Matteo Barbieri

Tiziana Liberati, Nitin Shukla, Matteo Barbieri et al.

Shor's algorithm proved that asymmetric cryptographic protocols based on the integer factorization and discrete logarithm problems are no longer safe in a world with large-scale quantum computers. As a result, Post-Quantum Cryptography (PQC) has been developed over the last few years, seeking cryptographic primitives resistant to quantum attacks. One of the main hard problems underlying PQC schemes is the Learning with Errors (LWE) problem, which is significantly more computationally intensive than its classical predecessors. In this work, we present a Key Encapsulation Mechanism (KEM) based on plain LWE and develop a GPU-oriented implementation using OpenACC. We evaluate the performance of our accelerated application in terms of both time-to-solution and energy-to-solution, considering bare-metal and containerized executions across multiple NVIDIA GPU models and generations. Our implementation achieves significant acceleration across all tested GPU platforms. In particular, on the NVIDIA Grace Hopper Superchip, it attains up to a $208\times$ speedup over a multithreaded CPU baseline and enables the execution of problem sizes that are impractical on CPU architectures due to memory and synchronization constraints. Energy consumption analysis also shows $\approx 2\times$ better efficiency when using the Superchip compared to systems equipped with x86-based CPUs and NVIDIA H100 GPUs. These results highlight the effectiveness of GPU acceleration for computationally demanding LWE-based cryptographic workloads.

Roberto Rocco, Simone Rizzo, Matteo Barbieri et al.

The integration of quantum computers within classical High-Performance Computing (HPC) infrastructures is receiving increasing attention, with the former expected to serve as accelerators for specific computational tasks. However, combining HPC and quantum computers presents significant technical challenges, including resource allocation. This paper presents a novel malleability-based approach, alongside a workflow-based strategy, to optimize resource utilization in hybrid HPC-quantum workloads. With both these approaches, we can release classical resources when computations are offloaded to the quantum computer and reallocate them once quantum processing is complete. Our experiments with a hybrid HPC-quantum use case show the benefits of dynamic allocation, highlighting the potential of those solutions.

Francesco Micucci, Matteo Barbieri, Gabriella Bettonte et al.

Molecular docking is a crucial step in the development of new drugs as it guides the positioning of a small molecule (ligand) within the pocket of a target protein. In the literature, a feasibility study explored the potential of D-Wave quantum annealers for purely geometric molecular docking, neglecting physicochemical interactions between the protein and the ligand and focusing solely on their simplified geometries. To achieve this, the ligands were represented as graphs incorporating their geometric properties and then mapped onto a grid that discretized the three-dimensional space of the protein pocket. The quality of the ligand pose on the protein pocket was evaluated through the isomorphism between the ligand graph and the spatial grid. This paper builds on the previous study by introducing physicochemical interactions between the protein-ligand pair into the QUBO problem to improve the accuracy of the docking results. This paper presents a novel QUBO formulation that includes Coulomb and van der Waals forces, together with components representing H-bond and hydrophobic interactions. We integrate these physical interactions as corrective terms to the previous purely geometric QUBO formulation, and provide experimental results using the D-Wave quantum annealers to demonstrate their impact on the accuracy of the docking results.

Agrin Hilmkil, Sebastian Callh, Matteo Barbieri et al.

Federated learning (FL) is a promising approach to distributed compute, as well as distributed data, and provides a level of privacy and compliance to legal frameworks. This makes FL attractive for both consumer and healthcare applications. While the area is actively being explored, few studies have examined FL in the context of larger language models and there is a lack of comprehensive reviews of robustness across tasks, architectures, numbers of clients, and other relevant factors. In this paper, we explore the fine-tuning of Transformer-based language models in a federated learning setting. We evaluate three popular BERT-variants of different sizes (BERT, ALBERT, and DistilBERT) on a number of text classification tasks such as sentiment analysis and author identification. We perform an extensive sweep over the number of clients, ranging up to 32, to evaluate the impact of distributed compute on task performance in the federated averaging setting. While our findings suggest that the large sizes of the evaluated models are not generally prohibitive to federated training, we found that the different models handle federated averaging to a varying degree. Most notably, DistilBERT converges significantly slower with larger numbers of clients, and under some circumstances, even collapses to chance level performance. Investigating this issue presents an interesting perspective for future research.

Ming Y. Lu, Drew F. K. Williamson, Tiffany Y. Chen et al.

The rapidly emerging field of computational pathology has the potential to enable objective diagnosis, therapeutic response prediction and identification of new morphological features of clinical relevance. However, deep learning-based computational pathology approaches either require manual annotation of gigapixel whole slide images (WSIs) in fully-supervised settings or thousands of WSIs with slide-level labels in a weakly-supervised setting. Moreover, whole slide level computational pathology methods also suffer from domain adaptation and interpretability issues. These challenges have prevented the broad adaptation of computational pathology for clinical and research purposes. Here we present CLAM - Clustering-constrained attention multiple instance learning, an easy-to-use, high-throughput, and interpretable WSI-level processing and learning method that only requires slide-level labels while being data efficient, adaptable and capable of handling multi-class subtyping problems. CLAM is a deep-learning-based weakly-supervised method that uses attention-based learning to automatically identify sub-regions of high diagnostic value in order to accurately classify the whole slide, while also utilizing instance-level clustering over the representative regions identified to constrain and refine the feature space. In three separate analyses, we demonstrate the data efficiency and adaptability of CLAM and its superior performance over standard weakly-supervised classification. We demonstrate that CLAM models are interpretable and can be used to identify well-known and new morphological features. We further show that models trained using CLAM are adaptable to independent test cohorts, cell phone microscopy images, and biopsies. CLAM is a general-purpose and adaptable method that can be used for a variety of different computational pathology tasks in both clinical and research settings.