arXiv subjects

Liudmila Prokhorenkova

Publications and source records attributed to Liudmila Prokhorenkova.

At least 19 recordsLinked to original sources

arXiv2026

GraphPFN: A Prior-Data Fitted Graph Foundation Model

Graph foundation models face several fundamental challenges including transferability across diverse domains and data scarcity, which calls into question the very feasibility of creating such models. However, despite similar challenges, the tabular domain has recently witnessed the emergence of the first successful foundation models such as TabPFN. These models are based on the prior-data fitted networks (PFN) framework, in which models are pretrained on carefully designed synthetic datasets to make predictions in an in-context learning setting. Recently, G2T-FM, a framework that converts graph node-level tasks into tabular tasks, has made the first step towards adopting PFNs for graphs, yet it is limited to hand-crafted features and was never pretrained on graph data. In this work, we make the next step by proposing GraphPFN, a PFN-based model designed and pretrained specifically for graph node-level tasks. Following the PFN framework, we first design a prior distribution of synthetic attributed graphs by using a novel combination of multi-level stochastic block models and a preferential attachment process for structure generation and graph-aware structured causal models for attribute generation. Then, we augment the tabular foundation model LimiX with attention-based graph neighborhood aggregation layers and train it on millions of synthetic graphs sampled from our prior. On diverse real-world graph datasets with node-level tasks, GraphPFN achieves state-of-the-art results in both in-context learning and finetuning regimes, outperforming G2T-FM, prior GFMs, and task-specific GNNs trained from scratch. More broadly, GraphPFN shows the potential of PFN-based models for building graph foundation models.

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arXiv2026

Cluster Attention for Graph Machine Learning

Message Passing Neural Networks have recently become the most popular approach to graph machine learning tasks; however, their receptive field is limited by the number of message passing layers. To increase the receptive field, Graph Transformers with global attention have been proposed; however, global attention does not take into account the graph topology and thus lacks graph-structure-based inductive biases, which are typically very important for graph machine learning tasks. In this work, we propose an alternative approach: cluster attention (CLATT). We divide graph nodes into clusters with off-the-shelf graph community detection algorithms and let each node attend to all other nodes in each cluster. CLATT provides large receptive fields while still having strong graph-structure-based inductive biases. We show that augmenting Message Passing Neural Networks or Graph Transformers with CLATT significantly improves their performance on a wide range of graph datasets including datasets from the recently introduced GraphLand benchmark representing real-world applications of graph machine learning.

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arXiv2026

Relevance-Based Embeddings: Lightweight Candidate Retrieval via Heavy-Ranker Calls

In many machine learning applications, the most relevant items for a query should be efficiently retrieved. The relevance function is usually an expensive similarity model, making the exhaustive search infeasible. A typical solution is to train another model that separately embeds queries and items to a vector space, where similarity is defined via the dot product or cosine similarity. This allows one to search the relevant items through fast approximate nearest neighbor search at the cost of some reduction in quality. To compensate for this reduction, the found items (candidates) are re-ranked by the expensive ranking model. In this paper, we investigate an alternative approach to candidate selection that utilizes the scores of the expensive model to improve the representations of queries and items. The idea is to describe each query (item) by its relevance to a set of support items (queries) and use these new representations to obtain query (item) embeddings. We theoretically prove that such embeddings are powerful enough to approximate any complex similarity model (under mild conditions). We also investigate the choice of support items, which is a crucial ingredient of the proposed approach. The experiments on diverse academic and production datasets illustrate the power of our method.

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arXiv2026

A Fair Evaluation of Graph Foundation Models for Node Property Prediction

Due to the wide use of graph-structured data in different fields of industry and science, the development of Graph Foundation Models (GFMs) has recently attracted a lot of attention. While many different types of models are called GFMs, particular interest has been paid to GFMs designed for node property prediction tasks, which is one of the most popular settings in Graph ML with lots of real-world applications from fraud detection in financial and social networks to recommendation systems for e-commerce and user-generated content platforms. While a number of GFMs for this task have been recently proposed, the field has not converged to a unified evaluation setting, and different works evaluate their models in widely different ways, preventing reliable comparison of GFMs with each other and with other types of models. In this work, we conduct a fair and rigorous reevaluation of 9 recent GFMs for node property prediction, comparing them to strong Graph Neural Network (GNN) baselines. We find that, among these GFMs, only the most recent ones based on the Prior-data Fitted Networks paradigm outperform well-tuned GNNs in predictive performance, although at a higher inference cost.

