Sequential design of real and computer experiments via Gaussian Process (GP) models has proven useful for parsimonious, goal-oriented data acquisition purposes. In this work, we focus on acquisition strategies for a GP model that needs to be accurate within a predefined range of the response of interest. Such an approach is useful in various fields including synthetic chemistry, where finding molecules with particular properties is essential for developing useful materials and effective medications. GP modeling and sequential design of experiments have been successfully applied to a plethora of domains, including molecule research. Our main contribution here is to use the threshold-weighted Continuous Ranked Probability Score (CRPS) as a basic building block for acquisition functions employed within sequential design. We study pointwise and integral criteria relying on two different weighting measures and benchmark them against competitors, demonstrating improved performance with respect to considered goals. The resulting acquisition strategies are applicable to a wide range of fields and pave the way to further developing sequential design relying on scoring rules.

Despite the ever-growing importance of online moderation, there has been no large-scale study evaluating the effectiveness of alternative moderation strategies. This is largely due to the lack of appropriate datasets, and the difficulty of getting human discussants, moderators, and evaluators involved in multiple experiments. In this paper, we propose a methodology for leveraging synthetic experiments performed exclusively by Large Language Models (LLMs) to initially bypass the need for human participation in experiments involving online moderation. We evaluate six LLM moderation configurations; two currently used real-life moderation strategies (guidelines issued for human moderators for online moderation and real-life facilitation), two baseline strategies (guidelines elicited for LLM alignment work, and LLM moderation with minimal prompting) a baseline with no moderator at all, as well as our own proposed strategy inspired by a Reinforcement Learning (RL) formulation of the problem. We find that our own moderation strategy significantly outperforms established moderation guidelines, as well as out-of-the-box LLM moderation. We also find that smaller LLMs, with less intensive instruction-tuning, can create more varied discussions than larger models. In order to run these experiments, we create and release an efficient, purpose-built, open-source Python framework, dubbed "SynDisco" to easily simulate hundreds of discussions using LLM user-agents and moderators. Additionally, we release the Virtual Moderation Dataset (VMD), a large dataset of LLM-generated and LLM-annotated discussions, generated by three families of open-source LLMs accompanied by an exploratory analysis of the dataset.

The structural analogies of ResNets and Multigrid (MG) methods such as common building blocks like convolutions and poolings where already pointed out by He et al.\ in 2016. Multigrid methods are used in the context of scientific computing for solving large sparse linear systems arising from partial differential equations. MG methods particularly rely on two main concepts: smoothing and residual restriction / coarsening. Exploiting these analogies, He and Xu developed the MgNet framework, which integrates MG schemes into the design of ResNets. In this work, we introduce a novel neural network building block inspired by polynomial smoothers from MG theory. Our polynomial block from an MG perspective naturally extends the MgNet framework to Poly-Mgnet and at the same time reduces the number of weights in MgNet. We present a comprehensive study of our polynomial block, analyzing the choice of initial coefficients, the polynomial degree, the placement of activation functions, as well as of batch normalizations. Our results demonstrate that constructing (quadratic) polynomial building blocks based on real and imaginary polynomial roots enhances Poly-MgNet's capacity in terms of accuracy. Furthermore, our approach achieves an improved trade-off of model accuracy and number of weights compared to ResNet as well as compared to specific configurations of MgNet.

While Large Language Models (LLMs) have significantly advanced natural language processing, aligning them with human preferences remains an open challenge. Although current alignment methods rely primarily on explicit feedback, eye-tracking (ET) data offers insights into real-time cognitive processing during reading. In this paper, we present OASST-ETC, a novel eye-tracking corpus capturing reading patterns from 24 participants, while evaluating LLM-generated responses from the OASST1 dataset. Our analysis reveals distinct reading patterns between preferred and non-preferred responses, which we compare with synthetic eye-tracking data. Furthermore, we examine the correlation between human reading measures and attention patterns from various transformer-based models, discovering stronger correlations in preferred responses. This work introduces a unique resource for studying human cognitive processing in LLM evaluation and suggests promising directions for incorporating eye-tracking data into alignment methods. The dataset and analysis code are publicly available.

