Agent-based modeling (ABM) is a well-established paradigm for simulating complex systems via interactions between constituent entities. Machine learning (ML) refers to approaches whereby statistical algorithms 'learn' from data on their own, without imposing a priori theories of system behavior. Biological systems -- from molecules, to cells, to entire organisms -- consist of vast numbers of entities, governed by complex webs of interactions that span many spatiotemporal scales and exhibit nonlinearity, stochasticity and intricate coupling between entities. The macroscopic properties and collective dynamics of such systems are difficult to capture via continuum modelling and mean-field formalisms. ABM takes a 'bottom-up' approach that obviates these difficulties by enabling one to easily propose and test a set of well-defined 'rules' to be applied to the individual entities (agents) in a system. Evaluating a system and propagating its state over discrete time-steps effectively simulates the system, allowing observables to be computed and system properties to be analyzed. Because the rules that govern an ABM can be difficult to abstract and formulate from experimental data, there is an opportunity to use ML to help infer optimal, system-specific ABM rules. Once such rule-sets are devised, ABM calculations can generate a wealth of data, and ML can be applied there too -- e.g., to probe statistical measures that meaningfully describe a system's stochastic properties. As an example of synergy in the other direction (from ABM to ML), ABM simulations can generate realistic datasets for training ML algorithms (e.g., for regularization, to mitigate overfitting). In these ways, one can envision various synergistic ABM$\rightleftharpoons$ML loops. This review summarizes how ABM and ML have been integrated in contexts that span spatiotemporal scales, from cellular to population-level epidemiology.

Prediction failures of machine learning models often arise from deficiencies in training data, such as incorrect labels, outliers, and selection biases. However, such data points that are responsible for a given failure mode are generally not known a priori, let alone a mechanism for repairing the failure. This work draws on the Bayesian view of continual learning, and develops a generic framework for both, identifying training examples which have given rise to the target failure, and fixing the model through erasing information about them. This framework naturally allows leveraging recent advances in continual learning to this new problem of model repairment, while subsuming the existing works on influence functions and data deletion as specific instances. Experimentally, the proposed approach outperforms the baselines for both identification of detrimental training data and fixing model failures in a generalisable manner.

Fairness-aware mining of massive data streams is a growing and challenging concern in the contemporary domain of machine learning. Many stream learning algorithms are used to replace humans at critical decision-making points e.g., hiring staff, assessing credit risk, etc. This calls for handling massive incoming information with minimum response delay while ensuring fair and high quality decisions. Recent discrimination-aware learning methods are optimized based on overall accuracy. However, the overall accuracy is biased in favor of the majority class; therefore, state-of-the-art methods mainly diminish discrimination by partially or completely ignoring the minority class. In this context, we propose a novel adaptation of Na\"ive Bayes to mitigate discrimination embedded in the streams while maintaining high predictive performance for both the majority and minority classes. Our proposed algorithm is simple, fast, and attains multi-objective optimization goals. To handle class imbalance and concept drifts, a dynamic instance weighting module is proposed, which gives more importance to recent instances and less importance to obsolete instances based on their membership in minority or majority class. We conducted experiments on a range of streaming and static datasets and deduced that our proposed methodology outperforms existing state-of-the-art fairness-aware methods in terms of both discrimination score and balanced accuracy.

Identifying novel drug-target interactions (DTI) is a critical and rate limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, we show that state-of-the-art models fail to generalize to novel (i.e., never-before-seen) structures. We first unveil the mechanisms responsible for this shortcoming, demonstrating how models rely on shortcuts that leverage the topology of the protein-ligand bipartite network, rather than learning the node features. Then, we introduce AI-Bind, a pipeline that combines network-based sampling strategies with unsupervised pre-training, allowing us to limit the annotation imbalance and improve binding predictions for novel proteins and ligands. We illustrate the value of AI-Bind by predicting drugs and natural compounds with binding affinity to SARS-CoV-2 viral proteins and the associated human proteins. We also validate these predictions via docking simulations and comparison with recent experimental evidence, and step up the process of interpreting machine learning prediction of protein-ligand binding by identifying potential active binding sites on the amino acid sequence. Overall, AI-Bind offers a powerful high-throughput approach to identify drug-target combinations, with the potential of becoming a powerful tool in drug discovery.

With most technical fields, there exists a delay between fundamental academic research and practical industrial uptake. Whilst some sciences have robust and well-established processes for commercialisation, such as the pharmaceutical practice of regimented drug trials, other fields face transitory periods in which fundamental academic advancements diffuse gradually into the space of commerce and industry. For the still relatively young field of Automated/Autonomous Machine Learning (AutoML/AutonoML), that transitory period is under way, spurred on by a burgeoning interest from broader society. Yet, to date, little research has been undertaken to assess the current state of this dissemination and its uptake. Thus, this review makes two primary contributions to knowledge around this topic. Firstly, it provides the most up-to-date and comprehensive survey of existing AutoML tools, both open-source and commercial. Secondly, it motivates and outlines a framework for assessing whether an AutoML solution designed for real-world application is 'performant'; this framework extends beyond the limitations of typical academic criteria, considering a variety of stakeholder needs and the human-computer interactions required to service them. Thus, additionally supported by an extensive assessment and comparison of academic and commercial case-studies, this review evaluates mainstream engagement with AutoML in the early 2020s, identifying obstacles and opportunities for accelerating future uptake.

