Agent-based modeling is indispensable for studying complex systems across many domains. However, existing simulation platforms exhibit two major issues: performance and modularity. Low performance prevents simulations with a large number of agents, increases development time, limits parameter exploration, and raises computing costs. Inflexible software designs motivate modelers to create their own tools, diverting valuable resources. This dissertation introduces a novel simulation platform called BioDynaMo and its significant improvement, TeraAgent, to alleviate these challenges via three major works. First, we lay the platform's foundation by defining abstractions, establishing software infrastructure, and implementing a multitude of features for agent-based modeling. We demonstrate BioDynaMo's modularity through use cases in neuroscience, epidemiology, and oncology. We validate these models and show the simplicity of adding new functionality with few lines of code. Second, we perform a rigorous performance analysis and identify challenges for shared-memory parallelism. Provided solutions include an optimized grid for neighbor searching, mechanisms to reduce the memory access latency, and exploiting domain knowledge to omit unnecessary work. These improvements yield up to three orders of magnitude speedups, enabling simulations of 1.7 billion agents on a single server. Third, we present TeraAgent, a distributed simulation engine that allows scaling out the computation of one simulation to multiple servers. We identify and address server communication bottlenecks and implement solutions for serialization and delta encoding to accelerate and reduce data transfer. TeraAgent can simulate 500 billion agents and scales to 84096 CPU cores. BioDynaMo has been widely adopted, including a prize-winning radiotherapy simulation recognized as a top 10 breakthrough in physics in 2024.

Histo-genomic multimodal survival prediction has garnered growing attention for its remarkable model performance and potential contributions to precision medicine. However, a significant challenge in clinical practice arises when only unimodal data is available, limiting the usability of these advanced multimodal methods. To address this issue, this study proposes a prototype-guided cross-modal knowledge enhancement (ProSurv) framework, which eliminates the dependency on paired data and enables robust learning and adaptive survival prediction. Specifically, we first introduce an intra-modal updating mechanism to construct modality-specific prototype banks that encapsulate the statistics of the whole training set and preserve the modality-specific risk-relevant features/prototypes across intervals. Subsequently, the proposed cross-modal translation module utilizes the learned prototypes to enhance knowledge representation for multimodal inputs and generate features for missing modalities, ensuring robust and adaptive survival prediction across diverse scenarios. Extensive experiments on four public datasets demonstrate the superiority of ProSurv over state-of-the-art methods using either unimodal or multimodal input, and the ablation study underscores its feasibility for broad applicability. Overall, this study addresses a critical practical challenge in computational pathology, offering substantial significance and potential impact in the field.

Despite classical statistical theory predicting severe overfitting, modern massively overparameterized neural networks still generalize well. This unexpected property is attributed to the network's so-called implicit bias, which describes its propensity to converge to solutions that generalize effectively, among the many possible that correctly label the training data. The aim of our research is to explore this bias from a new perspective, focusing on how non-linear activation functions contribute to shaping it. First, we introduce a reparameterization which removes a continuous weight rescaling symmetry. Second, in the kernel regime, we leverage this reparameterization to generalize recent findings that relate shallow Neural Networks to the Radon transform, deriving an explicit formula for the implicit bias induced by a broad class of activation functions. Specifically, by utilizing the connection between the Radon transform and the Fourier transform, we interpret the kernel regime's inductive bias as minimizing a spectral seminorm that penalizes high-frequency components, in a manner dependent on the activation function. Finally, in the adaptive regime, we demonstrate the existence of local dynamical attractors that facilitate the formation of clusters of hyperplanes where the input to a neuron's activation function is zero, yielding alignment between many neurons' response functions. We confirm these theoretical results with simulations. All together, our work provides a deeper understanding of the mechanisms underlying the generalization capabilities of overparameterized neural networks and its relation with the implicit bias, offering potential pathways for designing more efficient and robust models.

Discourse understanding is essential for many NLP tasks, yet most existing work remains constrained by framework-dependent discourse representations. This work investigates whether large language models (LLMs) capture discourse knowledge that generalizes across languages and frameworks. We address this question along two dimensions: (1) developing a unified discourse relation label set to facilitate cross-lingual and cross-framework discourse analysis, and (2) probing LLMs to assess whether they encode generalizable discourse abstractions. Using multilingual discourse relation classification as a testbed, we examine a comprehensive set of 23 LLMs of varying sizes and multilingual capabilities. Our results show that LLMs, especially those with multilingual training corpora, can generalize discourse information across languages and frameworks. Further layer-wise analyses reveal that language generalization at the discourse level is most salient in the intermediate layers. Lastly, our error analysis provides an account of challenging relation classes.

