Maciej Besta

Maciej Besta, Nils Blach, Ales Kubicek et al.

We introduce Graph of Thoughts (GoT): a framework that advances prompting capabilities in large language models (LLMs) beyond those offered by paradigms such as Chain-of-Thought or Tree of Thoughts (ToT). The key idea and primary advantage of GoT is the ability to model the information generated by an LLM as an arbitrary graph, where units of information ("LLM thoughts") are vertices, and edges correspond to dependencies between these vertices. This approach enables combining arbitrary LLM thoughts into synergistic outcomes, distilling the essence of whole networks of thoughts, or enhancing thoughts using feedback loops. We illustrate that GoT offers advantages over state of the art on different tasks, for example increasing the quality of sorting by 62% over ToT, while simultaneously reducing costs by >31%. We ensure that GoT is extensible with new thought transformations and thus can be used to spearhead new prompting schemes. This work brings the LLM reasoning closer to human thinking or brain mechanisms such as recurrence, both of which form complex networks.

Maciej Besta, Torsten Hoefler

Graph neural networks (GNNs) are among the most powerful tools in deep learning. They routinely solve complex problems on unstructured networks, such as node classification, graph classification, or link prediction, with high accuracy. However, both inference and training of GNNs are complex, and they uniquely combine the features of irregular graph processing with dense and regular computations. This complexity makes it very challenging to execute GNNs efficiently on modern massively parallel architectures. To alleviate this, we first design a taxonomy of parallelism in GNNs, considering data and model parallelism, and different forms of pipelining. Then, we use this taxonomy to investigate the amount of parallelism in numerous GNN models, GNN-driven machine learning tasks, software frameworks, or hardware accelerators. We use the work-depth model, and we also assess communication volume and synchronization. We specifically focus on the sparsity/density of the associated tensors, in order to understand how to effectively apply techniques such as vectorization. We also formally analyze GNN pipelining, and we generalize the established Message-Passing class of GNN models to cover arbitrary pipeline depths, facilitating future optimizations. Finally, we investigate different forms of asynchronicity, navigating the path for future asynchronous parallel GNN pipelines. The outcomes of our analysis are synthesized in a set of insights that help to maximize GNN performance, and a comprehensive list of challenges and opportunities for further research into efficient GNN computations. Our work will help to advance the design of future GNNs.

Maciej Besta, Patrick Iff, Florian Scheidl et al.

Graph databases (GDBs) enable processing and analysis of unstructured, complex, rich, and usually vast graph datasets. Despite the large significance of GDBs in both academia and industry, little effort has been made into integrating them with the predictive power of graph neural networks (GNNs). In this work, we show how to seamlessly combine nearly any GNN model with the computational capabilities of GDBs. For this, we observe that the majority of these systems are based on, or support, a graph data model called the Labeled Property Graph (LPG), where vertices and edges can have arbitrarily complex sets of labels and properties. We then develop LPG2vec, an encoder that transforms an arbitrary LPG dataset into a representation that can be directly used with a broad class of GNNs, including convolutional, attentional, message-passing, and even higher-order or spectral models. In our evaluation, we show that the rich information represented as LPG labels and properties is properly preserved by LPG2vec, and it increases the accuracy of predictions regardless of the targeted learning task or the used GNN model, by up to 34% compared to graphs with no LPG labels/properties. In general, LPG2vec enables combining predictive power of the most powerful GNNs with the full scope of information encoded in the LPG model, paving the way for neural graph databases, a class of systems where the vast complexity of maintained data will benefit from modern and future graph machine learning methods.

Maciej Besta, Afonso Claudino Catarino, Lukas Gianinazzi et al.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

Maciej Besta, Patrick Iff, Marcel Schneider et al.

