Biochemical reaction networks are an amalgamation of reactions where each reaction represents the interaction of different species. Generally, these networks exhibit a multi-scale behavior caused by the high variability in reaction rates and abundances of species. The so-called jump-diffusion approximation is a valuable tool in the modeling of such systems. The approximation is constructed by partitioning the reaction network into a fast and slow subgroup of fast and slow reactions, respectively. This enables the modeling of the dynamics using a Langevin equation for the fast group, while a Markov jump process model is kept for the dynamics of the slow group. Most often biochemical processes are poorly characterized in terms of parameters and population states. As a result of this, methods for estimating hidden quantities are of significant interest. In this paper, we develop a tractable Bayesian inference algorithm based on Markov chain Monte Carlo. The presented blocked Gibbs particle smoothing algorithm utilizes a sequential Monte Carlo method to estimate the latent states and performs distinct Gibbs steps for the parameters of a biochemical reaction network, by exploiting a jump-diffusion approximation model. The presented blocked Gibbs sampler is based on the two distinct steps of state inference and parameter inference. We estimate states via a continuous-time forward-filtering backward-smoothing procedure in the state inference step. By utilizing bootstrap particle filtering within a backward-smoothing procedure, we sample a smoothing trajectory. For estimating the hidden parameters, we utilize a separate Markov chain Monte Carlo sampler within the Gibbs sampler that uses the path-wise continuous-time representation of the reaction counters. Finally, the algorithm is numerically evaluated for a partially observed multi-scale birth-death process example.

The neural boom that has sparked natural language processing (NLP) research through the last decade has similarly led to significant innovations in data-to-text generation (DTG). This survey offers a consolidated view into the neural DTG paradigm with a structured examination of the approaches, benchmark datasets, and evaluation protocols. This survey draws boundaries separating DTG from the rest of the natural language generation (NLG) landscape, encompassing an up-to-date synthesis of the literature, and highlighting the stages of technological adoption from within and outside the greater NLG umbrella. With this holistic view, we highlight promising avenues for DTG research that not only focus on the design of linguistically capable systems but also systems that exhibit fairness and accountability.

Modeling and control of epidemics such as the novel Corona virus have assumed paramount importance at a global level. A natural and powerful dynamical modeling framework to use in this context is a continuous time Markov decision process (CTMDP) that encompasses classical compartmental paradigms such as the Susceptible-Infected-Recovered (SIR) model. The challenges with CTMDP based models motivate the need for a more efficient approach and the mean field approach offers an effective alternative. The mean field approach computes the collective behavior of a dynamical system comprising numerous interacting nodes (where nodes represent individuals in the population). This paper (a) presents an overview of the mean field approach to epidemic modeling and control and (b) provides a state-of-the-art update on recent advances on this topic. Our discussion in this paper proceeds along two specific threads. The first thread assumes that the individual nodes faithfully follow a socially optimal control policy prescribed by a regulatory authority. The second thread allows the individual nodes to exhibit independent, strategic behavior. In this case, the strategic interaction is modeled as a mean field game and the control is based on the associated mean field Nash equilibria. In this paper, we start with a discussion of modeling of epidemics using an extended compartmental model - SIVR and provide an illustrative example. We next provide a review of relevant literature, using a mean field approach, on optimal control of epidemics, dealing with how a regulatory authority may optimally contain epidemic spread in a population. Following this, we provide an update on the literature on the use of the mean field game based approach in the study of epidemic spread and control. We conclude the paper with relevant future research directions.

Despite their potential in real-world applications, multi-agent reinforcement learning (MARL) algorithms often suffer from high sample complexity. To address this issue, we present a novel model-based MARL algorithm, BiLL (Bi-Level Latent Variable Model-based Learning), that learns a bi-level latent variable model from high-dimensional inputs. At the top level, the model learns latent representations of the global state, which encode global information relevant to behavior learning. At the bottom level, it learns latent representations for each agent, given the global latent representations from the top level. The model generates latent trajectories to use for policy learning. We evaluate our algorithm on complex multi-agent tasks in the challenging SMAC and Flatland environments. Our algorithm outperforms state-of-the-art model-free and model-based baselines in sample efficiency, including on two extremely challenging Super Hard SMAC maps.

We consider the problem of cooperative exploration where multiple robots need to cooperatively explore an unknown region as fast as possible. Multi-agent reinforcement learning (MARL) has recently become a trending paradigm for solving this challenge. However, existing MARL-based methods adopt action-making steps as the metric for exploration efficiency by assuming all the agents are acting in a fully synchronous manner: i.e., every single agent produces an action simultaneously and every single action is executed instantaneously at each time step. Despite its mathematical simplicity, such a synchronous MARL formulation can be problematic for real-world robotic applications. It can be typical that different robots may take slightly different wall-clock times to accomplish an atomic action or even periodically get lost due to hardware issues. Simply waiting for every robot being ready for the next action can be particularly time-inefficient. Therefore, we propose an asynchronous MARL solution, Asynchronous Coordination Explorer (ACE), to tackle this real-world challenge. We first extend a classical MARL algorithm, multi-agent PPO (MAPPO), to the asynchronous setting and additionally apply action-delay randomization to enforce the learned policy to generalize better to varying action delays in the real world. Moreover, each navigation agent is represented as a team-size-invariant CNN-based policy, which greatly benefits real-robot deployment by handling possible robot lost and allows bandwidth-efficient intra-agent communication through low-dimensional CNN features. We first validate our approach in a grid-based scenario. Both simulation and real-robot results show that ACE reduces over 10% actual exploration time compared with classical approaches. We also apply our framework to a high-fidelity visual-based environment, Habitat, achieving 28% improvement in exploration efficiency.

