As a relatively new field, network neuroscience has tended to focus on aggregate behaviours of the brain averaged over many successive experiments or over long recordings in order to construct robust brain models. These models are limited in their ability to explain dynamic state changes in the brain which occurs spontaneously as a result of normal brain function. Hidden Markov Models (HMMs) trained on neuroimaging time series data have since arisen as a method to produce dynamical models that are easy to train but can be difficult to fully parametrise or analyse. We propose an interpretation of these neural HMMs as multiplex brain state graph models we term Hidden Markov Graph Models (HMGMs). This interpretation allows for dynamic brain activity to be analysed using the full repertoire of network analysis techniques. Furthermore, we propose a general method for selecting HMM hyperparameters in the absence of external data, based on the principle of maximum entropy, and use this to select the number of layers in the multiplex model. We produce a new tool for determining important communities of brain regions using a spatiotemporal random walk-based procedure that takes advantage of the underlying Markov structure of the model. Our analysis of real multi-subject fMRI data provides new results that corroborate the modular processing hypothesis of the brain at rest as well as contributing new evidence of functional overlap between and within dynamic brain state communities. Our analysis pipeline provides a way to characterise dynamic network activity of the brain under novel behaviours or conditions.

Solving general Markov decision processes (MDPs) is a computationally hard problem. Solving finite-horizon MDPs, on the other hand, is highly tractable with well known polynomial-time algorithms. What drives this extreme disparity, and do problems exist that lie between these diametrically opposed complexities? In this paper we identify and analyse a sub-class of stochastic shortest path problems (SSPs) for general state-action spaces whose dynamics satisfy a particular drift condition. This construction generalises the traditional, temporal notion of a horizon via decreasing reachability: a property called reductivity. It is shown that optimal policies can be recovered in polynomial-time for reductive SSPs -- via an extension of backwards induction -- with an efficient analogue in reductive MDPs. The practical considerations of the proposed approach are discussed, and numerical verification provided on a canonical optimal liquidation problem.

Markov chains are used to model probabilities using information that can be encoded in the current state. Each state has a certain probability of transitioning to each other state, so each time you are in a state and want to transition, a markov chain can predict outcomes based on pre-existing probability data. More technically, information is put into a matrix and a vector - also called a column matrix - and with many iterations, a collection of probability vectors makes up Markov chains. To determine the transition probabilities, you have to "train" your Markov Chain on some input corpus.

Prokaryotic viruses, which infect bacteria and archaea, are key players in microbial communities. Predicting the hosts of prokaryotic viruses helps decipher the dynamic relationship between microbes. Experimental methods for host prediction cannot keep pace with the fast accumulation of sequenced phages. Thus, there is a need for computational host prediction. Despite some promising results, computational host prediction remains a challenge because of the limited known interactions and the sheer amount of sequenced phages by high-throughput sequencing technologies. The state-of-the-art methods can only achieve 43\% accuracy at the species level. In this work, we formulate host prediction as link prediction in a knowledge graph that integrates multiple protein and DNA-based sequence features. Our implementation named CHERRY can be applied to predict hosts for newly discovered viruses and to identify viruses infecting targeted bacteria. We demonstrated the utility of CHERRY for both applications and compared its performance with 11 popular host prediction methods. To our best knowledge, CHERRY has the highest accuracy in identifying virus-prokaryote interactions. It outperforms all the existing methods at the species level with an accuracy increase of 37\%. In addition, CHERRY's performance on short contigs is more stable than other tools.

A new Bayesian modelling framework is introduced for piece-wise homogeneous variable-memory Markov chains, along with a collection of effective algorithmic tools for change-point detection and segmentation of discrete time series. Building on the recently introduced Bayesian Context Trees (BCT) framework, the distributions of different segments in a discrete time series are described as variable-memory Markov chains. Inference for the presence and location of change-points is then performed via Markov chain Monte Carlo sampling. The key observation that facilitates effective sampling is that, using one of the BCT algorithms, the prior predictive likelihood of the data can be computed exactly, integrating out all the models and parameters in each segment. This makes it possible to sample directly from the posterior distribution of the number and location of the change-points, leading to accurate estimates and providing a natural quantitative measure of uncertainty in the results. Estimates of the actual model in each segment can also be obtained, at essentially no additional computational cost. Results on both simulated and real-world data indicate that the proposed methodology performs better than or as well as state-of-the-art techniques.