The diversity of communication paths in a network, especially non-minimal paths, is a key enabler of performance at extreme scales. We present EvalNet, a toolchain for scalable generation and analysis of over 25 important network topologies, such as Slim Fly, PolarFly, and Orthogonal Fat Trees, with a strong focus on path diversity metrics. EvalNet provides an extensive and fine-grained analysis of shortest and non-shortest paths, including their multiplicities, lengths, and interference. It supports exact measurement and visualization of bandwidth and throughput between every router pair, enabling unprecedented insight into routing potential. EvalNet also includes detailed models for construction cost and power consumption, and interfaces seamlessly with established simulators, which we tune to support large-scale evaluations on low-cost hardware. Using EvalNet, we deliver the widest and most comprehensive path diversity study to date, demonstrating how path diversity underpins throughput and scalability, and facilitating progress towards new frontiers in extreme-scale network design.

Julia Bazinska, Andrei Ivanov, Tal Ben-Nun et al.

Graph Neural Networks (GNNs) are a powerful tool for handling structured graph data and addressing tasks such as node classification, graph classification, and clustering. However, the sparse nature of GNN computation poses new challenges for performance optimization compared to traditional deep neural networks. We address these challenges by providing a unified view of GNN computation, I/O, and memory. By analyzing the computational graphs of the Graph Convolutional Network (GCN) and Graph Attention (GAT) layers -- two widely used GNN layers -- we propose alternative computation strategies. We present adaptive operator reordering with caching, which achieves a speedup of up to 2.43x for GCN compared to the current state-of-the-art. Furthermore, an exploration of different caching schemes for GAT yields a speedup of up to 1.94x. The proposed optimizations save memory, are easily implemented across various hardware platforms, and have the potential to alleviate performance bottlenecks in training large-scale GNN models.

Patrick Iff, Paul Bruegger, Marcin Chrapek et al.

Advances in embedding models for text, image, audio, and video drive progress across multiple domains, including retrieval-augmented generation, recommendation systems, and others. Many of these applications require an efficient method to retrieve items that are close to a given query in the embedding space while satisfying a filter condition based on the item's attributes, a problem known as filtered approximate nearest neighbor search (FANNS). By performing an in-depth literature analysis on FANNS, we identify a key gap in the research landscape: publicly available datasets with embedding vectors from state-of-the-art transformer-based text embedding models that contain abundant real-world attributes covering a broad spectrum of attribute types and value distributions. To fill this gap, we introduce the arxiv-for-fanns dataset of transformer-based embedding vectors for the abstracts of over 2.7 million arXiv papers, enriched with 11 real-world attributes such as authors and categories. We benchmark eleven different FANNS methods on our new dataset to evaluate their performance across different filter types, numbers of retrieved neighbors, dataset scales, and query selectivities. We distill our findings into eight key observations that guide users in selecting the most suitable FANNS method for their specific use cases.

Patrick Iff, Tommaso Bonato, Maciej Besta et al.

Transformer-based large language models are increasingly constrained by data movement as communication bandwidth drops sharply beyond the chip boundary. Wafer-scale integration using wafer-on-wafer hybrid bonding alleviates this limitation by providing ultra-high bandwidth between reticles on bonded wafers. In this paper, we investigate how the physical placement of reticles on wafers influences the achievable network topology and the resulting communication performance. Starting from a 2D mesh-like baseline, we propose four reticle placements (Aligned, Interleaved, Rotated, and Contoured) that improve throughput by up to 250%, reduce latency by up to 36%, and decrease energy per transmitted byte by up to 38%.

Maciej Besta, Łukasz Jarmocik, Orest Hrycyna et al.

Graphs are foundational across domains but remain hard to use without deep expertise. LLMs promise accessible natural language (NL) graph analytics, yet they fail to process industry-scale property graphs effectively and efficiently: such datasets are large, highly heterogeneous, structurally complex, and evolve dynamically. To address this, we devise a novel abstraction for complex multi-query analytics over such graphs. Its key idea is to replace brittle generation of graph queries directly from NL with planning over a Semantic Catalog that describes both the graph schema and the graph operations. Concretely, this induces a clean separation between a Semantic Plane for LLM planning and broader reasoning, and an Execution Plane for deterministic, database-grade query execution over the full dataset and tool implementations. This design yields substantial gains in both token efficiency and task effectiveness even with small-context LLMs. We use this abstraction as the basis of the first LLM-enhanced graph analytics framework called GraphSeek. GraphSeek achieves substantially higher success rates (e.g., 86% over enhanced LangChain) and points toward the next generation of affordable and accessible graph analytics that unify LLM reasoning with database-grade execution over large and complex property graphs.

