Abstract--Computational protein design is experiencing a transformation driven by AI/ML. However, the range of potential protein sequences and structures is astronomically vast, even for moderately sized proteins. Hence, achieving convergence between generated and predicted structures demands substantial computational resources for sampling. The Integrated Machine-learning for Protein Structures at Scale (IMPRESS) offers methods and advanced computing systems for coupling AI to high-performance computing tasks, enabling the ability to evaluate the effectiveness of protein designs as they are developed, as well as the models and simulations used to generate data and train models. This paper introduces IMPRESS and demonstrates the development and implementation of an adaptive protein design protocol and its supporting computing infrastructure. This leads to increased consistency in the quality of protein design and enhanced throughput of protein design due to dynamic resource allocation and asynchronous workload execution.

Reward models (RMs) are central to the alignment of language models (LMs). An RM often serves as a proxy for human preferences to guide downstream LM behavior. However, our understanding of RM behavior is limited. Our work (i) formalizes a framework for measuring the alignment of opinions captured by RMs, (ii) investigates the extent to which RMs demonstrate sociodemographic biases, and (iii) explores the effects of prompting to steer rewards towards the preferences of a target group. We study the subjective and diverse perspectives on controversial topics, which allows us to quantify RM perspectives in terms of their opinions, attitudes, and values. We show that RMs are poorly aligned with several demographic groups and can systematically reward harmful stereotypes, and steering alone is not enough to overcome these limitations. Our findings underscore the need for more careful consideration of RM behavior in model alignment during preference learning to prevent the propagation of unwanted social biases in the language technologies that we use.

Generating stylistic text with specific attributes is a key problem in controllable text generation. Recently, diffusion models have emerged as a powerful paradigm for both visual and textual generation. Existing approaches can be broadly categorized into classifier-free guidance (CFG) and classifier guidance (CG) methods. While CFG effectively preserves semantic content, it often fails to provide effective attribute control. In contrast, CG modifies the denoising trajectory using classifier gradients, enabling better attribute alignment but incurring high computational costs during sampling and suffering from classifier generalization issues. In this work, we propose RegDiff, a regularized diffusion framework that leverages attribute features without requiring a pretrained classifier during sampling, thereby achieving controllable generation with reduced computational costs. Specifically, RegDiff employs a VAE-based encoder--decoder architecture to ensure reconstruction fidelity and a latent diffusion model trained with attribute supervision to enable controllable text generation. Attribute information is injected only during training. Experiments on five datasets spanning multiple stylistic attributes demonstrate that RegDiff outperforms strong baselines in generating stylistic texts. These results validate the effectiveness of RegDiff as an efficient solution for attribute-controllable text diffusion. Our code, datasets, and resources will be released upon publication at https://github.com/xxxx.

Far from equilibrium, neural systems self-organize across multiple scales. Exploiting multiscale self-organization in neuroscience and artificial intelligence requires a computational framework for modeling the effective non-equilibrium dynamics of stochastic neural trajectories. Non-equilibrium thermodynamics and representational geometry offer theoretical foundations, but we need scalable data-driven techniques for modeling collective properties of high-dimensional neural networks from partial subsampled observations. Renormalization is a coarse-graining technique central to studying emergent scaling properties of many-body and nonlinear dynamical systems. While widely applied in physics and machine learning, coarse-graining complex dynamical networks remains unsolved, affecting many computational sciences. Recent diffusion-based renormalization, inspired by quantum statistical mechanics, coarse-grains networks near entropy transitions marked by maximal changes in specific heat or information transmission. Here I explore diffusion-based renormalization of neural systems by generating symmetry-breaking representations across scales and offering scalable algorithms using tensor networks. Diffusion-guided renormalization bridges microscale and mesoscale dynamics of dissipative neural systems. For microscales, I developed a scalable graph inference algorithm for discovering community structure from subsampled neural activity. Using community-based node orderings, diffusion-guided renormalization generates renormalization group flow through metagraphs and joint probability functions. Towards mesoscales, diffusion-guided renormalization targets learning the effective non-equilibrium dynamics of dissipative neural trajectories occupying lower-dimensional subspaces, enabling coarse-to-fine control in systems neuroscience and artificial intelligence.

