ICLR 2025 Papers

In recent years, the design and transfer of neural network models have been widely studied due to their exceptional performance and capabilities. However, the complex nature of datasets and the vast architecture space pose significant challenges for both manual and automated algorithms in creating high-performance models. Inspired by researchers who design, train, and document the performance of various models across different datasets, this paper introduces a novel schema that transforms the benchmark data into a Knowledge Benchmark Graph (KBG), which primarily stores the facts in the form of performance(data, model). Constructing the KBG facilitates the structured storage of design knowledge, aiding subsequent model design and transfer. However, it is a non-trivial task to retrieve or design suitable neural networks based on the KBG, as real-world data are often off the records. To tackle this challenge, we propose transferring existing models stored in KBG by establishing correlations between unseen and previously seen datasets. Given that measuring dataset similarity is a complex and open-ended issue, we explore the potential for evaluating the correctness of the similarity function. Then, we further integrate the KBG with Large Language Models (LLMs), assisting LLMs to think and retrieve existing model knowledge in a manner akin to humans when designing or transferring models. We demonstrate our method specifically in the context of Graph Neural Network (GNN) architecture design, constructing a KBG (with 26,206 models, 211,669 performance records, and 2,540,064 facts) and validating the effectiveness of leveraging the KBG to promote GNN architecture design.

In neuroscience, identifying distinct patterns linked to neurological disorders, such as Alzheimer's and Autism, is critical for early diagnosis and effective intervention. Graph Neural Networks (GNNs) have shown promising in analyzing brain networks, but there are two major challenges in using GNNs: (1) distribution shifts in multi-site brain network data, leading to poor Out-of-Distribution (OOD) generalization, and (2) limited interpretability in identifying key brain regions critical to neurological disorders. Existing graph OOD methods, while effective in other domains, struggle with the unique characteristics of brain networks. To bridge these gaps, we introduce BrainOOD, a novel framework tailored for brain networks that enhances GNNs' OOD generalization and interpretability. BrainOOD framework consists of a feature selector and a structure extractor, which incorporates various auxiliary losses including an improved Graph Information Bottleneck (GIB) objective to recover causal subgraphs. By aligning structure selection across brain networks and filtering noisy features, BrainOOD offers reliable interpretations of critical brain regions. Our approach outperforms 16 existing methods and improves generalization to OOD subjects by up to 8.5%. Case studies highlight the scientific validity of the patterns extracted, which aligns with the findings in known neuroscience literature. We also propose the first OOD brain network benchmark, which provides a foundation for future research in this field. Our code is available at https://github.com/AngusMonroe/BrainOOD.

Graphs are a complex and versatile data structure used across various domains, with possibly multi-label nodes playing a particularly crucial role. Examples include proteins in PPI networks with multiple functions and users in social or e-commerce networks exhibiting diverse interests. Tackling multi-label node classification (MLNC) on graphs has led to the development of various approaches. Some methods leverage graph neural networks (GNNs) to exploit label co-occurrence correlations, while others incorporate label embeddings to capture label proximity. However, these approaches fail to account for the intricate influences between labels in non-Euclidean graph data. To address this issue, we decompose the message passing process in GNNs into two operations: propagation and transformation. We then conduct a comprehensive analysis and quantification of the influence correlations between labels in each operation. Building on these insights, we propose a novel model, Label Influence Propagation (LIP). Specifically, we construct a label influence graph based on the integrated label correlations. Then, we propagate high-order influences through this graph, dynamically adjusting the learning process by amplifying labels with positive contributions and mitigating those with negative influence. Finally, our framework is evaluated on comprehensive benchmark datasets, consistently outperforming SOTA methods across various settings, demonstrating its effectiveness on MLNC tasks.

Learning on graphs is one of the most active research topics in machine learning (ML). Among the key challenges in this field, effectively learning long-range dependencies in graphs has been particularly difficult. It has been observed that, in practice, the performance of many ML approaches, including various types of graph neural networks (GNNs), degrades significantly when the learning task involves long-range dependencies—that is, when the answer is determined by the presence of a certain path of significant length in the graph. This issue has been attributed to several phenomena, including over-smoothing, over-squashing, and vanishing gradient. A number of solutions have been proposed to mitigate these causes. However, evaluation of these solutions is currently challenging because existing benchmarks do not effectively test systems for their ability to learn tasks based on long-range dependencies in a transparent manner. In this paper, we introduce GLoRa, a synthetic benchmark that allows testing of systems for this ability in a systematic way. We then evaluate state-of-the-art systems using GLoRa and conclude that none of them can confidently claim to learn long-range dependencies well. We also observe that this weak performance cannot be attributed to any of the three causes, highlighting the need for further investigation.

