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.

A major concern of Machine Learning (ML) models is their opacity. They are deployed in an increasing number of applications where they often operate as black boxes that do not provide explanations for their predictions. Among others, the potential harms associated with the lack of understanding of the models' rationales include privacy violations, adversarial manipulations, and unfair discrimination. As a result, the accountability and transparency of ML models have been posed as critical desiderata by works in policy and law, philosophy, and computer science. In computer science, the decision-making process of ML models has been studied by developing accountability and transparency methods. Accountability methods, such as adversarial attacks and diagnostic datasets, expose vulnerabilities of ML models that could lead to malicious manipulations or systematic faults in their predictions. Transparency methods explain the rationales behind models' predictions gaining the trust of relevant stakeholders and potentially uncovering mistakes and unfairness in models' decisions. To this end, transparency methods have to meet accountability requirements as well, e.g., being robust and faithful to the underlying rationales of a model. This thesis presents my research that expands our collective knowledge in the areas of accountability and transparency of ML models developed for complex reasoning tasks over text.

Many recent perturbation studies have found unintuitive results on what does and does not matter when performing Natural Language Understanding (NLU) tasks in English. Coding properties, such as the order of words, can often be removed through shuffling without impacting downstream performances. Such insight may be used to direct future research into English NLP models. As many improvements in multilingual settings consist of wholesale adaptation of English approaches, it is important to verify whether those studies replicate or not in multilingual settings. In this work, we replicate a study on the importance of local structure, and the relative unimportance of global structure, in a multilingual setting. We find that the phenomenon observed on the English language broadly translates to over 120 languages, with a few caveats.

Large language models (LLMs) have led to a series of breakthroughs in natural language processing (NLP), owing to their excellent understanding and generation abilities. Remarkably, what further sets these models apart is the massive amounts of world knowledge they internalize during pretraining. While many downstream applications provide the model with an informational context to aid its performance on the underlying task, how the model's world knowledge interacts with the factual information presented in the context remains under explored. As a desirable behavior, an LLM should give precedence to the context whenever it contains task-relevant information that conflicts with the model's memorized knowledge. This enables model predictions to be grounded in the context, which can then be used to update or correct specific model predictions without frequent retraining. By contrast, when the context is irrelevant to the task, the model should ignore it and fall back on its internal knowledge. In this paper, we undertake a first joint study of the aforementioned two properties, namely controllability and robustness, in the context of LLMs. We demonstrate that state-of-the-art T5 and PaLM (both pretrained and finetuned) could exhibit poor controllability and robustness, which do not scale with increasing model size. As a solution, we propose a novel method - Knowledge Aware FineTuning (KAFT) - to strengthen both controllability and robustness by incorporating counterfactual and irrelevant contexts to standard supervised datasets. Our comprehensive evaluation showcases the utility of KAFT across model architectures and sizes.

We propose an algorithm for learning a conditional generative model of a molecule given a target. Specifically, given a receptor molecule that one wishes to bind to, the conditional model generates candidate ligand molecules that may bind to it. The distribution should be invariant to rigid body transformations that act $\textit{jointly}$ on the ligand and the receptor; it should also be invariant to permutations of either the ligand or receptor atoms. Our learning algorithm is based on a continuous normalizing flow. We establish semi-equivariance conditions on the flow which guarantee the aforementioned invariance conditions on the conditional distribution. We propose a graph neural network architecture which implements this flow, and which is designed to learn effectively despite the vast differences in size between the ligand and receptor. We evaluate our method on the CrossDocked2020 dataset, attaining a significant improvement in binding affinity over competing methods.

A key challenge in science and engineering is to design experiments to learn about some unknown quantity of interest. Classical experimental design optimally allocates the experimental budget to maximize a notion of utility (e.g., reduction in uncertainty about the unknown quantity). We consider a rich setting, where the experiments are associated with states in a {\em Markov chain}, and we can only choose them by selecting a {\em policy} controlling the state transitions. This problem captures important applications, from exploration in reinforcement learning to spatial monitoring tasks. We propose an algorithm -- \textsc{markov-design} -- that efficiently selects policies whose measurement allocation \emph{provably converges to the optimal one}. The algorithm is sequential in nature, adapting its choice of policies (experiments) informed by past measurements. In addition to our theoretical analysis, we showcase our framework on applications in ecological surveillance and pharmacology.

Providing better language tools for low-resource and endangered languages is imperative for equitable growth. Recent progress with massively multilingual pretrained models has proven surprisingly effective at performing zero-shot transfer to a wide variety of languages. However, this transfer is not universal, with many languages not currently understood by multilingual approaches. It is estimated that only 72 languages possess a "small set of labeled datasets" on which we could test a model's performance, the vast majority of languages not having the resources available to simply evaluate performances on. In this work, we attempt to clarify which languages do and do not currently benefit from such transfer. To that end, we develop a general approach that requires only unlabelled text to detect which languages are not well understood by a cross-lingual model. Our approach is derived from the hypothesis that if a model's understanding is insensitive to perturbations to text in a language, it is likely to have a limited understanding of that language. We construct a cross-lingual sentence similarity task to evaluate our approach empirically on 350, primarily low-resource, languages.

Misinformation spread over social media has become an undeniable infodemic. However, not all spreading claims are made equal. If propagated, some claims can be destructive, not only on the individual level, but to organizations and even countries. Detecting claims that should be prioritized for fact-checking is considered the first step to fight against spread of fake news. With training data limited to a handful of languages, developing supervised models to tackle the problem over lower-resource languages is currently infeasible. Therefore, our work aims to investigate whether we can use existing datasets to train models for predicting worthiness of verification of claims in tweets in other languages. We present a systematic comparative study of six approaches for cross-lingual check-worthiness estimation across pairs of five diverse languages with the help of Multilingual BERT (mBERT) model. We run our experiments using a state-of-the-art multilingual Twitter dataset. Our results show that for some language pairs, zero-shot cross-lingual transfer is possible and can perform as good as monolingual models that are trained on the target language. We also show that in some languages, this approach outperforms (or at least is comparable to) state-of-the-art models.

Our team, Hibikino-Musashi@Home (the shortened name is HMA), was founded in 2010. It is based in the Kitakyushu Science and Research Park, Japan. We have participated in the RoboCup@Home Japan open competition open platform league every year since 2010. Moreover, we participated in the RoboCup 2017 Nagoya as open platform league and domestic standard platform league teams. Currently, the Hibikino-Musashi@Home team has 20 members from seven different laboratories based in the Kyushu Institute of Technology. In this paper, we introduce the activities of our team and the technologies.

Streets networks provide an invaluable source of information about the different temporal and spatial patterns emerging in our cities. These streets are often represented as graphs where intersections are modelled as nodes and streets as links between them. Previous work has shown that raster representations of the original data can be created through a learning algorithm on low-dimensional representations of the street networks. In contrast, models that capture high-level urban network metrics can be trained through convolutional neural networks. However, the detailed topological data is lost through the rasterisation of the street network. The models cannot recover this information from the image alone, failing to capture complex street network features. This paper proposes a model capable of inferring good representations directly from the street network. Specifically, we use a variational autoencoder with graph convolutional layers and a decoder that outputs a probabilistic fully-connected graph to learn latent representations that encode both local network structure and the spatial distribution of nodes. We train the model on thousands of street network segments and use the learnt representations to generate synthetic street configurations. Finally, we proposed a possible application to classify the urban morphology of different network segments by investigating their common characteristics in the learnt space.