Lev Telyatnikov

Mathilde Papillon, Mustafa Hajij, Helen Jenne et al.

This paper presents the computational challenge on topological deep learning that was hosted within the ICML 2023 Workshop on Topology and Geometry in Machine Learning. The competition asked participants to provide open-source implementations of topological neural networks from the literature by contributing to the python packages TopoNetX (data processing) and TopoModelX (deep learning). The challenge attracted twenty-eight qualifying submissions in its two-month duration. This paper describes the design of the challenge and summarizes its main findings.

Raffael Theiler, Lev Telyatnikov, Leandro Von Krannichfeldt et al.

Data-driven Prognostics and Health Management (PHM) uses time-varying condition-monitoring data to diagnose system states and estimate remaining useful life in engineered assets. These tasks are central to maintenance planning, but industrial PHM data are often fragmented, partially observed, and poorly labeled, which hinders supervised learning. Foundation models offer a route toward reusable predictive systems, yet most time-series foundation models are designed for forecasting and assume long, coherent, regularly sampled sequences. To address this gap, we propose a framework for applying Tabular Foundation Models to industrial time series using in-context learning, and we evaluate them on a variety of PHM tasks. By converting raw unit-level signals into tabular rows, we show that these models perform well across multiple tasks - including prognostics, and diagnostics - and are highly data efficient. We compare them directly with sequence models, transformer baselines, and gradient-boosted trees under a common evaluation protocol. The results indicate that tabular foundation models achieve the best average ranks across prognostic and diagnostic tasks. Our findings further show that PFN-based models are competitive in low-data regimes, that temporal context can be preserved in the tabular representation, and that performance depends on representative context construction under subsampling. These results demonstrate that tabular foundation models provide a practical and general interface for heterogeneous PHM problems.

Lev Telyatnikov, Simone Scardapane

Missing data imputation (MDI) is crucial when dealing with tabular datasets across various domains. Autoencoders can be trained to reconstruct missing values, and graph autoencoders (GAE) can additionally consider similar patterns in the dataset when imputing new values for a given instance. However, previously proposed GAEs suffer from scalability issues, requiring the user to define a similarity metric among patterns to build the graph connectivity beforehand. In this paper, we leverage recent progress in latent graph imputation to propose a novel EdGe Generation Graph AutoEncoder (EGG-GAE) for missing data imputation that overcomes these two drawbacks. EGG-GAE works on randomly sampled mini-batches of the input data (hence scaling to larger datasets), and it automatically infers the best connectivity across the mini-batch for each architecture layer. We also experiment with several extensions, including an ensemble strategy for inference and the inclusion of what we call prototype nodes, obtaining significant improvements, both in terms of imputation error and final downstream accuracy, across multiple benchmarks and baselines.

Lev Telyatnikov, Maria Sofia Bucarelli, Guillermo Bernardez et al.

Most of the current hypergraph learning methodologies and benchmarking datasets in the hypergraph realm are obtained by lifting procedures from their graph analogs, leading to overshadowing specific characteristics of hypergraphs. This paper attempts to confront some pending questions in that regard: Q1 Can the concept of homophily play a crucial role in Hypergraph Neural Networks (HNNs)? Q2 Is there room for improving current HNN architectures by carefully addressing specific characteristics of higher-order networks? Q3 Do existing datasets provide a meaningful benchmark for HNNs? To address them, we first introduce a novel conceptualization of homophily in higher-order networks based on a Message Passing (MP) scheme, unifying both the analytical examination and the modeling of higher-order networks. Further, we investigate some natural, yet mostly unexplored, strategies for processing higher-order structures within HNNs such as keeping hyperedge-dependent node representations, or performing node/hyperedge stochastic samplings, leading us to the most general MP formulation up to date -MultiSet-, as well as to an original architecture design, MultiSetMixer. Finally, we conduct an extensive set of experiments that contextualize our proposals and successfully provide insights about our inquiries.

Lev Telyatnikov, Raffael Theiler, Leandro Von Krannichfeldt et al.