Corresponding Author Abstract--Replicating human-level intelligence in the execution of embodied tasks remains challenging due to the unconstrained nature of real-world environments. Novel use of large language models (LLMs) for task planning seeks to address the previously intractable state/action space of complex planning tasks, but hallucinations limit their reliability, and thus, viability beyond a research context. Additionally, the prompt engineering required to achieve adequate system performance lacks transparency, and thus, repeatability. In contrast to LLM planning, symbolic planning methods offer strong reliability and repeatability guarantees, but struggle to scale to the complexity and ambiguity of real-world tasks. We introduce a new robotic planning method that augments LLM planners with symbolic planning oversight to improve reliability and repeatability, and provide a transparent approach to defining hard constraints with considerably stronger clarity than traditional prompt engineering. Importantly, these augmentations preserve the reasoning capabilities of LLMs and retain impressive generalization in open-world environments. We demonstrate our approach in simulated and real-world environments. On the ALFWorld planning benchmark, our approach outperforms current state-of-the-art methods, achieving a near-perfect 99% success rate. Deployment of our method to a real-world quadruped robot resulted in 100% task success compared to 50% and 30% for pure LLM and symbolic planners across embodied pick and place tasks. Our approach presents an effective strategy to enhance the reliability, repeatability and transparency of LLM-based robot planners while retaining their key strengths: flexibility and generalizability to complex real-world environments. We hope that this work will contribute to the broad goal of building resilient embodied intelligent systems. By leveraging the strengths of both emerging Large Language Model (LLM)-based and well-understood symbolic planning components, we present a novel, hybrid approach to high-level embodied planning that allows for explicit and rigid constraint definition while preserving the adaptability and common-sense reasoning of its LLM components to enable a highly adaptable, reliable, repeatable, and transparent planning solution for use in unconstrained open-world environments. NABLING the reliable autonomy of embodied agents in complex and potentially unknown environments is a long-standing goal in robotics. Achieving this goal requires seamless interaction and understanding between a variety of system components including perception, control, navigation, and high-level planning.

Magnetic Resonance Imaging (MRI) is a critical tool in modern medical diagnostics, yet its prolonged acquisition time remains a critical limitation, especially in time-sensitive clinical scenarios. While undersampling strategies can accelerate image acquisition, they often result in image artifacts and degraded quality. Recent diffusion models have shown promise for reconstructing high-fidelity images from undersampled data by learning powerful image priors; however, most existing approaches either (i) rely on unsupervised score functions without paired supervision or (ii) apply data consistency only as a post-processing step. In this work, we introduce a conditional denoising diffusion framework with iterative data-consistency correction, which differs from prior methods by embedding the measurement model directly into every reverse diffusion step and training the model on paired undersampled-ground truth data. This hybrid design bridges generative flexibility with explicit enforcement of MRI physics. Experiments on the fastMRI dataset demonstrate that our framework consistently outperforms recent state-of-the-art deep learning and diffusion-based methods in SSIM, PSNR, and LPIPS, with LPIPS capturing perceptual improvements more faithfully. These results demonstrate that integrating conditional supervision with iterative consistency updates yields substantial improvements in both pixel-level fidelity and perceptual realism, establishing a principled and practical advance toward robust, accelerated MRI reconstruction.