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arXiv2026

Turning Tabular Foundation Models into Graph Foundation Models

While foundation models have revolutionized fields such as natural language processing and computer vision, their potential in graph machine learning remains largely unexplored. One of the key challenges in designing graph foundation models (GFMs) is handling diverse node features that can vary across different graph datasets. While many works on GFMs have focused exclusively on text-attributed graphs, the problem of handling arbitrary features of other types in GFMs has not been fully addressed. However, this problem is not unique to the graph domain, as it also arises in the field of machine learning for tabular data. In this work, motivated by the recent success of tabular foundation models (TFMs) like TabPFNv2 and LimiX, we propose G2T-FM, a simple framework that allows tabular foundation models to be applied to graph node-level tasks. Specifically, G2T-FM augments the original node features with neighborhood feature aggregation, adds structural embeddings, and then applies a TFM to the constructed node representations. Even in the in-context learning setting, our model achieves strong results when combined with a strong TFM, outperforming both prior GFMs and well-tuned GNNs trained from scratch. Moreover, after finetuning, G2T-FM consistently surpasses well-tuned GNN baselines, often by a significant margin. In summary, our paper reveals the potential of a previously overlooked direction: utilizing tabular foundation models for graph machine learning tasks.

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arXiv2026

Metropolis-Scale Road Network Datasets for Fine-Grained Urban Traffic Modeling

Modeling traffic dynamics is a critical challenge for urban computing, with applications from real-time traffic management to infrastructure planning. However, progress in this area is fundamentally constrained by a lack of large-scale public datasets that capture the subtle properties of real city road networks. Existing benchmarks are often limited by their small scale, reliance on sparse highway traffic sensors, absence of true road connectivity information, and lack of information about road properties. To address this issue, we introduce datasets representing fine-grained road networks of two major cities, which are unique in their scale (up to 100,000 road segments), use of real road connectivity, presence of time series measurements for both traffic speed and volume at a 5-minute resolution, and inclusion of rich static road attributes. These datasets enable in-depth analysis of spatiotemporal traffic patterns and can serve as benchmarks for various ML applications. As a practical demonstration of the utility of our datasets and the challenges they present, we use them for the task of traffic forecasting. The size of the real-world road networks in our datasets reveals significant scalability issues in current traffic forecasting models. To address them, we propose a simple and efficient baseline that not only scales to large road graphs but also achieves forecasting performance competitive with other established spatiotemporal models. We hope that the proposed datasets will serve as a foundational resource for a broad range of research in traffic modeling, urban computing, and smart city development.

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arXiv2026

GraphLand: Evaluating Graph Machine Learning Models on Diverse Industrial Data

Although data that can be naturally represented as graphs is widespread in real-world applications across diverse industries, popular graph ML benchmarks for node property prediction only cover a surprisingly narrow set of data domains, and graph neural networks (GNNs) are often evaluated on just a few academic citation networks. This issue is particularly pressing in light of the recent growing interest in designing graph foundation models. These models are supposed to be able to transfer to diverse graph datasets from different domains, and yet the proposed graph foundation models are often evaluated on a very limited set of datasets from narrow applications. To alleviate this issue, we introduce GraphLand: a benchmark of 14 diverse graph datasets for node property prediction from a range of different industrial applications. GraphLand allows evaluating graph ML models on a wide range of graphs with diverse sizes, structural characteristics, and feature sets, all in a unified setting. Further, GraphLand allows investigating such previously underexplored research questions as how realistic temporal distributional shifts under transductive and inductive settings influence graph ML model performance. To mimic realistic industrial settings, we use GraphLand to compare GNNs with gradient-boosted decision trees (GBDT) models that are popular in industrial applications and show that GBDTs provided with additional graph-based input features can sometimes be very strong baselines. Further, we evaluate currently available general-purpose graph foundation models and find that they fail to produce competitive results on our proposed datasets.

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arXiv2025

Discrete Neural Algorithmic Reasoning

Neural algorithmic reasoning aims to capture computations with neural networks by training models to imitate the execution of classical algorithms. While common architectures are expressive enough to contain the correct model in the weight space, current neural reasoners struggle to generalize well on out-of-distribution data. On the other hand, classical computations are not affected by distributional shifts as they can be described as transitions between discrete computational states. In this work, we propose to force neural reasoners to maintain the execution trajectory as a combination of finite predefined states. To achieve this, we separate discrete and continuous data flows and describe the interaction between them. Trained with supervision on the algorithm's state transitions, such models are able to perfectly align with the original algorithm. To show this, we evaluate our approach on multiple algorithmic problems and achieve perfect test scores both in single-task and multitask setups. Moreover, the proposed architectural choice allows us to prove the correctness of the learned algorithms for any test data.