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.

Maciej Besta, Shriram Chandran, Robert Gerstenberger et al.

We introduce MBTI-in-Thoughts, a framework for enhancing the effectiveness of Large Language Model (LLM) agents through psychologically grounded personality conditioning. Drawing on the Myers-Briggs Type Indicator (MBTI), our method primes agents with distinct personality archetypes via prompt engineering, enabling control over behavior along two foundational axes of human psychology, cognition and affect. We show that such personality priming yields consistent, interpretable behavioral biases across diverse tasks: emotionally expressive agents excel in narrative generation, while analytically primed agents adopt more stable strategies in game-theoretic settings. Our framework supports experimenting with structured multi-agent communication protocols and reveals that self-reflection prior to interaction improves cooperation and reasoning quality. To ensure trait persistence, we integrate the official 16Personalities test for automated verification. While our focus is on MBTI, we show that our approach generalizes seamlessly to other psychological frameworks such as Big Five, HEXACO, or Enneagram. By bridging psychological theory and LLM behavior design, we establish a foundation for psychologically enhanced AI agents without any fine-tuning.

Patrik Okanovic, Sameer Deshmukh, Grzegorz Kwasniewski et al.

The energy consumption of large-scale ML models is dominated by data movement, shuffling billions of parameters across memory hierarchies and data centers. Sparsification offers a principled way to mitigate these costs by pruning redundant weights and activations, thereby reducing data movement. Effective sparsification to prune redundant parameters is still challenging: existing methods incur significant accuracy degradation, performance overhead, or both. We introduce (Bl)ock (a)nd (S)parse (T)ransformers (BLaST), a general, robust, and reliable method for sparsification, applicable to linear layers in all settings. Our method iteratively sparsifies weight matrices into a block sparsity pattern suitable for efficient sparse matrix-matrix (SpMM) multiplication. BLaST achieves up to 95% sparsity in MLP weights with negligible accuracy loss (majority <2.25%). We show a 2.2x inference speedup for Llama 3.2 with 16 GPUs, and up to 4.45x reduction in inference memory footprint resulting in a 2.9x reduction in GPU setup and operating costs.

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, Florian Scheidl, Lukas Gianinazzi et al.

Higher-order graph neural networks (HOGNNs) and the related architectures from Topological Deep Learning are an important class of GNN models that harness polyadic relations between vertices beyond plain edges. They have been used to eliminate issues such as over-smoothing or over-squashing, to significantly enhance the accuracy of GNN predictions, to improve the expressiveness of GNN architectures, and for numerous other goals. A plethora of HOGNN models have been introduced, and they come with diverse neural architectures, and even with different notions of what the "higher-order" means. This richness makes it very challenging to appropriately analyze and compare HOGNN models, and to decide in what scenario to use specific ones. To alleviate this, we first design an in-depth taxonomy and a blueprint for HOGNNs. This facilitates designing models that maximize performance. Then, we use our taxonomy to analyze and compare the available HOGNN models. The outcomes of our analysis are synthesized in a set of insights that help to select the most beneficial GNN model in a given scenario, and a comprehensive list of challenges and opportunities for further research into more powerful HOGNNs.

Maciej Besta, Ales Kubicek, Robert Gerstenberger et al.

Retrieval-Augmented Generation (RAG) improves Large Language Models (LLMs) by retrieving supporting documents into the prompt, but existing methods do not explicitly target queries that require fetching multiple documents with substantially different content. Such multi-aspect queries are challenging because relevant documents can be far apart in embedding space, making joint retrieval difficult. We introduce Multi-Head RAG (MRAG), which addresses this gap with a simple yet powerful idea: using Transformer multi-head attention activations rather than the standard decoder-layer embedding, as retrieval keys. It leverages the observation that different heads capture different semantic aspects. This yields multi-aspect embeddings for both documents and queries, improving retrieval accuracy on complex queries. We show MRAG's design advantages over 18 RAG baselines, up to 20% higher retrieval success ratios for real-world use cases, and improved downstream LLM generation. MRAG integrates seamlessly with existing RAG frameworks and benchmarks.