Subject of this thesis is the implementation of an AI-based Gaze Tracking system using RGBD images that contain both color (RGB) and depth (D) information. To fuse the features extracted from the images, a module based on the Transformer architecture is used. The combination of RGBD input images and Transformers was chosen because it has not yet been investigated. Furthermore, a new dataset is created for training the AI models as existing datasets either do not contain depth information or only contain labels for Gaze Point Estimation that are not suitable for the task of Gaze Angle Estimation. Various model configurations are trained, validated and evaluated on a total of three different datasets. The trained models are then to be used in a real-time pipeline to estimate the gaze direction and thus the gaze point of a person in front of a computer screen. The AI model architecture used in this thesis is based on an earlier work by Lian et al. It uses a Generative Adversarial Network (GAN) to simultaneously remove depth map artifacts and extract head pose features. Lian et al. achieve a mean Euclidean error of 38.7mm on their own dataset ShanghaiTechGaze+. In this thesis, a model architecture with a Transformer module for feature fusion achieves a mean Euclidean error of 55.3mm on the same dataset, but we show that using no pre-trained GAN module leads to a mean Euclidean error of 30.1mm. Replacing the Transformer module with a Multilayer Perceptron (MLP) improves the error to 26.9mm. These results are coherent with the ones on the other two datasets. On the ETH-XGaze dataset, the model with Transformer module achieves a mean angular error of 3.59° and without Transformer module 3.26°, whereas the fundamentally different model architecture used by the dataset authors Zhang et al. achieves a mean angular error of 2.04°. On the OTH-Gaze-Estimation dataset created for...

High-resolution (4K) image-to-image synthesis has become increasingly important for mobile applications. Existing diffusion models for image editing face significant challenges, in terms of memory and image quality, when deployed on resource-constrained devices. In this paper, we present MobilePicasso, a novel system that enables efficient image editing at high resolutions, while minimising computational cost and memory usage. MobilePicasso comprises three stages: (i) performing image editing at a standard resolution with hallucination-aware loss, (ii) applying latent projection to overcome going to the pixel space, and (iii) upscaling the edited image latent to a higher resolution with adaptive context-preserving tiling. Our user study with 46 participants reveals that MobilePicasso not only improves image quality by 18-48% but reduces hallucinations by 14-51% over existing methods. MobilePicasso demonstrates significantly lower latency, e.g., up to 55.8$\times$ speed-up, yet with a small increase in runtime memory, e.g., a mere 9% increase over prior work. Surprisingly, the on-device runtime of MobilePicasso is observed to be faster than a server-based high-resolution image editing model running on an A100 GPU.

The widespread use of GPS devices has driven advances in spatiotemporal data mining, enabling machine learning models to simulate human decision making and generate realistic trajectories, addressing both data collection costs and privacy concerns. Recent studies have shown the promise of diffusion models for high-quality trajectory generation. However, most existing methods rely on convolution based architectures (e.g. UNet) to predict noise during the diffusion process, which often results in notable deviations and the loss of fine-grained street-level details due to limited model capacity. In this paper, we propose Trajectory Transformer, a novel model that employs a transformer backbone for both conditional information embedding and noise prediction. We explore two GPS coordinate embedding strategies, location embedding and longitude-latitude embedding, and analyze model performance at different scales. Experiments on two real-world datasets demonstrate that Trajectory Transformer significantly enhances generation quality and effectively alleviates the deviation issues observed in prior approaches.

Today's AI models learn primarily through mimicry and sharpening, so it is not surprising that they struggle to solve problems beyond the limits set by existing data. To solve novel problems, agents should acquire skills for exploring and learning through experience. Finding a scalable learning mechanism for developing agents that learn through interaction remains a major open problem. In this work, we introduce BuilderBench, a benchmark to accelerate research into agent pre-training that centers open-ended exploration. BuilderBench requires agents to learn how to build any structure using blocks. BuilderBench is equipped with $(1)$ a hardware accelerated simulator of a robotic agent interacting with various physical blocks, and $(2)$ a task-suite with over 42 diverse target structures that are carefully curated to test an understanding of physics, mathematics, and long-horizon planning. During training, agents have to explore and learn general principles about the environment without any external supervision. During evaluation, agents have to build the unseen target structures from the task suite. Solving these tasks requires a sort of \emph{embodied reasoning} that is not reflected in words but rather in actions, experimenting with different strategies and piecing them together. Our experiments show that many of these tasks challenge the current iteration of algorithms. Hence, we also provide a ``training wheels'' protocol, in which agents are trained and evaluated to build a single target structure from the task suite. Finally, we provide single-file implementations of six different algorithms as a reference point for researchers.