A Poisson Hidden Markov Model is a mixture of two regression models: A Poisson regression model which is visible and a Markov model which is ‘hidden’.

Understanding kinetics and thermodynamics profile of biomolecules is necessary to understand their functional roles which has a major impact in mechanism driven drug discovery. Molecular dynamics simulation has been routinely used to understand conformational dynamics and molecular recognition in biomolecules. Statistical analysis of high-dimensional spatiotemporal data generated from molecular dynamics simulation requires identification of few low-dimensional variables which can describe essential dynamics of a system without significant loss of informations. In physical chemistry, these low-dimensional variables often called collective variables. Collective variables are used to generated reduced representation of free energy surface and calculate transition probabilities between different metastable basins. However the choice of collective variables is not trivial for complex systems. Collective variables ranges from geometric criteria's such as distances, dihedral angles to abstract ones such as weighted linear combinations of multiple geometric variables. Advent of machine learning algorithms led to increasing use of abstract collective variables to represent biomolecular dynamics. In this review, I will highlight several nuances of commonly used collective variables ranging from geometric to abstract ones. Further, I will put forward some cases where machine learning based collective variables were used to describe simple systems which in principle could have been described by geometric ones. Finally, I will put forward my thoughts on artificial general intelligence and how it can be used to discover and predict collective variables from spatiotemporal data generated by molecular dynamics simulations.

In these notes we will tackle the problem of finding optimal policies for Markov decision processes (MDPs) which are not fully known to us. Our intention is to slowly transition from an offline setting to an online (learning) setting. Namely, we are moving towards reinforcement learning. As a reminder, a (stationary) MDP M is a 4-tuple (S,A,P,r) where: - S is a finite set of states, - A is a finite set of actions. For intuition, this is just a graph-based way of saying that the reachable part of the Markov chain induced by the policy has a single closed communicating class. Let M be a communicating MDP and i one of its states.

Model-based reinforcement learning methods achieve significant sample efficiency in many tasks, but their performance is often limited by the existence of the model error. To reduce the model error, previous works use a single well-designed network to fit the entire environment dynamics, which treats the environment dynamics as a black box. However, these methods lack to consider the environmental decomposed property that the dynamics may contain multiple sub-dynamics, which can be modeled separately, allowing us to construct the world model more accurately. In this paper, we propose the Environment Dynamics Decomposition (ED2), a novel world model construction framework that models the environment in a decomposing manner. ED2 contains two key components: sub-dynamics discovery (SD2) and dynamics decomposition prediction (D2P). SD2 discovers the sub-dynamics in an environment and then D2P constructs the decomposed world model following the sub-dynamics. ED2 can be easily combined with existing MBRL algorithms and empirical results show that ED2 significantly reduces the model error and boosts the performance of the state-of-the-art MBRL algorithms on various tasks.

The Internet generates large volumes of data at a high rate, in particular, posts on social networks. Although social network data has numerous semantic adulterations, and is not intended to be a source of geo-spatial information, in the text of posts we find pieces of important information about how people relate to their environment, which can be used to identify interesting aspects of how human beings interact with portions of land based on their activities. This research proposes a methodology for the identification of land uses using Natural Language Processing (NLP) from the contents of the popular social network Twitter. It will be approached by identifying keywords with linguistic patterns from the text, and the geographical coordinates associated with the publication. Context-specific innovations are introduced to deal with data across South America and, in particular, in the city of Arequipa, Peru. The objective is to identify the five main land uses: residential, commercial, institutional-governmental, industrial-offices and unbuilt land. Within the framework of urban planning and sustainable urban management, the methodology contributes to the optimization of the identification techniques applied for the updating of land use cadastres, since the results achieved an accuracy of about 90%, which motivates its application in the real context. In addition, it would allow the identification of land use categories at a more detailed level, in situations such as a complex/mixed distribution building based on the amount of data collected. Finally, the methodology makes land use information available in a more up-to-date fashion and, above all, avoids the high economic cost of the non-automatic production of land use maps for cities, mostly in developing countries.