Policies generated by Reinforcement Learning (RL) algorithms can be difficult to describe to users, as they result from the interplay between complex reward structures and neural network-based representations. This combination often leads to unpredictable behaviors, making policies challenging to analyze and posing significant obstacles to fostering human trust in real-world applications. Global policy summarization methods aim to describe agent behavior through a demonstration of actions in a subset of world-states. However, users can only watch a limited number of demonstrations, restricting their understanding of policies. Moreover, those methods overly rely on user interpretation, as they do not synthesize observations into coherent patterns. In this work, we present SySLLM (Synthesized Summary using LLMs), a novel method that employs synthesis summarization, utilizing large language models' (LLMs) extensive world knowledge and ability to capture patterns, to generate textual summaries of policies. Specifically, an expert evaluation demonstrates that the proposed approach generates summaries that capture the main insights generated by experts while not resulting in significant hallucinations. Additionally, a user study shows that SySLLM summaries are preferred over demonstration-based policy summaries and match or surpass their performance in objective agent identification tasks.

Continual learning algorithms aim to learn from a sequence of tasks, making the training distribution non-stationary. The majority of existing continual learning approaches in the literature rely on heuristics and do not provide learning guarantees for the continual learning setup. In this paper, we present a new method called 'Continual Pick-to-Learn' (CoP2L), which is able to retain the most representative samples for each task in an efficient way. The algorithm is adapted from the Pick-to-Learn algorithm, rooted in the sample compression theory. This allows us to provide high-confidence upper bounds on the generalization loss of the learned predictors, numerically computable after every update of the learned model. We also empirically show on several standard continual learning benchmarks that our algorithm is able to outperform standard experience replay, significantly mitigating catastrophic forgetting.

Islands are diversity hotspots and vulnerable to environmental degradation, climate variations, land use changes and societal crises. These factors can exhibit interactive impacts on ecosystem services. The study reviewed a large number of papers on the climate change-islands-ecosystem services topic worldwide. Potential inclusion of land use changes and other drivers of impacts on ecosystem services were sequentially also recorded. The study sought to investigate the impacts of climate change, land use change, and other non-climatic driver changes on island ecosystem services. Explanatory variables examined were divided into two categories: environmental variables and methodological ones. Environmental variables include sea zone geographic location, ecosystem, ecosystem services, climate, land use, other driver variables, Methodological variables include consideration of policy interventions, uncertainty assessment, cumulative effects of climate change, synergistic effects of climate change with land use change and other anthropogenic and environmental drivers, and the diversity of variables used in the analysis. Machine learning and statistical methods were used to analyze their effects on island ecosystem services. Negative climate change impacts on ecosystem services are better quantified by land use change or other non-climatic driver variables than by climate variables. The synergy of land use together with climate changes is modulating the impact outcome and critical for a better impact assessment. Analyzed together, there is little evidence of more pronounced for a specific sea zone, ecosystem, or ecosystem service. Climate change impacts may be underestimated due to the use of a single climate variable deployed in most studies. Policy interventions exhibit low classification accuracy in quantifying impacts indicating insufficient efficacy or integration in the studies.

Bio-loggers, electronic devices used to track animal behaviour through various sensors, have become essential in wildlife research. Despite continuous improvements in their capabilities, bio-loggers still face significant limitations in storage, processing, and data transmission due to the constraints of size and weight, which are necessary to avoid disturbing the animals. This study aims to explore how selective data transmission, guided by machine learning, can reduce the energy consumption of bio-loggers, thereby extending their operational lifespan without requiring hardware modifications.

AI alignment, the challenge of ensuring AI systems act in accordance with human values, has emerged as a critical problem in the development of systems such as foundation models and recommender systems. Still, the current dominant approach, reinforcement learning with human feedback (RLHF) faces known theoretical limitations in aggregating diverse human preferences. Social choice theory provides a framework to aggregate preferences, but was not developed for the multidimensional applications typical of AI. Leveraging insights from a recently published urn process, this work introduces a preference aggregation strategy that adapts to the user's context and that inherits the good properties of the maximal lottery, a Condorcet-consistent solution concept.

Time series forecasting (TSF) has long been a crucial task in both industry and daily life. Most classical statistical models may have certain limitations when applied to practical scenarios in fields such as energy, healthcare, traffic, meteorology, and economics, especially when high accuracy is required. With the continuous development of deep learning, numerous new models have emerged in the field of time series forecasting in recent years. However, existing surveys have not provided a unified summary of the wide range of model architectures in this field, nor have they given detailed summaries of works in feature extraction and datasets. To address this gap, in this review, we comprehensively study the previous works and summarize the general paradigms of Deep Time Series Forecasting (DTSF) in terms of model architectures. Besides, we take an innovative approach by focusing on the composition of time series and systematically explain important feature extraction methods. Additionally, we provide an overall compilation of datasets from various domains in existing works. Finally, we systematically emphasize the significant challenges faced and future research directions in this field.