Marcin Copik

Afif Boudaoud, Lisa Gaedke-Merzhäuser, Alexandros Nikolaos Ziogas et al.

Spatio-temporal Bayesian inference drives environmental and health sciences using latent Gaussian models. Integrated Nested Laplace Approximations (INLA) enable inference for these models at HPC scale but rely on derivative-based optimization over $d$ hyperparameters. State-of-the-art INLA implementations approximate derivatives via central finite differences (FD), requiring $2d{+}1$ evaluations. These evaluations are embarrassingly parallel, but total work and energy grow with $d$, limiting time-to-solution under fixed budgets. Reverse-mode automatic differentiation (AD) computes exact gradients independently of $d$, but its efficient application to INLA's structured-sparse kernels is an open challenge. We present ADELIA, the first AD-enabled INLA implementation with a structure-exploiting multi-GPU backward pass leveraging model sparsity. We evaluate ADELIA on ten benchmark models, including real-world air-pollution monitoring. We achieve $4.2$--$7.9\times$ per-gradient speedups and reliable convergence on production-scale models with up to 1.9M latent variables, where FD struggles. Even when scaled to 16--32 GPUs to match ADELIA's wall-clock time, FD consumes $5$--$8\times$ more energy.

Maciej Besta, Julia Barth, Eric Schreiber et al.

Reasoning language models (RLMs), also known as Large Reasoning Models (LRMs), such as OpenAI's o1 and o3, DeepSeek-R1, and Alibaba's QwQ, have redefined AI's problem-solving capabilities by extending LLMs with advanced reasoning mechanisms. Yet, their high costs, proprietary nature, and complex architectures - uniquely combining reinforcement learning (RL), search heuristics, and LLMs - present accessibility and scalability challenges. To address these, we propose a comprehensive blueprint that organizes RLM components into a modular framework, based on a survey and analysis of all RLM works. This blueprint incorporates diverse reasoning structures (chains, trees, graphs, and nested forms), reasoning strategies (e.g., Monte Carlo Tree Search, Beam Search), RL concepts (policy, value models and others), supervision schemes (Outcome-Based and Process-Based Supervision), and other related concepts (e.g., Test-Time Compute, Retrieval-Augmented Generation, agent tools). We also provide detailed mathematical formulations and algorithmic specifications to simplify RLM implementation. By showing how schemes like LLaMA-Berry, QwQ, Journey Learning, and Graph of Thoughts fit as special cases, we demonstrate the blueprint's versatility and unifying potential. To illustrate its utility, we introduce x1, a modular implementation for rapid RLM prototyping and experimentation. Using x1 and a literature review, we provide key insights, such as multi-phase training for policy and value models, and the importance of familiar training distributions. Finally, we discuss scalable RLM cloud deployments and we outline how RLMs can integrate with a broader LLM ecosystem. Our work demystifies RLM construction, democratizes advanced reasoning capabilities, and fosters innovation, aiming to mitigate the gap between "rich AI" and "poor AI" by lowering barriers to RLM design and experimentation.

Maciej Besta, Lorenzo Paleari, Jia Hao Andrea Jiang et al.

Large Language Models (LLMs) are revolutionizing the development of AI assistants capable of performing diverse tasks across domains. However, current state-of-the-art LLM-driven agents face significant challenges, including high operational costs and limited success rates on complex benchmarks like GAIA. To address these issues, we propose Knowledge Graph of Thoughts (KGoT), an innovative AI assistant architecture that integrates LLM reasoning with dynamically constructed knowledge graphs (KGs). KGoT extracts and structures task-relevant knowledge into a dynamic KG representation, iteratively enhanced through external tools such as math solvers, web crawlers, and Python scripts. Such structured representation of task-relevant knowledge enables low-cost models to solve complex tasks effectively while also minimizing bias and noise. For example, KGoT achieves a 29% improvement in task success rates on the GAIA benchmark compared to Hugging Face Agents with GPT-4o mini. Moreover, harnessing a smaller model dramatically reduces operational costs by over 36x compared to GPT-4o. Improvements for other models (e.g., Qwen2.5-32B and Deepseek-R1-70B) and benchmarks (e.g., SimpleQA) are similar. KGoT offers a scalable, affordable, versatile, and high-performing solution for AI assistants.