Collaborative learning of large language models (LLMs) has emerged as a new paradigm for utilizing private data from different parties to guarantee efficiency and privacy. Meanwhile, Knowledge Editing (KE) for LLMs has also garnered increased attention due to its ability to manipulate the behaviors of LLMs explicitly, yet leaves the collaborative KE case—in which knowledge edits of multiple parties are aggregated in a privacy-preserving and continual manner—unexamined. To this end, this manuscript dives into the first investigation of collaborative KE, in which we start by carefully identifying the unique three challenges therein, including knowledge overlap, knowledge conflict, and knowledge forgetting. We then propose a non-destructive collaborative KE framework, COLLABEDIT, which employs a novel model merging mechanism to mimic the global KE behavior while preventing the severe performance drop. Extensive experiments on two canonical datasets demonstrate the superiority of COLLABEDIT compared to other destructive baselines, and results shed light on addressing three collaborative KE challenges and future applications. Our code is available at [https://github.com/LINs-lab/CollabEdit](https://github.com/LINs-lab/CollabEdit).

Can integrating spectral and curvature signals unlock new potential in graph representation learning? Non-Euclidean geometries, particularly Riemannian manifolds such as hyperbolic (negative curvature) and spherical (positive curvature), offer powerful inductive biases for embedding complex graph structures like scale-free, hierarchical, and cyclic patterns. Meanwhile, spectral filtering excels at processing signal variations across graphs, making it effective in homophilic and heterophilic settings. Leveraging both can significantly enhance the learned representations. To this end, we propose Spectro-Riemannian Graph Neural Networks (CUSP) - the first graph representation learning paradigm that unifies both CUrvature (geometric) and SPectral insights. CUSP is a mixed-curvature spectral GNN that learns spectral filters to optimize node embeddings in products of constant curvature manifolds (hyperbolic, spherical, and Euclidean). Specifically, CUSP introduces three novel components: (a) Cusp Laplacian, an extension of the traditional graph Laplacian based on Ollivier-Ricci curvature, designed to capture the curvature signals better; (b) Cusp Filtering, which employs multiple Riemannian graph filters to obtain cues from various bands in the eigenspectrum; and (c) Cusp Pooling, a hierarchical attention mechanism combined with a curvature-based positional encoding to assess the relative importance of differently curved substructures in our graph. Empirical evaluation across eight homophilic and heterophilic datasets demonstrates the superiority of CUSP in node classification and link prediction tasks, with a gain of up to 5.3\% over state-of-the-art models.

Existing benchmarks like NLGraph and GraphQA evaluate LLMs on graphs by focusing mainly on pairwise relationships, overlooking the high-order correlations found in real-world data. Hypergraphs, which can model complex beyond-pairwise relationships, offer a more robust framework but are still underexplored in the context of LLMs. To address this gap, we introduce LLM4Hypergraph, the first comprehensive benchmark comprising 21,500 problems across eight low-order, five high-order, and two isomorphism tasks, utilizing both synthetic and real-world hypergraphs from citation networks and protein structures. We evaluate six prominent LLMs, including GPT-4o, demonstrating our benchmark’s effectiveness in identifying model strengths and weaknesses. Our specialized prompt- ing framework incorporates seven hypergraph languages and introduces two novel techniques, Hyper-BAG and Hyper-COT, which enhance high-order reasoning and achieve an average 4% (up to 9%) performance improvement on structure classification tasks. This work establishes a foundational testbed for integrating hypergraph computational capabilities into LLMs, advancing their comprehension.