This paper revisits the work of Rauch et al. (1965) and develops a novel method for recursive maximum likelihood particle filtering for general state-space models. The new method is based on statistical analysis of incomplete observations of the systems. Score function and conditional observed information of the incomplete observations/data are introduced and their distributional properties are discussed. Some identities concerning the score function and information matrices of the incomplete data are derived. Maximum likelihood estimation of state-vector is presented in terms of the score function and observed information matrices. In particular, to deal with nonlinear state-space, a sequential Monte Carlo method is developed. It is given recursively by an EM-gradient-particle filtering which extends the work of Lange (1995) for state estimation. To derive covariance matrix of state-estimation errors, an explicit form of observed information matrix is proposed. It extends Louis (1982) general formula for the same matrix to state-vector estimation. Under (Neumann) boundary conditions of state transition probability distribution, the inverse of this matrix coincides with the Cramer-Rao lower bound on the covariance matrix of estimation errors of unbiased state-estimator. In the case of linear models, the method shows that the Kalman filter is a fully efficient state estimator whose covariance matrix of estimation error coincides with the Cramer-Rao lower bound. Some numerical examples are discussed to exemplify the main results.

Sampling-based inference techniques are central to modern cosmological data analysis; these methods, however, scale poorly with dimensionality and typically require approximate or intractable likelihoods. In this paper we describe how Truncated Marginal Neural Ratio Estimation (TMNRE) (a new approach in so-called simulation-based inference) naturally evades these issues, improving the $(i)$ efficiency, $(ii)$ scalability, and $(iii)$ trustworthiness of the inferred posteriors. Using measurements of the Cosmic Microwave Background (CMB), we show that TMNRE can achieve converged posteriors using orders of magnitude fewer simulator calls than conventional Markov Chain Monte Carlo (MCMC) methods. Remarkably, the required number of samples is effectively independent of the number of nuisance parameters. In addition, a property called \emph{local amortization} allows the performance of rigorous statistical consistency checks that are not accessible to sampling-based methods. TMNRE promises to become a powerful tool for cosmological data analysis, particularly in the context of extended cosmologies, where the timescale required for conventional sampling-based inference methods to converge can greatly exceed that of simple cosmological models such as $\Lambda$CDM. To perform these computations, we use an implementation of TMNRE via the open-source code \texttt{swyft}.

Causal structure learning from observational data remains a non-trivial task due to various factors such as finite sampling, unobserved confounding factors, and measurement errors. Constraint-based and score-based methods tend to suffer from high computational complexity due to the combinatorial nature of estimating the directed acyclic graph (DAG). Motivated by the `Cause-Effect Pair' NIPS 2013 Workshop on Causality Challenge, in this paper, we take a different approach and generate a probability distribution over all possible graphs informed by the cause-effect pair features proposed in response to the workshop challenge. The goal of the paper is to propose new methods based on this probabilistic information and compare their performance with traditional and state-of-the-art approaches. Our experiments, on both synthetic and real datasets, show that our proposed methods not only have statistically similar or better performances than some traditional approaches but also are computationally faster.

In natural language understanding (NLU) production systems, users' evolving needs necessitate the addition of new features over time, indexed by new symbols added to the meaning representation space. This requires additional training data and results in ever-growing datasets. We present the first systematic investigation of this incremental symbol learning scenario. Our analysis reveals a troubling quirk in building broad-coverage NLU systems: as the training dataset grows, performance on the new symbol often decreases if we do not accordingly increase its training data. This suggests that it becomes more difficult to learn new symbols with a larger training dataset. We show that this trend holds for multiple mainstream models on two common NLU tasks: intent recognition and semantic parsing. Rejecting class imbalance as the sole culprit, we reveal that the trend is closely associated with an effect we call source signal dilution, where strong lexical cues for the new symbol become diluted as the training dataset grows. Selectively dropping training examples to prevent dilution often reverses the trend, showing the over-reliance of mainstream neural NLU models on simple lexical cues. Code, models, and data are available at https://aka.ms/nlu-incremental-symbol-learning

Mission teams are exposed to the emotional toll of life and death decisions. These are small groups of specially trained people supported by intelligent machines for dealing with stressful environments and scenarios. We developed a composite model for stress monitoring in such teams of human and autonomous machines. This modelling aims to identify the conditions that may contribute to mission failure. The proposed model is composed of three parts: 1) a computational logic part that statically describes the stress states of teammates; 2) a decision part that manifests the mission status at any time; 3) a stress propagation part based on standard Susceptible-Infected-Susceptible (SIS) paradigm. In contrast to the approaches such as agent-based, random-walk and game models, the proposed model combines various mechanisms to satisfy the conditions of stress propagation in small groups. Our core approach involves data structures such as decision tables and decision diagrams. These tools are adaptable to human-machine teaming as well.