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arXiv2025

Measuring Diversity: Axioms and Challenges

This paper addresses the problem of quantifying diversity for a set of objects. First, we conduct a systematic review of existing diversity measures and explore their undesirable behavior in certain cases. Based on this review, we formulate three desirable properties (axioms) of a reliable diversity measure: monotonicity, uniqueness, and continuity. We show that none of the existing measures has all three properties and thus these measures are not suitable for quantifying diversity. Then, we construct two examples of measures that have all the desirable properties, thus proving that the list of axioms is not self-contradictory. Unfortunately, the constructed examples are too computationally expensive (NP-hard) for practical use. Thus, we pose an open problem of constructing a diversity measure that has all the listed properties and can be computed in practice or proving that all such measures are NP-hard to compute.

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arXiv2024

Revisiting Graph Homophily Measures

Homophily is a graph property describing the tendency of edges to connect similar nodes. There are several measures used for assessing homophily but all are known to have certain drawbacks: in particular, they cannot be reliably used for comparing datasets with varying numbers of classes and class size balance. To show this, previous works on graph homophily suggested several properties desirable for a good homophily measure, also noting that no existing homophily measure has all these properties. Our paper addresses this issue by introducing a new homophily measure - unbiased homophily - that has all the desirable properties and thus can be reliably used across datasets with different label distributions. The proposed measure is suitable for undirected (and possibly weighted) graphs. We show both theoretically and via empirical examples that the existing homophily measures have serious drawbacks while unbiased homophily has a desirable behavior for the considered scenarios. Finally, when it comes to directed graphs, we prove that some desirable properties contradict each other and thus a measure satisfying all of them cannot exist.

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arXiv2024

Challenges of Generating Structurally Diverse Graphs

For many graph-related problems, it can be essential to have a set of structurally diverse graphs. For instance, such graphs can be used for testing graph algorithms or their neural approximations. However, to the best of our knowledge, the problem of generating structurally diverse graphs has not been explored in the literature. In this paper, we fill this gap. First, we discuss how to define diversity for a set of graphs, why this task is non-trivial, and how one can choose a proper diversity measure. Then, for a given diversity measure, we propose and compare several algorithms optimizing it: we consider approaches based on standard random graph models, local graph optimization, genetic algorithms, and neural generative models. We show that it is possible to significantly improve diversity over basic random graph generators. Additionally, our analysis of generated graphs allows us to better understand the properties of graph distances: depending on which diversity measure is used for optimization, the obtained graphs may possess very different structural properties which gives a better understanding of the graph distance underlying the diversity measure.

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arXiv2024

Characterizing Graph Datasets for Node Classification: Homophily-Heterophily Dichotomy and Beyond

Homophily is a graph property describing the tendency of edges to connect similar nodes; the opposite is called heterophily. It is often believed that heterophilous graphs are challenging for standard message-passing graph neural networks (GNNs), and much effort has been put into developing efficient methods for this setting. However, there is no universally agreed-upon measure of homophily in the literature. In this work, we show that commonly used homophily measures have critical drawbacks preventing the comparison of homophily levels across different datasets. For this, we formalize desirable properties for a proper homophily measure and verify which measures satisfy which properties. In particular, we show that a measure that we call adjusted homophily satisfies more desirable properties than other popular homophily measures while being rarely used in graph machine learning literature. Then, we go beyond the homophily-heterophily dichotomy and propose a new characteristic that allows one to further distinguish different sorts of heterophily. The proposed label informativeness (LI) characterizes how much information a neighbor's label provides about a node's label. We prove that this measure satisfies important desirable properties. We also observe empirically that LI better agrees with GNN performance compared to homophily measures, which confirms that it is a useful characteristic of the graph structure.

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arXiv2024

A critical look at the evaluation of GNNs under heterophily: Are we really making progress?

Node classification is a classical graph machine learning task on which Graph Neural Networks (GNNs) have recently achieved strong results. However, it is often believed that standard GNNs only work well for homophilous graphs, i.e., graphs where edges tend to connect nodes of the same class. Graphs without this property are called heterophilous, and it is typically assumed that specialized methods are required to achieve strong performance on such graphs. In this work, we challenge this assumption. First, we show that the standard datasets used for evaluating heterophily-specific models have serious drawbacks, making results obtained by using them unreliable. The most significant of these drawbacks is the presence of a large number of duplicate nodes in the datasets Squirrel and Chameleon, which leads to train-test data leakage. We show that removing duplicate nodes strongly affects GNN performance on these datasets. Then, we propose a set of heterophilous graphs of varying properties that we believe can serve as a better benchmark for evaluating the performance of GNNs under heterophily. We show that standard GNNs achieve strong results on these heterophilous graphs, almost always outperforming specialized models. Our datasets and the code for reproducing our experiments are available at https://github.com/yandex-research/heterophilous-graphs