In this thesis, we focus on the design of an automatic algorithms that provide personalized ranking by adapting to the current conditions. To demonstrate the empirical efficiency of the proposed approaches we investigate their applications for decision making in recommender systems and energy systems domains. For the former, we propose novel algorithm called SAROS that take into account both kinds of feedback for learning over the sequence of interactions. The proposed approach consists in minimizing pairwise ranking loss over blocks constituted by a sequence of non-clicked items followed by the clicked one for each user. We also explore the influence of long memory on the accurateness of predictions. SAROS shows highly competitive and promising results based on quality metrics and also it turn out faster in terms of loss convergence than stochastic gradient descent and batch classical approaches. Regarding power systems, we propose an algorithm for faulted lines detection based on focusing of misclassifications in lines close to the true event location. The proposed idea of taking into account the neighbour lines shows statistically significant results in comparison with the initial approach based on convolutional neural networks for faults detection in power grid.

Abstract--Balancing the trade-off between safety and efficiency paths in uncertain environments, especially under nonconvex and is of significant importance for path planning under uncertainty. The initial paths are often of poor Many risk-aware path planners have been developed to explicitly quality as well. Therefore, we propose the NR-RRT algorithm limit the probability of collision to an acceptable bound in to rapidly find near-optimal solutions with guaranteed bounded uncertain environments. It utilizes an informed bidirectional search strategy after uncertainties are usually assumed to make the problem tractable having past experiences in those challenging environments. These assumptions limit the generalization RRT can be applied in not only seen but also unseen uncertain and application of path planners in real-world implementations. However, the algorithm cannot handle entirely unseen In this article, we propose to apply deep learning methods to environments that contain new or additional obstacles. In future the sampling-based planner, developing a novel risk bounded research, we will address the problem of planning under robot near-optimal path planning algorithm named neural risk-aware model uncertainty. Specifically, a deterministic risk contours map is Index Terms--Planning under uncertainty, Sampling-based maintained by perceiving the probabilistic nonconvex obstacles, path planning, Learning from demonstration. and a neural network sampler is proposed to predict the next most-promising safe state.

Humanity has been waiting for self-driving cars for several decades. Thanks to the extremely fast evolution of technology, this idea recently went from "possible" to "commercially available in a Tesla". Deep learning is one of the main technologies that enabled self-driving. It's a versatile tool that can solve almost any problem – it can be used in physics, for example, the proton-proton collision in the Large Hadron Collider, just as well as in Google Lens to classify pictures. Deep learning is a technology that can help solve almost any type of science or engineering problem. CNN is the primary algorithm that these systems use to recognize and classify different parts of the road, and to make appropriate decisions. Along the way, we'll see how Tesla, Waymo, and Nvidia use CNN algorithms to make their cars driverless or autonomous. The first self-driving car was invented in 1989, it was the Automatic Land Vehicle in Neural Network (ALVINN). It used neural networks to detect lines, segment the environment, navigate itself, and drive. It worked well, but it was limited by slow processing powers and insufficient data.

Autonomous systems that operate in the open world often use incomplete models of their environment. Model incompleteness is inevitable due to the practical limitations in precise model specification and data collection about open-world environments. Due to the limited fidelity of the model, agent actions may produce negative side effects (NSEs) when deployed. Negative side effects are undesirable, unmodeled effects of agent actions on the environment. NSEs are inherently challenging to identify at design time and may affect the reliability, usability and safety of the system. We present two complementary approaches to mitigate the NSE via: (1) learning from feedback, and (2) environment shaping. The solution approaches target settings with different assumptions and agent responsibilities. In learning from feedback, the agent learns a penalty function associated with a NSE. We investigate the efficiency of different feedback mechanisms, including human feedback and autonomous exploration. The problem is formulated as a multi-objective Markov decision process such that optimizing the agent’s assigned task is prioritized over mitigating NSE. A slack parameter denotes the maximum allowed deviation from the optimal expected reward for the agent’s task in order to mitigate NSE. In environment shaping, we examine how a human can assist an agent, beyond providing feedback, and utilize their broader scope of knowledge to mitigate the impacts of NSE. We formulate the problem as a human-agent collaboration with decoupled objectives. The agent optimizes its assigned task and may produce NSE during its operation. The human assists the agent by performing modest reconfigurations of the environment so as to mitigate the impacts of NSE, without affecting the agent’s ability to complete its assigned task. We present an algorithm for shaping and analyze its properties. Empirical evaluations demonstrate the trade-offs in the performance of different approaches in mitigating NSE in different settings.

Deep reinforcement learning (DRL) has made significant achievements in many real-world applications. But these real-world applications typically can only provide partial observations for making decisions due to occlusions and noisy sensors. However, partial state observability can be used to hide malicious behaviors for backdoors. In this paper, we explore the sequential nature of DRL and propose a novel temporal-pattern backdoor attack to DRL, whose trigger is a set of temporal constraints on a sequence of observations rather than a single observation, and effect can be kept in a controllable duration rather than in the instant. We validate our proposed backdoor attack to a typical job scheduling task in cloud computing. Numerous experimental results show that our backdoor can achieve excellent effectiveness, stealthiness, and sustainability. Our backdoor's average clean data accuracy and attack success rate can reach 97.8% and 97.5%, respectively.