Mechanistic interpretability has made great strides in identifying neural network features (e.g., directions in hidden activation space) that mediate concepts(e.g., the birth year of a person) and enable predictable manipulation. Distributed alignment search (DAS) leverages supervision from counterfactual data to learn concept features within hidden states, but DAS assumes we can afford to conduct a brute force search over potential feature locations. To address this, we present HyperDAS, a transformer-based hypernetwork architecture that (1) automatically locates the token-positions of the residual stream that a concept is realized in and (2) constructs features of those residual stream vectors for the concept. In experiments with Llama3-8B, HyperDAS achieves state-of-the-art performance on the RAVEL benchmark for disentangling concepts in hidden states. In addition, we review the design decisions we made to mitigate the concern that HyperDAS (like all powerful interpretabilty methods) might inject new information into the target model rather than faithfully interpreting it.

Earth observation (EO) data features diverse sensing platforms with varying spectral bands, spatial resolutions, and sensing modalities. While most prior work has constrained inputs to fixed sensors, a new class of any-sensor foundation models able to process arbitrary sensors has recently emerged. Contributing to this line of work, we propose Panopticon, an any-sensor foundation model built on the DINOv2 framework. We extend DINOv2 by (1) treating images of the same geolocation across sensors as natural augmentations, (2) subsampling channels to diversify spectral input, and (3) adding a cross attention over channels as a flexible patch embedding mechanism. By encoding the wavelength and modes of optical and synthetic aperture radar sensors, respectively, Panopticon can effectively process any combination of arbitrary channels. In extensive evaluations, we achieve state-of-the-art performance on GEO-Bench, especially on the widely-used Sentinel-1 and Sentinel-2 sensors, while out-competing other any-sensor models, as well as domain adapted fixed-sensor models on unique sensor configurations. Panopticon enables immediate generalization to both existing and future satellite platforms, advancing sensor-agnostic EO.

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.

Software testing and verification are critical for ensuring the reliability and security of modern software systems. Traditionally, formal verification techniques, such as model checking and theorem proving, have provided rigorous frameworks for detecting bugs and vulnerabilities. However, these methods often face scalability challenges when applied to complex, real-world programs. Recently, the advent of Large Language Models (LLMs) has introduced a new paradigm for software analysis, leveraging their ability to understand insecure coding practices. Although LLMs demonstrate promising capabilities in tasks such as bug prediction and invariant generation, they lack the formal guarantees of classical methods. This paper presents a comprehensive study of state-of-the-art software testing and verification, focusing on three key approaches: classical formal methods, LLM-based analysis, and emerging hybrid techniques, which combine their strengths. We explore each approach's strengths, limitations, and practical applications, highlighting the potential of hybrid systems to address the weaknesses of standalone methods. We analyze whether integrating formal rigor with LLM-driven insights can enhance the effectiveness and scalability of software verification, exploring their viability as a pathway toward more robust and adaptive testing frameworks.

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.

Transformer models have demonstrated exceptional performance across a wide range of applications. Though forming the foundation of Transformer models, the dot-product attention does not scale well to long-context data since its time requirement grows quadratically with context length. In this work, we propose Radar, a training-free approach that accelerates inference by dynamically searching for the most important context tokens. For any pre-trained Transformer, Radar can reduce the decoding time complexity without training or heuristically evicting tokens. Moreover, we provide theoretical justification for our approach, demonstrating that Radar can reliably identify the most important tokens with high probability. We conduct extensive comparisons with the previous methods on a wide range of tasks. The results demonstrate that Radar achieves the state-of-the-art performance across different architectures with reduced time complexity, offering a practical solution for efficient long-context processing of Transformers. The code is publicly available at https://github.com/BorealisAI/ In particular, Transformer models take each input as a sequence of tokens and compute the embedding of each token for downstream tasks. Among all components, the dot-product attention has been shown to be critical to the success of Transformer models (Choromanski et al., 2021). It not only enables parallel computation of sequences during training (Vyas et al., 2020), but also provides a high-quality method for sequence modeling (Sanford et al., 2023). Despite being at the core of Transformer models, the dot-product attention is not ideal for long-context data: the time to process each token increases with context lengths, significantly slowing down the throughput on long-context data. Moreover, the maximum context length is limited during training, resulting in an inability to perform inference on long-context tasks. Y et, many real-world applications are naturally long-context (Tay et al., 2021; Beltagy et al., 2020; Wu et al., 2024). For example, a code file could have more than 10K tokens (Lozhkov et al., 2024; Kocetkov et al., 2022).