Coresets have become an invaluable tool for solving $k$-means and kernel $k$-means clustering problems on large datasets with small numbers of clusters. On the other hand, spectral clustering works well on sparse graphs and has recently been extended to scale efficiently to large numbers of clusters. We exploit the connection between kernel $k$-means and the normalised cut problem to combine the benefits of both. Our main result is a coreset spectral clustering algorithm for graphs that clusters a coreset graph to infer a good labelling of the original graph. We prove that an $\alpha$-approximation for the normalised cut problem on the coreset graph is an $O(\alpha)$-approximation on the original. We also improve the running time of the state-of-the-art coreset algorithm for kernel $k$-means on sparse kernels, from $\tilde{O}(nk)$ to $\tilde{O}(n\cdot \min (k, d_{avg}))$, where $d_{avg}$ is the average number of non-zero entries in each row of the $n\times n$ kernel matrix. Our experiments confirm our coreset algorithm is asymptotically faster on large real-world graphs with many clusters, and show that our clustering algorithm overcomes the main challenge faced by coreset kernel $k$-means on sparse kernels which is getting stuck in local optima.

The foundation model (FM) paradigm is transforming Machine Learning Force Fields (MLFFs), leveraging general-purpose representations and scalable training to perform a variety of computational chemistry tasks. Although MLFF FMs have begun to close the accuracy gap relative to first-principles methods, there is still a strong need for faster inference speed. Additionally, while research is increasingly focused on general-purpose models which transfer across chemical space, practitioners typically only study a small subset of systems at a given time. At test time, MLFFs must also obey physical constraints unique to the downstream use case, such as energy conservation for molecular dynamics simulations. This underscores the need for fast, specialized MLFFs relevant to specific downstream applications, which preserve test-time physical soundness while maintaining train-time scalability. In this work, we introduce a method for transferring general-purpose representations from MLFF foundation models to smaller, faster MLFFs specialized to specific regions of chemical space. We formulate our approach as an architecture-agnostic knowledge distillation procedure, where the smaller "student" MLFF is trained to match the Hessians of the energy predictions of the "teacher" foundation model. We demonstrate our approach across multiple recent foundation models, large-scale datasets, chemical subsets, and downstream tasks. Our specialized MLFFs can be up to 20 times faster than the original foundation model, while retaining, and in some cases exceeding, its performance and that of undistilled models. We also show that distilling from a teacher model with a direct force parameterization into a student model trained with conservative forces (i.e., computed as derivatives of the potential energy) successfully leverages the representations from the large-scale teacher for improved accuracy, while maintaining energy conservation during test-time molecular dynamics simulations. More broadly, our work suggests a new paradigm for MLFF development, in which foundation models are released along with smaller, specialized simulation ``engines" for common chemical subsets. The implementation of our method is available at https://github.com/ASK-Berkeley/MLFF-distill.

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 encountering ( ABC ) together, showcasing the generalization ability of human intelligence. In this paper, we introduce a synthetic learning task, "FTCT" (Fragmented at Training, Chained at Testing), to validate the potential of Transformers in replicating this skill and interpret its inner mechanism. During training, data consist of separated knowledge fragments from an overall causal graph. In testing, Transformers must combine these fragments to infer complete causal traces. Our findings demonstrate that few-shot Chain-of-Thought prompting enables Transformers to perform compositional reasoning on FTCT by revealing correct combinations of fragments, even if such combinations were absent in training data. Furthermore, the emergence of compositional reasoning ability is strongly correlated with model complexity and training-testing data similarity. We propose, both theoretically and empirically, that Transformers learn an underlying generalizable program from training, enabling effective compositional reasoning during testing.

One fundamental challenge in graph machine learning is generalizing to new graphs. Many existing methods following the inductive setup can generalize to test graphs with new structures, but assuming the feature and label spaces remain the same as the training ones. This paper introduces a fully-inductive setup, where models should perform inference on arbitrary test graphs with new structures, feature and label spaces. We propose GraphAny as the first attempt at this challenging setup. GraphAny models inference on a new graph as an analytical solution to a LinearGNN, which can be naturally applied to graphs with any feature and label spaces. To further build a stronger model with learning capacity, we fuse multiple LinearGNN predictions with learned inductive attention scores. Specifically, the attention module is carefully parameterized as a function of the entropy-normalized distance features between pairs of LinearGNN predictions to ensure generalization to new graphs. Empirically, GraphAny trained on a single Wisconsin dataset with only 120 labeled nodes can generalize to 30 new graphs with an average accuracy of 67.26%, surpassing not only all inductive baselines, but also strong transductive methods trained separately on each of the 30 test graphs.