Interpretability of AI models allows for user safety checks to build trust in these models. In particular, decision trees (DTs) provide a global view on the learned model and clearly outlines the role of the features that are critical to classify a given data. However, interpretability is hindered if the DT is too large. To learn compact trees, a Reinforcement Learning (RL) framework has been recently proposed to explore the space of DTs. A given supervised classification task is modeled as a Markov decision problem (MDP) and then augmented with additional actions that gather information about the features, equivalent to building a DT. By appropriately penalizing these actions, the RL agent learns to optimally trade-off size and performance of a DT. However, to do so, this RL agent has to solve a partially observable MDP. The main contribution of this paper is to prove that it is sufficient to solve a fully observable problem to learn a DT optimizing the interpretability-performance trade-off. As such any planning or RL algorithm can be used. We demonstrate the effectiveness of this approach on a set of classical supervised classification datasets and compare our approach with other interpretability-performance optimizing methods.

The Markov decision process (MDP) provides a mathematical framework for modeling sequential decision-making problems, many of which are crucial to security and safety, such as autonomous driving and robot control. The rapid development of artificial intelligence research has created efficient methods for solving MDPs, such as deep neural networks (DNNs), reinforcement learning (RL), and imitation learning (IL). However, these popular models solving MDPs are neither thoroughly tested nor rigorously reliable. We present MDPFuzz, the first blackbox fuzz testing framework for models solving MDPs. MDPFuzz forms testing oracles by checking whether the target model enters abnormal and dangerous states. During fuzzing, MDPFuzz decides which mutated state to retain by measuring if it can reduce cumulative rewards or form a new state sequence. We design efficient techniques to quantify the "freshness" of a state sequence using Gaussian mixture models (GMMs) and dynamic expectation-maximization (DynEM). We also prioritize states with high potential of revealing crashes by estimating the local sensitivity of target models over states. MDPFuzz is evaluated on five state-of-the-art models for solving MDPs, including supervised DNN, RL, IL, and multi-agent RL. Our evaluation includes scenarios of autonomous driving, aircraft collision avoidance, and two games that are often used to benchmark RL. During a 12-hour run, we find over 80 crash-triggering state sequences on each model. We show inspiring findings that crash-triggering states, though they look normal, induce distinct neuron activation patterns compared with normal states. We further develop an abnormal behavior detector to harden all the evaluated models and repair them with the findings of MDPFuzz to significantly enhance their robustness without sacrificing accuracy.

We consider online reinforcement learning in Mean-Field Games (MFGs). Unlike traditional approaches, we alleviate the need for a mean-field oracle by developing an algorithm that approximates the Mean-Field Equilibrium (MFE) using the single sample path of the generic agent. We call this {\it Sandbox Learning}, as it can be used as a warm-start for any agent learning in a multi-agent non-cooperative setting. We adopt a two time-scale approach in which an online fixed-point recursion for the mean-field operates on a slower time-scale, in tandem with a control policy update on a faster time-scale for the generic agent. Given that the underlying Markov Decision Process (MDP) of the agent is communicating, we provide finite sample convergence guarantees in terms of convergence of the mean-field and control policy to the mean-field equilibrium. The sample complexity of the Sandbox learning algorithm is $\tilde{\mathcal{O}}(\epsilon^{-4})$ where $\epsilon$ is the MFE approximation error. This is similar to works which assume access to oracle. Finally, we empirically demonstrate the effectiveness of the sandbox learning algorithm in diverse scenarios, including those where the MDP does not necessarily have a single communicating class.

This work proposes a data driven learning model for the synthesis of keystroke biometric data. The proposed method is compared with two statistical approaches based on Universal and User-dependent models. These approaches are validated on the bot detection task, using the keystroke synthetic data to improve the training process of keystroke-based bot detection systems. Our experimental framework considers a dataset with 136 million keystroke events from 168 thousand subjects. We have analyzed the performance of the three synthesis approaches through qualitative and quantitative experiments. Different bot detectors are considered based on several supervised classifiers (Support Vector Machine, Random Forest, Gaussian Naive Bayes and a Long Short-Term Memory network) and a learning framework including human and synthetic samples. The experiments demonstrate the realism of the synthetic samples. The classification results suggest that in scenarios with large labeled data, these synthetic samples can be detected with high accuracy. However, in few-shot learning scenarios it represents an important challenge. Furthermore, these results show the great potential of the presented models.

We develop a latent variable model and an efficient spectral algorithm motivated by the recent emergence of very large data sets of chromatin marks from multiple human cell types. A natural model for chromatin data in one cell type is a Hidden Markov Model (HMM); we model the relationship between multiple cell types by connecting their hidden states by a fixed tree of known structure. The main challenge with learning parameters of such models is that iterative methods such as EM are very slow, while naive spectral methods result in time and space complexity exponential in the number of cell types. We exploit properties of the tree structure of the hidden states to provide spectral algorithms that are more computationally efficient for current biological datasets. We provide sample complexity bounds for our algorithm and evaluate it experimentally on biological data from nine human cell types. Finally, we show that beyond our specific model, some of our algorithmic ideas can be applied to other graphical models.