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arXiv2023

Evaluating Robustness and Uncertainty of Graph Models Under Structural Distributional Shifts

In reliable decision-making systems based on machine learning, models have to be robust to distributional shifts or provide the uncertainty of their predictions. In node-level problems of graph learning, distributional shifts can be especially complex since the samples are interdependent. To evaluate the performance of graph models, it is important to test them on diverse and meaningful distributional shifts. However, most graph benchmarks considering distributional shifts for node-level problems focus mainly on node features, while structural properties are also essential for graph problems. In this work, we propose a general approach for inducing diverse distributional shifts based on graph structure. We use this approach to create data splits according to several structural node properties: popularity, locality, and density. In our experiments, we thoroughly evaluate the proposed distributional shifts and show that they can be quite challenging for existing graph models. We also reveal that simple models often outperform more sophisticated methods on the considered structural shifts. Finally, our experiments provide evidence that there is a trade-off between the quality of learned representations for the base classification task under structural distributional shift and the ability to separate the nodes from different distributions using these representations.

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arXiv2023

Neural Algorithmic Reasoning Without Intermediate Supervision

Neural algorithmic reasoning is an emerging area of machine learning focusing on building models that can imitate the execution of classic algorithms, such as sorting, shortest paths, etc. One of the main challenges is to learn algorithms that are able to generalize to out-of-distribution data, in particular with significantly larger input sizes. Recent work on this problem has demonstrated the advantages of learning algorithms step-by-step, giving models access to all intermediate steps of the original algorithm. In this work, we instead focus on learning neural algorithmic reasoning only from the input-output pairs without appealing to the intermediate supervision. We propose simple but effective architectural improvements and also build a self-supervised objective that can regularise intermediate computations of the model without access to the algorithm trajectory. We demonstrate that our approach is competitive to its trajectory-supervised counterpart on tasks from the CLRS Algorithmic Reasoning Benchmark and achieves new state-of-the-art results for several problems, including sorting, where we obtain significant improvements. Thus, learning without intermediate supervision is a promising direction for further research on neural reasoners.

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arXiv2023

Which Tricks Are Important for Learning to Rank?

Nowadays, state-of-the-art learning-to-rank methods are based on gradient-boosted decision trees (GBDT). The most well-known algorithm is LambdaMART which was proposed more than a decade ago. Recently, several other GBDT-based ranking algorithms were proposed. In this paper, we thoroughly analyze these methods in a unified setup. In particular, we address the following questions. Is direct optimization of a smoothed ranking loss preferable over optimizing a convex surrogate? How to properly construct and smooth surrogate ranking losses? To address these questions, we compare LambdaMART with YetiRank and StochasticRank methods and their modifications. We also propose a simple improvement of the YetiRank approach that allows for optimizing specific ranking loss functions. As a result, we gain insights into learning-to-rank techniques and obtain a new state-of-the-art algorithm.

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arXiv2023

Gradient Boosting Performs Gaussian Process Inference

This paper shows that gradient boosting based on symmetric decision trees can be equivalently reformulated as a kernel method that converges to the solution of a certain Kernel Ridge Regression problem. Thus, we obtain the convergence to a Gaussian Process' posterior mean, which, in turn, allows us to easily transform gradient boosting into a sampler from the posterior to provide better knowledge uncertainty estimates through Monte-Carlo estimation of the posterior variance. We show that the proposed sampler allows for better knowledge uncertainty estimates leading to improved out-of-domain detection.

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arXiv2022

Overlapping Spaces for Compact Graph Representations

Various non-trivial spaces are becoming popular for embedding structured data such as graphs, texts, or images. Following spherical and hyperbolic spaces, more general product spaces have been proposed. However, searching for the best configuration of product space is a resource-intensive procedure, which reduces the practical applicability of the idea. We generalize the concept of product space and introduce an overlapping space that does not have the configuration search problem. The main idea is to allow subsets of coordinates to be shared between spaces of different types (Euclidean, hyperbolic, spherical). As a result, parameter optimization automatically learns the optimal configuration. Additionally, overlapping spaces allow for more compact representations since their geometry is more complex. Our experiments confirm that overlapping spaces outperform the competitors in graph embedding tasks. Here, we consider both distortion setup, where the aim is to preserve distances, and ranking setup, where the relative order should be preserved. The proposed method effectively solves the problem and outperforms the competitors in both settings. We also perform an empirical analysis in a realistic information retrieval task, where we compare all spaces by incorporating them into DSSM. In this case, the proposed overlapping space consistently achieves nearly optimal results without any configuration tuning. This allows for reducing training time, which can be significant in large-scale applications.

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