Progress in Prognostics and Health Management (PHM) is hindered by the lack of standardized and reusable evaluation practices across tasks, datasets, and application domains. Reported results are often difficult to reproduce and compare, as key protocol choices, such as data splits, preprocessing, label alignment, temporal windowing, and metrics, are often implicit or implemented ad hoc. We introduce \picid, a modular evaluation infrastructure that formalizes the PHM evaluation pipeline as an explicit, executable, and reproducible protocol. Through well-defined abstractions, \picid enforces deterministic, leakage-safe dataset construction while remaining flexible across diverse PHM settings. The framework supports fault detection, diagnostics, and prognostics through a unified interface and can be extended to new datasets and model classes without violating protocol invariants. By standardizing data contracts and evaluation boundaries, \picid also enables fair cross-task comparisons across diagnostics (classification) and prognostics (regression), allowing identical model families to be evaluated consistently across heterogeneous settings. We demonstrate \picid through an empirical evaluation of thirteen models on twelve datasets spanning batteries, bearings, turbofan engines, hydraulics, filtration systems, and buildings. This work establishes a reusable foundation for standardized, fair and reproducible evaluation in PHM.

Raffael Theiler, Ludovico Comito, David Leko et al.

Industrial Prognostics and Health Management (PHM) provides a representative case study for a broader challenge in applied machine learning: translating published papers into executable, benchmark-ready implementations. Reproducing under-specified methods in PHM is particularly difficult due to restricted access to industrial datasets, incomplete reporting of preprocessing and evaluation protocols, and implicit design choices (e.g., windowing, target construction, data splits) that critically affect performance. Existing paper-to-code systems generate implementations for individual papers, but these artifacts are often not directly comparable due to inconsistencies in assumptions and evaluation settings. We introduce \emph{agentic, framework-based PHM paper reproduction}, where an agent translates a paper into a shared PHM benchmark framework via a \emph{slot-binding interface}. This interface maps equations and protocol descriptions into structured components (task definitions, dataset adapters, windowing, targets, models, and evaluators), while explicitly recording unresolved assumptions. The resulting implementations are validated against standardized task contracts and evaluation hooks, enabling consistent and comparable benchmarking. We evaluate this approach on 16 PHM papers, comparing framework-enhanced, skill-based and prompt-based agentic reproduction against a recent framework-free paper-reproduction agent. We assess reproduction success, model-based code evaluation, framework binding of paper assumptions, and cross-paper benchmark comparability under standardized protocols. Our results show that coupling agentic generation with a shared framework transforms paper reproduction from isolated code synthesis into executable, assumption-aware, and systematically comparable benchmark implementations.

Guillermo Bernárdez, Lev Telyatnikov, Eduard Alarcón et al.

Recently emerged Topological Deep Learning (TDL) methods aim to extend current Graph Neural Networks (GNN) by naturally processing higher-order interactions, going beyond the pairwise relations and local neighborhoods defined by graph representations. In this paper we propose a novel TDL-based method for compressing signals over graphs, consisting in two main steps: first, disjoint sets of higher-order structures are inferred based on the original signal --by clustering $N$ datapoints into $K\ll N$ collections; then, a topological-inspired message passing gets a compressed representation of the signal within those multi-element sets. Our results show that our framework improves both standard GNN and feed-forward architectures in compressing temporal link-based signals from two real-word Internet Service Provider Networks' datasets --from $30\%$ up to $90\%$ better reconstruction errors across all evaluation scenarios--, suggesting that it better captures and exploits spatial and temporal correlations over the whole graph-based network structure.

Guillermo Bernárdez, Lev Telyatnikov, Marco Montagna et al.

This paper describes the 2nd edition of the ICML Topological Deep Learning Challenge that was hosted within the ICML 2024 ELLIS Workshop on Geometry-grounded Representation Learning and Generative Modeling (GRaM). The challenge focused on the problem of representing data in different discrete topological domains in order to bridge the gap between Topological Deep Learning (TDL) and other types of structured datasets (e.g. point clouds, graphs). Specifically, participants were asked to design and implement topological liftings, i.e. mappings between different data structures and topological domains --like hypergraphs, or simplicial/cell/combinatorial complexes. The challenge received 52 submissions satisfying all the requirements. This paper introduces the main scope of the challenge, and summarizes the main results and findings.