Marcin Chrapek, Marcin Copik, Etienne Mettaz et al.

Large Language Models (LLMs) are increasingly deployed on converged Cloud and High-Performance Computing (HPC) infrastructure. However, as LLMs handle confidential inputs and are fine-tuned on costly, proprietary datasets, their heightened security requirements slow adoption in privacy-sensitive sectors such as healthcare and finance. We investigate methods to address this gap and propose Trusted Execution Environments (TEEs) as a solution for securing end-to-end LLM inference. We validate their practicality by evaluating these compute-intensive workloads entirely within CPU and GPU TEEs. On the CPU side, we conduct an in-depth study running full Llama2 inference pipelines (7B, 13B, 70B) inside Intel's TDX and SGX, accelerated by Advanced Matrix Extensions (AMX). We derive 12 insights, including that across various data types, batch sizes, and input lengths, CPU TEEs impose under 10% throughput and 20% latency overheads, further reduced by AMX. We run LLM inference on NVIDIA H100 Confidential Compute GPUs, contextualizing our CPU findings and observing throughput penalties of 4-8% that diminish as batch and input sizes grow. By comparing performance, cost, and security trade-offs, we show how CPU TEEs can be more cost-effective or secure than their GPU counterparts. To our knowledge, our work is the first to comprehensively demonstrate the performance and practicality of modern TEEs across both CPUs and GPUs for enabling confidential LLMs (cLLMs).

Pedro Garcia Lopez, Daniel Barcelona Pons, Marcin Copik et al.

The strategic importance of artificial intelligence is driving a global push toward Sovereign AI initiatives. Nationwide governments are increasingly developing dedicated infrastructures, called AI Factories (AIF), to achieve technological autonomy and secure the resources necessary to sustain robust local digital ecosystems. In Europe, the EuroHPC Joint Undertaking is investing hundreds of millions of euros into several AI Factories, built atop existing high-performance computing (HPC) supercomputers. However, while HPC systems excel in raw performance, they are not inherently designed for usability, accessibility, or serving as public-facing platforms for AI services such as inference or agentic applications. In contrast, AI practitioners are accustomed to cloud-native technologies like Kubernetes and object storage, tools that are often difficult to integrate within traditional HPC environments. This article advocates for a dual-stack approach within supercomputers: integrating both HPC and cloud-native technologies. Our goal is to bridge the divide between HPC and cloud computing by combining high performance and hardware acceleration with ease of use and service-oriented front-ends. This convergence allows each paradigm to amplify the other. To this end, we will study the cloud challenges of HPC (Serverless HPC) and the HPC challenges of cloud technologies (High-performance Cloud).

Afif Boudaoud, Alexandru Calotoiu, Marcin Copik et al.

Automatic differentiation (AD) is a set of techniques that systematically applies the chain rule to compute the gradients of functions without requiring human intervention. Although the fundamentals of this technology were established decades ago, it is experiencing a renaissance as it plays a key role in efficiently computing gradients for backpropagation in machine learning algorithms. AD is also crucial for many applications in scientific computing domains, particularly emerging techniques that integrate machine learning models within scientific simulations and schemes. Existing AD frameworks have four main limitations: limited support of programming languages, requiring code modifications for AD compatibility, limited performance on scientific computing codes, and a naive store-all solution for forward-pass data required for gradient calculations. These limitations force domain scientists to manually compute the gradients for large problems. This work presents DaCe AD, a general, efficient automatic differentiation engine that requires no code modifications. DaCe AD uses a novel ILP-based algorithm to optimize the trade-off between storing and recomputing to achieve maximum performance within a given memory constraint. We showcase the generality of our method by applying it to NPBench, a suite of HPC benchmarks with diverse scientific computing patterns, where we outperform JAX, a Python framework with state-of-the-art general AD capabilities, by more than 92 times on average without requiring any code changes.

