Designing new protein structures is fundamental to computational biology, enabling advances in therapeutic molecule discovery and enzyme engineering. Existing diffusion-based generative models typically operate in Cartesian coordinate space, where adding noise disrupts strict geometric constraints such as fixed bond lengths and angles, often producing physically invalid structures. To address this limitation, we propose a Torsion-Space Diffusion Model that generates protein backbones by denoising torsion angles, ensuring perfect local geometry by construction. A differentiable forward-kinematics module reconstructs 3D coordinates with fixed 3.8 Angstrom backbone bond lengths while a constrained post-processing refinement optimizes global compactness via Radius of Gyration (Rg) correction, without violating bond constraints. Experiments on standard PDB proteins demonstrate 100% bond-length accuracy and significantly improved structural compactness, reducing Rg error from 70% to 18.6% compared to Cartesian diffusion baselines. Overall, this hybrid torsion-diffusion plus geometric-refinement framework generates physically valid and compact protein backbones, providing a promising path toward full-atom protein generation.

Molecular dynamics simulations are an essential tool in understanding protein structure, dynamics, and function at the atomic level. However, preparing high quality input files for MD simulations can be a time consuming and error prone process. In this work, we introduce an automated pipeline that leverages Large Language Models (LLMs), specifically Gemini 2.0 Flash, in conjunction with python scripting and Selenium based web automation to streamline the generation of MD input files. The pipeline exploits CHARMM GUI's comprehensive web-based interface for preparing simulation-ready inputs for NAMD. By integrating Gemini's code generation and iterative refinement capabilities, simulation scripts are automatically written, executed, and revised to navigate CHARMM GUI, extract appropriate parameters, and produce the required NAMD input files. Post processing is performed using additional software to further refine the simulation outputs, thereby enabling a complete and largely hands free workflow. Our results demonstrate that this approach reduces setup time, minimizes manual errors, and offers a scalable solution for handling multiple protein systems in parallel. This automated framework paves the way for broader application of LLMs in computational structural biology, offering a robust and adaptable platform for future developments in simulation automation.

3D Geometric Graph Neural Networks (GNNs) have emerged as transformative tools for modeling molecular data. Despite their predictive power, these models often suffer from limited interpretability, raising concerns for scientific applications that require reliable and transparent insights. While existing methods have primarily focused on explaining molecular substructures in 2D GNNs, the transition to 3D GNNs introduces unique challenges, such as handling the implicit dense edge structures created by a cut-off radius. To tackle this, we introduce a novel explanation method specifically designed for 3D GNNs, which localizes the explanation to the immediate neighborhood of each node within the 3D space. Each node is assigned an radius of influence, defining the localized region within which message passing captures spatial and structural interactions crucial for the model's predictions. This method leverages the spatial and geometric characteristics inherent in 3D graphs. By constraining the subgraph to a localized radius of influence, the approach not only enhances interpretability but also aligns with the physical and structural dependencies typical of 3D graph applications, such as molecular learning.

Mobile network operators constantly optimize their networks to ensure superior service quality and coverage. This optimization is crucial for maintaining an optimal user experience and requires extensive data collection and analysis. One of the primary methods for gathering this data is through drive tests, where technical teams use specialized equipment to collect signal information across various regions. However, drive tests are both costly and time-consuming, and they face challenges such as traffic conditions, environmental factors, and limited access to certain areas. These constraints make it difficult to replicate drive tests under similar conditions. In this study, we propose a method that enables operators to predict received signal strength at specific locations using data from other drive test points. By reducing the need for widespread drive tests, this approach allows operators to save time and resources while still obtaining the necessary data to optimize their networks and mitigate the challenges associated with traditional drive tests.

The Problem-oriented AutoML in Clustering (PoAC) framework introduces a novel, flexible approach to automating clustering tasks by addressing the shortcomings of traditional AutoML solutions. Conventional methods often rely on predefined internal Clustering Validity Indexes (CVIs) and static meta-features, limiting their adaptability and effectiveness across diverse clustering tasks. In contrast, PoAC establishes a dynamic connection between the clustering problem, CVIs, and meta-features, allowing users to customize these components based on the specific context and goals of their task. At its core, PoAC employs a surrogate model trained on a large meta-knowledge base of previous clustering datasets and solutions, enabling it to infer the quality of new clustering pipelines and synthesize optimal solutions for unseen datasets. Unlike many AutoML frameworks that are constrained by fixed evaluation metrics and algorithm sets, PoAC is algorithm-agnostic, adapting seamlessly to different clustering problems without requiring additional data or retraining. Experimental results demonstrate that PoAC not only outperforms state-of-the-art frameworks on a variety of datasets but also excels in specific tasks such as data visualization, and highlight its ability to dynamically adjust pipeline configurations based on dataset complexity.