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.

Lukas Gianinazzi, Maximilian Fries, Nikoli Dryden et al.

We present a novel neural architecture to solve graph optimization problems where the solution consists of arbitrary node labels, allowing us to solve hard problems like graph coloring. We train our model using reinforcement learning, specifically policy gradients, which gives us both a greedy and a probabilistic policy. Our architecture builds on a graph attention network and uses several inductive biases to improve solution quality. Our learned deterministic heuristics for graph coloring give better solutions than classical degree-based greedy heuristics and only take seconds to apply to graphs with tens of thousands of vertices. Moreover, our probabilistic policies outperform all greedy state-of-the-art coloring baselines and a machine learning baseline. Finally, we show that our approach also generalizes to other problems by evaluating it on minimum vertex cover and outperforming two greedy heuristics.

Maciej Besta, Raphael Grob, Cesare Miglioli et al.

Link prediction is one of the central problems in graph mining. However, recent studies highlight the importance of higher-order network analysis, where complex structures called motifs are the first-class citizens. We first show that existing link prediction schemes fail to effectively predict motifs. To alleviate this, we establish a general motif prediction problem and we propose several heuristics that assess the chances for a specified motif to appear. To make the scores realistic, our heuristics consider - among others - correlations between links, i.e., the potential impact of some arriving links on the appearance of other links in a given motif. Finally, for highest accuracy, we develop a graph neural network (GNN) architecture for motif prediction. Our architecture offers vertex features and sampling schemes that capture the rich structural properties of motifs. While our heuristics are fast and do not need any training, GNNs ensure highest accuracy of predicting motifs, both for dense (e.g., k-cliques) and for sparse ones (e.g., k-stars). We consistently outperform the best available competitor by more than 10% on average and up to 32% in area under the curve. Importantly, the advantages of our approach over schemes based on uncorrelated link prediction increase with the increasing motif size and complexity. We also successfully apply our architecture for predicting more arbitrary clusters and communities, illustrating its potential for graph mining beyond motif analysis.

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.

Maciej Besta, Dimitri Stanojevic, Tijana Zivic et al.

Today's graphs used in domains such as machine learning or social network analysis may contain hundreds of billions of edges. Yet, they are not necessarily stored efficiently, and standard graph representations such as adjacency lists waste a significant number of bits while graph compression schemes such as WebGraph often require time-consuming decompression. To address this, we propose Log(Graph): a graph representation that combines high compression ratios with very low-overhead decompression to enable cheaper and faster graph processing. The key idea is to encode a graph so that the parts of the representation approach or match the respective storage lower bounds. We call our approach "graph logarithmization" because these bounds are usually logarithmic. Our high-performance Log(Graph) implementation based on modern bitwise operations and state-of-the-art succinct data structures achieves high compression ratios as well as performance. For example, compared to the tuned Graph Algorithm Processing Benchmark Suite (GAPBS), it reduces graph sizes by 20-35% while matching GAPBS' performance or even delivering speedups due to reducing amounts of transferred data. It approaches the compression ratio of the established WebGraph compression library while enabling speedups of up to more than 2x. Log(Graph) can improve the design of various graph processing engines or libraries on single NUMA nodes as well as distributed-memory systems.

Tal Ben-Nun, Maciej Besta, Simon Huber et al.

We introduce Deep500: the first customizable benchmarking infrastructure that enables fair comparison of the plethora of deep learning frameworks, algorithms, libraries, and techniques. The key idea behind Deep500 is its modular design, where deep learning is factorized into four distinct levels: operators, network processing, training, and distributed training. Our evaluation illustrates that Deep500 is customizable (enables combining and benchmarking different deep learning codes) and fair (uses carefully selected metrics). Moreover, Deep500 is fast (incurs negligible overheads), verifiable (offers infrastructure to analyze correctness), and reproducible. Finally, as the first distributed and reproducible benchmarking system for deep learning, Deep500 provides software infrastructure to utilize the most powerful supercomputers for extreme-scale workloads.