Marco Montagna, Simone Scardapane, Lev Telyatnikov

Graph Neural Networks based on the message-passing (MP) mechanism are a dominant approach for handling graph-structured data. However, they are inherently limited to modeling only pairwise interactions, making it difficult to explicitly capture the complexity of systems with $n$-body relations. To address this, topological deep learning has emerged as a promising field for studying and modeling higher-order interactions using various topological domains, such as simplicial and cellular complexes. While these new domains provide powerful representations, they introduce new challenges, such as effectively modeling the interactions among higher-order structures through higher-order MP. Meanwhile, structured state-space sequence models have proven to be effective for sequence modeling and have recently been adapted for graph data by encoding the neighborhood of a node as a sequence, thereby avoiding the MP mechanism. In this work, we propose a novel architecture designed to operate with simplicial complexes, utilizing the Mamba state-space model as its backbone. Our approach generates sequences for the nodes based on the neighboring cells, enabling direct communication between all higher-order structures, regardless of their rank. We extensively validate our model, demonstrating that it achieves competitive performance compared to state-of-the-art models developed for simplicial complexes.

Lev Telyatnikov, Guillermo Bernardez, Marco Montagna et al.

This work introduces TopoBench, an open-source library designed to standardize benchmarking and accelerate research in topological deep learning (TDL). TopoBench decomposes TDL into a sequence of independent modules for data generation, loading, transforming and processing, as well as model training, optimization and evaluation. This modular organization provides flexibility for modifications and facilitates the adaptation and optimization of various TDL pipelines. A key feature of TopoBench is its support for transformations and lifting across topological domains. Mapping the topology and features of a graph to higher-order topological domains, such as simplicial and cell complexes, enables richer data representations and more fine-grained analyses. The applicability of TopoBench is demonstrated by benchmarking several TDL architectures across diverse tasks and datasets.

Mustafa Hajij, Mathilde Papillon, Florian Frantzen et al.

We introduce TopoX, a Python software suite that provides reliable and user-friendly building blocks for computing and machine learning on topological domains that extend graphs: hypergraphs, simplicial, cellular, path and combinatorial complexes. TopoX consists of three packages: TopoNetX facilitates constructing and computing on these domains, including working with nodes, edges and higher-order cells; TopoEmbedX provides methods to embed topological domains into vector spaces, akin to popular graph-based embedding algorithms such as node2vec; TopoModelX is built on top of PyTorch and offers a comprehensive toolbox of higher-order message passing functions for neural networks on topological domains. The extensively documented and unit-tested source code of TopoX is available under MIT license at https://pyt-team.github.io/}{https://pyt-team.github.io/.

Martin Carrasco, Guillermo Bernardez, Marco Montagna et al.

While Graph Neural Networks (GNNs) have proven highly effective at modeling relational data, pairwise connections cannot fully capture multi-way relationships naturally present in complex real-world systems. In response to this, Topological Deep Learning (TDL) leverages more general combinatorial representations -- such as simplicial or cellular complexes -- to accommodate higher-order interactions. Existing TDL methods often extend GNNs through Higher-Order Message Passing (HOMP), but face critical \emph{scalability challenges} due to \textit{(i)} a combinatorial explosion of message-passing routes, and \textit{(ii)} significant complexity overhead from the propagation mechanism. This work presents HOPSE (Higher-Order Positional and Structural Encoder), an alternative method to solve tasks involving higher-order interactions \emph{without message passing}. Instead, HOPSE breaks \emph{arbitrary higher-order domains} into their neighborhood relationships using a Hasse graph decomposition. This method shows that decoupling the representation learning of neighborhood topology from that of attributes results in lower computational complexity, casting doubt on the need for HOMP. The experiments on molecular graph tasks and topological benchmarks show that HOPSE matches performance on traditional TDL datasets and outperforms HOMP methods on topological tasks, achieving up to $7\times$ speedups over HOMP-based models, opening a new path for scalable TDL.

Claudio Battiloro, Indro Spinelli, Lev Telyatnikov et al.

Latent Graph Inference (LGI) relaxed the reliance of Graph Neural Networks (GNNs) on a given graph topology by dynamically learning it. However, most of LGI methods assume to have a (noisy, incomplete, improvable, ...) input graph to rewire and can solely learn regular graph topologies. In the wake of the success of Topological Deep Learning (TDL), we study Latent Topology Inference (LTI) for learning higher-order cell complexes (with sparse and not regular topology) describing multi-way interactions between data points. To this aim, we introduce the Differentiable Cell Complex Module (DCM), a novel learnable function that computes cell probabilities in the complex to improve the downstream task. We show how to integrate DCM with cell complex message passing networks layers and train it in a end-to-end fashion, thanks to a two-step inference procedure that avoids an exhaustive search across all possible cells in the input, thus maintaining scalability. Our model is tested on several homophilic and heterophilic graph datasets and it is shown to outperform other state-of-the-art techniques, offering significant improvements especially in cases where an input graph is not provided.