensive to obtain (Small Data regime). We formulate the coarse-graining process by employing a probabilistic state-space model and account for the aforementioned equality constraints as virtual observables in the associated densities. We demonstrate how probabilistic inference tools can be employed to identify the coarse-grained variables in combination with deep neural nets and their evolution model without ever needing to define a fine-to-coarse (restriction) projection and without needing time-derivatives of state variables. Furthermore, it is capable of reconstructing the evolution of the full, fine-scale system and therefore the observables of interest need not be selected a priori. We demonstrate the efficacy of the proposed framework by applying it to systems of interacting particles and an image-series of a nonlinear pendulum

Uncertainty Aware AI ML: Why and How

This paper argues the need for research to realize uncertainty-aware artificial intelligence and machine learning (AI\&ML) systems for decision support by describing a number of motivating scenarios. Furthermore, the paper defines uncertainty-awareness and lays out the challenges along with surveying some promising research directions. A theoretical demonstration illustrates how two emerging uncertainty-aware ML and AI technologies could be integrated and be of value for a route planning operation.Comment: Presented at AAAI FSS-18: Artificial Intelligence in Government and Public Sector, Arlington, Virginia, US

Predictive Coarse-Graining

We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the CG process. Furthermore, it can be readily extended to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo - Expectation-Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model

Bayesian Modeling of Intersectional Fairness: The Variance of Bias

Intersectionality is a framework that analyzes how interlocking systems of power and oppression affect individuals along overlapping dimensions including race, gender, sexual orientation, class, and disability. Intersectionality theory therefore implies it is important that fairness in artificial intelligence systems be protected with regard to multi-dimensional protected attributes. However, the measurement of fairness becomes statistically challenging in the multi-dimensional setting due to data sparsity, which increases rapidly in the number of dimensions, and in the values per dimension. We present a Bayesian probabilistic modeling approach for the reliable, data-efficient estimation of fairness with multi-dimensional protected attributes, which we apply to two existing intersectional fairness metrics. Experimental results on census data and the COMPAS criminal justice recidivism dataset demonstrate the utility of our methodology, and show that Bayesian methods are valuable for the modeling and measurement of fairness in an intersectional context

Attribute-aware Collaborative Filtering: Survey and Classification

Attribute-aware CF models aims at rating prediction given not only the historical rating from users to items, but also the information associated with users (e.g. age), items (e.g. price), or even ratings (e.g. rating time). This paper surveys works in the past decade developing attribute-aware CF systems, and discovered that mathematically they can be classified into four different categories. We provide the readers not only the high level mathematical interpretation of the existing works in this area but also the mathematical insight for each category of models. Finally we provide in-depth experiment results comparing the effectiveness of the major works in each category

Inferring Complementary Products from Baskets and Browsing Sessions

Complementary products recommendation is an important problem in e-commerce. Such recommendations increase the average order price and the number of products in baskets. Complementary products are typically inferred from basket data. In this study, we propose the BB2vec model. The BB2vec model learns vector representations of products by analyzing jointly two types of data - Baskets and Browsing sessions (visiting web pages of products). These vector representations are used for making complementary products recommendation. The proposed model alleviates the cold start problem by delivering better recommendations for products having few or no purchases. We show that the BB2vec model has better performance than other models which use only basket data.Comment: Workshop on Intelligent Recommender Systems by Knowledge Transfer and Learning (RecSysKTL'18

Stacking with Neural network for Cryptocurrency investment

Predicting the direction of assets have been an active area of study and a difficult task. Machine learning models have been used to build robust models to model the above task. Ensemble methods is one of them showing results better than a single supervised method. In this paper, we have used generative and discriminative classifiers to create the stack, particularly 3 generative and 6 discriminative classifiers and optimized over one-layer Neural Network to model the direction of price cryptocurrencies. Features used are technical indicators used are not limited to trend, momentum, volume, volatility indicators, and sentiment analysis has also been used to gain useful insight combined with the above features. For Cross-validation, Purged Walk forward cross-validation has been used. In terms of accuracy, we have done a comparative analysis of the performance of Ensemble method with Stacking and Ensemble method with blending. We have also developed a methodology for combined features importance for the stacked model. Important indicators are also identified based on feature importance.Comment: 20 pages,7 figue

A Price Driven Hazard Approach to User Retention

Customer loyalty is crucial for internet services since retaining users of a service to ensure the staying time of the service is of significance for increasing revenue. It demands the retention of customers to be high enough to meet the needs for yielding profit for the internet servers. Besides, the growing of rich purchasing interaction feedback helps in uncovering the inner mechanism of purchasing intent of the customers. In this work, we exploit the rich interaction data of user to build a customers retention evaluation model focusing on the return time of a user to a product. Three aspects, namely the consilience between user and product, the sensitivity of the user to price and the external influence the user might receive, are promoted to effect the purchase intents, which are jointly modeled by a probability model based on Cox's proportional hazard approach. The hazard based model provides benefits in the dynamics in user retention and it can conveniently incorporate covariates in the model. Extensive experiments on real world purchasing data have demonstrated the superiority of the proposed model over state-of-the-art algorithms.Comment: 11 page

Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities

New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties describing genome, epigenome, transcriptome, microbiome, phenotype, and lifestyle. No single data type, however, can capture the complexity of all the factors relevant to understanding a phenomenon such as a disease. Integrative methods that combine data from multiple technologies have thus emerged as critical statistical and computational approaches. The key challenge in developing such approaches is the identification of effective models to provide a comprehensive and relevant systems view. An ideal method can answer a biological or medical question, identifying important features and predicting outcomes, by harnessing heterogeneous data across several dimensions of biological variation. In this Review, we describe the principles of data integration and discuss current methods and available implementations. We provide examples of successful data integration in biology and medicine. Finally, we discuss current challenges in biomedical integrative methods and our perspective on the future development of the field