A structural equation model (SEM) is an effective framework to reason over causal relationships represented via a directed acyclic graph (DAG). Recent advances have enabled effective maximum-likelihood point estimation of DAGs from observational data. However, a point estimate may not accurately capture the uncertainty in inferring the underlying graph in practical scenarios, wherein the true DAG is non-identifiable and/or the observed dataset is limited. We propose Bayesian Causal Discovery Nets (BCD Nets), a variational inference framework for estimating a distribution over DAGs characterizing a linear-Gaussian SEM. Developing a full Bayesian posterior over DAGs is challenging due to the the discrete and combinatorial nature of graphs. We analyse key design choices for scalable VI over DAGs, such as 1) the parametrization of DAGs via an expressive variational family, 2) a continuous relaxation that enables low-variance stochastic optimization, and 3) suitable priors over the latent variables. We provide a series of experiments on real and synthetic data showing that BCD Nets outperform maximum-likelihood methods on standard causal discovery metrics such as structural Hamming distance in low data regimes.

This work explores the potency of stochastic competition-based activations, namely Stochastic Local Winner-Takes-All (LWTA), against powerful (gradient-based) white-box and black-box adversarial attacks; we especially focus on Adversarial Training settings. In our work, we replace the conventional ReLU-based nonlinearities with blocks comprising locally and stochastically competing linear units. The output of each network layer now yields a sparse output, depending on the outcome of winner sampling in each block. We rely on the Variational Bayesian framework for training and inference; we incorporate conventional PGD-based adversarial training arguments to increase the overall adversarial robustness. As we experimentally show, the arising networks yield state-of-the-art robustness against powerful adversarial attacks while retaining very high classification rate in the benign case.

Data-driven forecasts of air quality have recently achieved more accurate short-term predictions. Despite their success, most of the current data-driven solutions lack proper quantifications of model uncertainty that communicate how much to trust the forecasts. Recently, several practical tools to estimate uncertainty have been developed in probabilistic deep learning. However, there have not been empirical applications and extensive comparisons of these tools in the domain of air quality forecasts. Therefore, this work applies state-of-the-art techniques of uncertainty quantification in a real-world setting of air quality forecasts. Through extensive experiments, we describe training probabilistic models and evaluate their predictive uncertainties based on empirical performance, reliability of confidence estimate, and practical applicability. We also propose improving these models using "free" adversarial training and exploiting temporal and spatial correlation inherent in air quality data. Our experiments demonstrate that the proposed models perform better than previous works in quantifying uncertainty in data-driven air quality forecasts. Overall, Bayesian neural networks provide a more reliable uncertainty estimate but can be challenging to implement and scale. Other scalable methods, such as deep ensemble, Monte Carlo (MC) dropout, and stochastic weight averaging-Gaussian (SWAG), can perform well if applied correctly but with different tradeoffs and slight variations in performance metrics. Finally, our results show the practical impact of uncertainty estimation and demonstrate that, indeed, probabilistic models are more suitable for making informed decisions. Code and dataset are available at \url{https://github.com/Abdulmajid-Murad/deep_probabilistic_forecast}

Intention recognition is an important step to facilitate collaboration in multi-agent systems. Existing work mainly focuses on intention recognition in a single-agent setting and uses a descriptive model, e.g. Bayesian networks, in the recognition process. In this paper, we resort to a prescriptive approach to model agents' behaviour where which their intentions are hidden in implementing their plans. We introduce landmarks into the behavioural model therefore enhancing informative features for identifying common intentions for multiple agents. We further refine the model by focusing only action sequences in their plan and provide a light model for identifying and comparing their intentions. The new models provide a simple approach of grouping agents' common intentions upon partial plans observed in agents' interactions. We provide experimental results in support.

KNN can easily be mapped to our real lives. If you want to learn about a person, of whom you have no information, you might like to find out about his close friends and the circles he moves in and gain access to his/her information!