Peyman Baghershahi

Peyman Baghershahi, Reshad Hosseini, Hadi Moradi

Numerous Graph Neural Networks (GNNs) have been developed to tackle the challenge of Knowledge Graph Embedding (KGE). However, many of these approaches overlook the crucial role of relation information and inadequately integrate it with entity information, resulting in diminished expressive power. In this paper, we propose a novel knowledge graph encoder that incorporates tensor decomposition within the aggregation function of Relational Graph Convolutional Network (R-GCN). Our model enhances the representation of neighboring entities by employing projection matrices of a low-rank tensor defined by relation types. This approach facilitates multi-task learning, thereby generating relation-aware representations. Furthermore, we introduce a low-rank estimation technique for the core tensor through CP decomposition, which effectively compresses and regularizes our model. We adopt a training strategy inspired by contrastive learning, which relieves the training limitation of the 1-N method inherent in handling vast graphs. We outperformed all our competitors on two common benchmark datasets, FB15k-237 and WN18RR, while using low-dimensional embeddings for entities and relations.

Angelo Zangari, Peyman Baghershahi, Sourav Medya

Graph problems are fundamentally challenging for large language models (LLMs). While LLMs excel at processing unstructured text, graph tasks require reasoning over explicit structure, permutation invariance, and computationally complex relationships, creating a mismatch with the representations of text-based models. Our work investigates how LLMs can be effectively applied to graph problems despite these barriers. We introduce a human-interpretable structural encoding strategy for graph-to-text translation that injects graph structure directly into natural language prompts. Our method involves computing a variant of Weisfeiler-Lehman (WL) similarity classes and maps them to human-like color tokens rather than numeric labels. The key insight is that semantically meaningful and human-interpretable cues may be more effectively processed by LLMs than opaque symbolic encoding. Experimental results on multiple algorithmic and predictive graph tasks show the considerable improvements by our method on both synthetic and real-world datasets. By capturing both local and global-range dependencies, our method enhances LLM performance especially on graph tasks that require reasoning over global graph structure.

Peyman Baghershahi, Fangxin Wang, Debmalya Mandal et al.

Conformal prediction (CP) provides a distribution-free approach to uncertainty quantification with finite-sample guarantees. However, applying CP to graph neural networks (GNNs) remains challenging as the combinatorial nature of graphs often leads to insufficiently certain predictions and indiscriminative embeddings. Existing methods primarily rely on embedding-space proximity for localization, which can be unreliable for graphs and yield inefficient prediction sets. We propose GRAPHLCP, a proximity-based localized CP framework that explicitly incorporates graph topology and inter-node dependencies into localization and weighting. Our approach introduces a feature-aware densification step to mitigate locality bias in sparse graphs, followed by a Personalized PageRank-based kernel computation to model structural proximity. This enables topology-dependent anchor sampling and calibration weighting that captures both local and long-range dependencies. Extensive experiments on several regression and classification datasets demonstrate that GRAPHLCP guarantees marginal coverage with finite samples while efficiently attaining favorable test conditional coverage across various conditioning scenarios.

Peyman Baghershahi, Gregoire Fournier, Pranav Nyati et al.

Graph Neural Networks (GNNs) have emerged as powerful tools for learning over structured data, including text-attributed graphs, which are common in domains such as citation networks, social platforms, and knowledge graphs. GNNs are not inherently interpretable and thus, many explanation methods have been proposed. However, existing explanation methods often struggle to generate interpretable, fine-grained rationales, especially when node attributes include rich natural language. In this work, we introduce LOGIC, a lightweight, post-hoc framework that uses large language models (LLMs) to generate faithful and interpretable explanations for GNN predictions. LOGIC projects GNN node embeddings into the LLM embedding space and constructs hybrid prompts that interleave soft prompts with textual inputs from the graph structure. This enables the LLM to reason about GNN internal representations and produce natural language explanations along with concise explanation subgraphs. Our experiments across four real-world TAG datasets demonstrate that LOGIC achieves a favorable trade-off between fidelity and sparsity, while significantly improving human-centric metrics such as insightfulness. LOGIC sets a new direction for LLM-based explainability in graph learning by aligning GNN internals with human reasoning.

Pantea Habibi, Peyman Baghershahi, Sourav Medya et al.