Maciej Besta, Shriram Chandran, Jakub Cudak et al.

Recent advances in graph databases (GDBs) have been driving interest in large-scale analytics, yet current systems fail to support higher-order (HO) interactions beyond first-order (one-hop) relations, which are crucial for tasks such as subgraph counting, polyadic modeling, and HO graph learning. We address this by introducing a new class of systems, higher-order graph databases (HO-GDBs) that use lifting and lowering paradigms to seamlessly extend traditional GDBs with HO. We provide a theoretical analysis of OLTP and OLAP queries, ensuring correctness, scalability, and ACID compliance. We implement a lightweight, modular, and parallelizable HO-GDB prototype that offers native support for hypergraphs, node-tuples, subgraphs, and other HO structures under a unified API. The prototype scales to large HO OLTP & OLAP workloads and shows how HO improves analytical tasks, for example enhancing accuracy of graph neural networks within a GDB by 44%. Our work ensures low latency and high query throughput, and generalizes both ACID-compliant and eventually consistent systems.

Maciej Besta, Lorenzo Paleari, Marcin Copik et al.

Large Language Models (LLMs) are transforming a wide range of domains, yet verifying their outputs remains a significant challenge, especially for complex open-ended tasks such as consolidation, summarization, and knowledge extraction. To address this, we introduce CheckEmbed (CE): a simple, scalable, and accurate verification method. CE reduces each LLM answer to a single embedding vector using powerful modern embedding LLM models like SFR-Embedding-Mistral. Prior methods such as BERTScore and SelfCheckGPT relied on weaker encoders like BERT, forcing them to operate at token or sentence granularity. In contrast, CE performs fast, semantically rich comparisons directly at the whole-answer level, overcoming key limitations in both accuracy and scalability. We conduct a comprehensive design and time complexity analysis across 13 verification baselines, including classical text scorers (e.g., BLEU), stability-based methods (e.g., SelfCheckGPT), and generative evaluators (e.g., LLM-as-a-Judge), which highlights the effectiveness, efficiency, versatility, and simplicity of CE. Empirical results show that CE reliably detects hallucinations in both closed and open-ended tasks. We further present evidence that CE generalizes beyond text to other modalities such as vision, establishing it as a practical and versatile verification framework.

Maciej Besta, Florim Memedi, Zhenyu Zhang et al.

The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and other parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

Maciej Besta, Zur Vonarburg-Shmaria, Yannick Schaffner et al.

We propose GraphMineSuite (GMS): the first benchmarking suite for graph mining that facilitates evaluating and constructing high-performance graph mining algorithms. First, GMS comes with a benchmark specification based on extensive literature review, prescribing representative problems, algorithms, and datasets. Second, GMS offers a carefully designed software platform for seamless testing of different fine-grained elements of graph mining algorithms, such as graph representations or algorithm subroutines. The platform includes parallel implementations of more than 40 considered baselines, and it facilitates developing complex and fast mining algorithms. High modularity is possible by harnessing set algebra operations such as set intersection and difference, which enables breaking complex graph mining algorithms into simple building blocks that can be separately experimented with. GMS is supported with a broad concurrency analysis for portability in performance insights, and a novel performance metric to assess the throughput of graph mining algorithms, enabling more insightful evaluation. As use cases, we harness GMS to rapidly redesign and accelerate state-of-the-art baselines of core graph mining problems: degeneracy reordering (by up to >2x), maximal clique listing (by up to >9x), k-clique listing (by 1.1x), and subgraph isomorphism (by up to 2.5x), also obtaining better theoretical performance bounds.