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The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared…

Machine Learning · Computer Science 2021-11-25 Chengxuan Ying , Tianle Cai , Shengjie Luo , Shuxin Zheng , Guolin Ke , Di He , Yanming Shen , Tie-Yan Liu

We introduce Attention Graphs, a new tool for mechanistic interpretability of Graph Neural Networks (GNNs) and Graph Transformers based on the mathematical equivalence between message passing in GNNs and the self-attention mechanism in…

Machine Learning · Computer Science 2025-02-26 Batu El , Deepro Choudhury , Pietro Liò , Chaitanya K. Joshi

Transformers have exhibited exceptional capabilities in sequence modeling tasks, leveraging self-attention and in-context learning. Critical to this success are induction heads, attention circuits that enable copying tokens based on their…

Machine Learning · Computer Science 2025-09-11 Francesco D'Angelo , Francesco Croce , Nicolas Flammarion

Many real-world interactions (e.g., researcher collaborations and email communication) occur among multiple entities. These group interactions are naturally modeled as hypergraphs. In graphs, transitivity is helpful to understand the…

Social and Information Networks · Computer Science 2023-10-27 Sunwoo Kim , Fanchen Bu , Minyoung Choe , Jaemin Yoo , Kijung Shin

Several recent works demonstrate that transformers can implement algorithms like gradient descent. By a careful construction of weights, these works show that multiple layers of transformers are expressive enough to simulate iterations of…

Machine Learning · Computer Science 2023-11-13 Kwangjun Ahn , Xiang Cheng , Hadi Daneshmand , Suvrit Sra

Transformers have the capacity to act as supervised learning algorithms: by properly encoding a set of labeled training ("in-context") examples and an unlabeled test example into an input sequence of vectors of the same dimension, the…

Machine Learning · Computer Science 2024-12-16 Spencer Frei , Gal Vardi

Stepwise inference protocols, such as scratchpads and chain-of-thought, help language models solve complex problems by decomposing them into a sequence of simpler subproblems. Despite the significant gain in performance achieved via these…

Machine Learning · Computer Science 2024-02-13 Mikail Khona , Maya Okawa , Jan Hula , Rahul Ramesh , Kento Nishi , Robert Dick , Ekdeep Singh Lubana , Hidenori Tanaka

Graph neural networks are powerful architectures for structured datasets. However, current methods struggle to represent long-range dependencies. Scaling the depth or width of GNNs is insufficient to broaden receptive fields as larger GNNs…

Machine Learning · Computer Science 2022-01-24 Zhanghao Wu , Paras Jain , Matthew A. Wright , Azalia Mirhoseini , Joseph E. Gonzalez , Ion Stoica

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections…

Machine Learning · Computer Science 2021-01-26 Vijay Prakash Dwivedi , Xavier Bresson

Graph Transformers have recently been successful in various graph representation learning tasks, providing a number of advantages over message-passing Graph Neural Networks. Utilizing Graph Transformers for learning the representation of…

Neurons and Cognition · Quantitative Biology 2023-12-27 Byung-Hoon Kim , Jungwon Choi , EungGu Yun , Kyungsang Kim , Xiang Li , Juho Lee

Much theoretical work has described the ability of transformers to represent formal languages. However, linking theoretical results to empirical performance is not straightforward due to the complex interplay between the architecture, the…

Computation and Language · Computer Science 2024-10-07 Anej Svete , Nadav Borenstein , Mike Zhou , Isabelle Augenstein , Ryan Cotterell

Graph Transformers (GTs) have demonstrated a strong capability in modeling graph structures by addressing the intrinsic limitations of graph neural networks (GNNs), such as over-smoothing and over-squashing. Recent studies have proposed…

Machine Learning · Computer Science 2025-02-28 Chaohao Yuan , Kangfei Zhao , Ercan Engin Kuruoglu , Liang Wang , Tingyang Xu , Wenbing Huang , Deli Zhao , Hong Cheng , Yu Rong

Humans exhibit remarkable compositional reasoning by integrating knowledge from various sources. For example, if someone learns ( B = f(A) ) from one source and ( C = g(B) ) from another, they can deduce ( C=g(B)=g(f(A)) ) even without…

Artificial Intelligence · Computer Science 2025-10-14 Yutong Yin , Zhaoran Wang

Graph Transformers excel in long-range dependency modeling, but generally require quadratic memory complexity in the number of nodes in an input graph, and hence have trouble scaling to large graphs. Sparse attention variants such as…

Machine Learning · Computer Science 2024-11-26 Hamed Shirzad , Honghao Lin , Balaji Venkatachalam , Ameya Velingker , David Woodruff , Danica Sutherland

Neural networks have in recent years shown promise for helping software engineers write programs and even formally verify them. While semantic information plays a crucial part in these processes, it remains unclear to what degree popular…

Machine Learning · Computer Science 2023-06-27 Shizhuo Dylan Zhang , Curt Tigges , Stella Biderman , Maxim Raginsky , Talia Ringer

Multi-graph learning is crucial for extracting meaningful signals from collections of heterogeneous graphs. However, effectively integrating information across graphs with differing topologies, scales, and semantics, often in the absence of…

Machine Learning · Computer Science 2026-02-02 Zahra Moslemi , Ziyi Liang , Norbert Fortin , Babak Shahbaba

Transformers have achieved remarkable success across domains, motivating the rise of Graph Transformers (GTs) as attention-based architectures for graph-structured data. A key design choice in GTs is the use of Graph Neural Network…

Machine Learning · Computer Science 2026-05-29 Javier Porras-Valenzuela , Zhiyang Wang , Xiaotao Shang , Yusu Wang , Alejandro Ribeiro

When trained on language data, do transformers learn some arbitrary computation that utilizes the full capacity of the architecture or do they learn a simpler, tree-like computation, hypothesized to underlie compositional meaning systems…

Computation and Language · Computer Science 2022-11-07 Shikhar Murty , Pratyusha Sharma , Jacob Andreas , Christopher D. Manning

Local neighborhoods play a crucial role in embedding generation in graph-based learning. It is commonly believed that nodes ought to have embeddings that resemble those of their neighbors. In this research, we try to carefully expand the…

Social and Information Networks · Computer Science 2024-01-04 Yassin Mohamadi , Mostafa Haghir Chehreghani

Transformer architectures, capable of capturing sequential dependencies in the history of user interactions, have become the dominant approach in sequential recommender systems. Despite their success, such models consider sequence elements…

Information Retrieval · Computer Science 2026-03-02 Artur Gimranov , Viacheslav Yusupov , Elfat Sabitov , Tatyana Matveeva , Anton Lysenko , Ruslan Israfilov , Evgeny Frolov