Graph neural networks (GNNs) are powerful graph-based machine-learning models that are popular in various domains, e.g., social media, transportation, and drug discovery. However, owing to complex data representations, GNNs do not easily allow for human-intelligible explanations of their predictions, which can decrease trust in them as well as deter any collaboration opportunities between the AI expert and non-technical, domain expert. Here, we first discuss the two papers that aim to provide GNN explanations to domain experts in an accessible manner and then establish a set of design requirements for human-centered GNN explanations. Finally, we offer two example prototypes to demonstrate some of those proposed requirements.

Fangxin Wang, Peyman Baghershahi, Langzhou He et al.

Gradient-based data selection offers a principled framework for estimating sample utility in large language model (LLM) fine-tuning, but existing methods are mostly designed for offline settings. They are therefore less suited to online fine-tuning, where data arrives sequentially, sample utility is step-dependent, and the effective update geometry is shaped by adaptive optimizers. We propose an optimizer-aware framework for gradient-based online data selection and reweighting in LLM fine-tuning. Our key idea is to view online selection not as static sample ranking, but as shaping the next target-oriented update under the optimizer state. We formulate this as an optimizer-aware update-matching problem, establish its connection to second-order target utility, and show why subset-level construction must account for interactions and redundancy among selected samples. Based on this view, we develop a two-stage Filter-then-Weight algorithm that first filters geometrically useful candidates and then optimizes their coefficients. To make the framework practical for LLMs, we introduce a factorized outer-product gradient representation and optimized matrix computations for long-context data. Experiments show that our method consistently improves convergence and downstream performance over existing online data selection baselines under the same data budget.

Peyman Baghershahi, Sourav Medya

Prompt tuning methods for Graph Neural Networks (GNNs) have become popular to address the semantic gap between pre-training and fine-tuning steps. However, existing GNN prompting methods rely on labeled data and involve lightweight fine-tuning for downstream tasks. Meanwhile, in-context learning methods for Large Language Models (LLMs) have shown promising performance with no parameter updating and no or minimal labeled data. Inspired by these approaches, in this work, we first introduce a challenging problem setup to evaluate GNN prompting methods. This setup encourages a prompting function to enhance a pre-trained GNN's generalization to a target dataset under covariate shift without updating the GNN's parameters and with no labeled data. Next, we propose a fully unsupervised prompting method based on consistency regularization through pseudo-labeling. We use two regularization techniques to align the prompted graphs' distribution with the original data and reduce biased predictions. Through extensive experiments under our problem setting, we demonstrate that our unsupervised approach outperforms the state-of-the-art prompting methods that have access to labels.

Rochana Chaturvedi, Peyman Baghershahi, Sourav Medya et al.

Temporal information extraction from unstructured text is essential for contextualizing events and deriving actionable insights, particularly in the medical domain. We address the task of extracting clinical events and their temporal relations using the well-studied I2B2 2012 Temporal Relations Challenge corpus. This task is inherently challenging due to complex clinical language, long documents, and sparse annotations. We introduce GRAPHTREX, a novel method integrating span-based entity-relation extraction, clinical large pre-trained language models (LPLMs), and Heterogeneous Graph Transformers (HGT) to capture local and global dependencies. Our HGT component facilitates information propagation across the document through innovative global landmarks that bridge distant entities. Our method improves the state-of-the-art with 5.5% improvement in the tempeval $F_1$ score over the previous best and up to 8.9% improvement on long-range relations, which presents a formidable challenge. We further demonstrate generalizability by establishing a strong baseline on the E3C corpus. This work not only advances temporal information extraction but also lays the groundwork for improved diagnostic and prognostic models through enhanced temporal reasoning.

Peyman Baghershahi, Reshad Hosseini, Hadi Moradi

A few models have tried to tackle the link prediction problem, also known as knowledge graph completion, by embedding knowledge graphs in comparably lower dimensions. However, the state-of-the-art results are attained at the cost of considerably increasing the dimensionality of embeddings which causes scalability issues in the case of huge knowledge bases. Transformers have been successfully used recently as powerful encoders for knowledge graphs, but available models still have scalability issues. To address this limitation, we introduce a Transformer-based model to gain expressive low-dimensional embeddings. We utilize a large number of self-attention heads as the key to applying query-dependent projections to capture mutual information between entities and relations. Empirical results on WN18RR and FB15k-237 as standard link prediction benchmarks demonstrate that our model has favorably comparable performance with the current state-of-the-art models. Notably, we yield our promising results with a significant reduction of 66.9% in the dimensionality of embeddings compared to the five best recent state-of-the-art competitors on average.