This project explores adversarial training techniques to develop fairer Deep Neural Networks (DNNs) to mitigate the inherent bias they are known to exhibit. DNNs are susceptible to inheriting bias with respect to sensitive attributes such as race and gender, which can lead to life-altering outcomes (e.g., demographic bias in facial recognition software used to arrest a suspect). We propose a robust optimization problem, which we demonstrate can improve fairness in several datasets, both synthetic and real-world, using an affine linear model. Leveraging second order information, we are able to find a solution to our optimization problem more efficiently than a purely first order method.

Leveraging the unique properties of quantum mechanics, Quantum Machine Learning (QML) promises computational breakthroughs and enriched perspectives where traditional systems reach their boundaries. However, similarly to classical machine learning, QML is not immune to adversarial attacks. Quantum adversarial machine learning has become instrumental in highlighting the weak points of QML models when faced with adversarial crafted feature vectors. Diving deep into this domain, our exploration shines light on the interplay between depolarization noise and adversarial robustness. While previous results enhanced robustness from adversarial threats through depolarization noise, our findings paint a different picture. Interestingly, adding depolarization noise discontinued the effect of providing further robustness for a multi-class classification scenario. Consolidating our findings, we conducted experiments with a multi-class classifier adversarially trained on gate-based quantum simulators, further elucidating this unexpected behavior.

Deterministic methods for motion planning guarantee safety amidst uncertainty in obstacle locations by trying to restrict the robot from operating in any possible location that an obstacle could be in. Unfortunately, this can result in overly conservative behavior. Chance-constrained optimization can be applied to improve the performance of motion planning algorithms by allowing for a user-specified amount of bounded constraint violation. However, state-of-the-art methods rely either on moment-based inequalities, which can be overly conservative, or make it difficult to satisfy assumptions about the class of probability distributions used to model uncertainty. To address these challenges, this work proposes a real-time, risk-aware reachability-based motion planning framework called RADIUS. The method first generates a reachable set of parameterized trajectories for the robot offline. At run time, RADIUS computes a closed-form over-approximation of the risk of a collision with an obstacle. This is done without restricting the probability distribution used to model uncertainty to a simple class (e.g., Gaussian). Then, RADIUS performs real-time optimization to construct a trajectory that can be followed by the robot in a manner that is certified to have a risk of collision that is less than or equal to a user-specified threshold. The proposed algorithm is compared to several state-of-the-art chance-constrained and deterministic methods in simulation, and is shown to consistently outperform them in a variety of driving scenarios. A demonstration of the proposed framework on hardware is also provided.

In robotic-assisted partial nephrectomy, surgeons remove a part of a kidney often due to the presence of a mass. A drop-in ultrasound probe paired to a surgical robot is deployed to execute multiple swipes over the kidney surface to localise the mass and define the margins of resection. This sub-task is challenging and must be performed by a highly skilled surgeon. Automating this sub-task may reduce cognitive load for the surgeon and improve patient outcomes. The overall goal of this work is to autonomously move the ultrasound probe on the surface of the kidney taking advantage of the use of the Pneumatically Attachable Flexible (PAF) rail system, a soft robotic device used for organ scanning and repositioning. First, we integrate a shape-sensing optical fibre into the PAF rail system to evaluate the curvature of target organs in robotic-assisted laparoscopic surgery. Then, we investigate the impact of the stiffness of the material of the PAF rail on the curvature sensing accuracy, considering that soft targets are present in the surgical field. Finally, we use shape sensing to plan the trajectory of the da Vinci surgical robot paired with a drop-in ultrasound probe and autonomously generate an Ultrasound scan of a kidney phantom.

Despite impressive successes, deep reinforcement learning (RL) systems still fall short of human performance on generalization to new tasks and environments that differ from their training. As a benchmark tailored for studying RL generalization, we introduce Avalon, a set of tasks in which embodied agents in highly diverse procedural 3D worlds must survive by navigating terrain, hunting or gathering food, and avoiding hazards. Avalon is unique among existing RL benchmarks in that the reward function, world dynamics, and action space are the same for every task, with tasks differentiated solely by altering the environment; its 20 tasks, ranging in complexity from eat and throw to hunt and navigate, each create worlds in which the agent must perform specific skills in order to survive. This setup enables investigations of generalization within tasks, between tasks, and to compositional tasks that require combining skills learned from previous tasks. Avalon includes a highly efficient simulator, a library of baselines, and a benchmark with scoring metrics evaluated against hundreds of hours of human performance, all of which are open-source and publicly available. We find that standard RL baselines make progress on most tasks but are still far from human performance, suggesting Avalon is challenging enough to advance the quest for generalizable RL.