ICLR 2026 论文列表

International Conference on Learning Representations

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5,358篇论文

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  • Oral
    2244.2%
  • Poster
    5,13495.8%

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On the Expressive Power of GNNs for Boolean Satisfiability

Saku Peltonen, Roger Wattenhofer

展开摘要

Machine learning approaches to solving Boolean Satisfiability (SAT) aim to replace handcrafted heuristics with learning-based models. Graph Neural Networks have emerged as the main architecture for SAT solving, due to the natural graph representation of Boolean formulas. We analyze the expressive power of GNNs for SAT solving through the lens of the Weisfeiler-Leman (WL) test. As our main result, we prove that the full WL hierarchy cannot, in general, distinguish between satisfiable and unsatisfiable instances. We show that indistinguishability under higher-order WL carries over to practical limitations for WL-bounded solvers that set variables sequentially. We further study the expressivity required for several important families of SAT instances, including regular, random and planar instances. To quantify expressivity needs in practice, we conduct experiments on random instances from the G4SAT benchmark and industrial instances from the 2024 SAT competition. Our results suggest that while random instances are largely distinguishable, industrial instances often require more expressivity to predict a satisfying assignment.

Poster
Disentangling Knowledge Representations for Large Language Model Editing

Mengqi Zhang, Zisheng Zhou, Xiaotian Ye, Qiang Liu, Zhaochun Ren, Zhumin Chen, Pengjie Ren

展开摘要

Knowledge Editing has emerged as a promising solution for efficiently updating embedded knowledge in large language models (LLMs). While existing approaches demonstrate effectiveness in integrating new knowledge and preserving the original capabilities of LLMs, they fail to maintain fine-grained irrelevant knowledge facts that share the same subject as edited knowledge but differ in relation and object. This challenge arises because subject representations inherently encode multiple attributes, causing the target and fine-grained irrelevant knowledge to become entangled in the representation space, and thus vulnerable to unintended alterations during editing. To address this, we propose DiKE, a novel approach that Disentangles Knowledge representations for LLM Editing (DiKE). DiKE consists of two key components: a Knowledge Representation Disentanglement (KRD) module that decomposes the subject representation into target-knowledgerelated and -unrelated components, and a Disentanglement-based Knowledge Edit (DKE) module that updates only the target-related component while explicitly preserving the unrelated one. We further derive a closed-form, rank-one parameter update based on matrix theory to enable efficient and minimally invasive edits. To rigorously evaluate fine-grained irrelevant knowledge preservation, we construct FINE-KED, a new benchmark comprising fine-grained irrelevant knowledge at different levels of relational similarity to the edited knowledge. Extensive experiments across multiple LLMs demonstrate that DiKE substantially improves fine-grained irrelevant knowledge preservation while maintaining competitive general editing performance.

Poster
When Silence Is Golden: Can LLMs Learn to Abstain in Temporal QA and Beyond?

Xinyu Zhou, Chang Jin, Carsten Eickhoff, Zhijiang Guo, Seyed Ali Bahrainian

展开摘要

Large language models (LLMs) rarely admit uncertainty, often producing fluent but misleading answers, rather than abstaining (i.e., refusing to answer). This weakness is even evident in temporal question answering (QA), where models frequently ignore time-sensitive evidence and conflate facts across different time-periods. In this paper, we present the first empirical study of training LLMs with abstention ability while reasoning about temporal QA. Existing approaches such as calibration might be unreliable in capturing uncertainty in complex reasoning. We instead frame abstention as a teachable skill and introduce a pipeline that couples Chain-of-Thought (CoT) supervision with Reinforcement Learning (RL) guided by abstention-aware rewards. Our goal is to systematically analyze how different information types and training techniques affect temporal reasoning with abstention behavior in LLMs. Through extensive experiments studying various methods, we find that RL yields strong empirical gains on reasoning: a model initialized by Qwen2.5-1.5B-Instruct surpasses GPT-4o by 3.46% and 5.80% in Exact Match on TimeQA-Easy and Hard, respectively. Moreover, it improves the True Positive rate on unanswerable questions by 20% over a pure supervised fine-tuned (SFT) variant. Beyond performance, our analysis shows that SFT induces overconfidence and harms reliability, while RL improves prediction accuracy but exhibits similar risks. Finally, by comparing implicit reasoning cues (e.g., original context, temporal sub-context, knowledge graphs) with explicit CoT supervision, we find that implicit information provides limited benefit for reasoning with abstention. Our study provides new insights into how abstention and reasoning can be jointly optimized, providing a foundation for building more reliable LLMs.

Poster
Spectral-guided Physical Dynamics Distillation

Youjin Kim, Dagyeong Na, Jae Yong Lee, Junseok Kwon

展开摘要

The problem of physical dynamics, which involves predicting the 3D trajectories of particles, is a fundamental task with wide-ranging applications across science and engineering. However, accurately forecasting long-horizon trajectories from initial states remains challenging, due to complex particle interactions and entangled multi-scale dynamics involving both low- and high-frequency components. To address this, we propose a novel knowledge-distillation-based framework, SGDD (Spectral-Guided Dynamics Distillation), which integrates a spectral-guided enhancement to adaptively prioritize key frequency components within a unified spatio-temporal representation. Through knowledge distillation, SGDD leverages future trajectories as privileged information during training, guiding a teacher encoder to generate comprehensive dynamics representations while a student encoder approximates them using only the initial state. This enables the student to generate effective dynamics representations at inference, even without privileged information, thereby enabling accurate long-horizon trajectory prediction. Experimental results on molecule, protein, and human motion datasets demonstrate that our method achieves more accurate and stable long-term predictions than previous physical dynamics models, successfully capturing the complex spatio-temporal structures of real-world systems.

Poster
Minimax Sample Complexity of Graph Neural Networks: Lower Bounds and Structural Effects

Ahmad Ghasemi, Hossein Pishro-Nik

展开摘要

Graph Neural Networks (GNNs) achieve strong empirical performance across domains, yet their fundamental statistical behavior remains poorly understood. This paper develops a minimax analysis of ReLU message-passing GNNs with explicit architectural assumptions, in both inductive (graph-level) and transductive (node-level) settings. For arbitrary graphs without structural constraints, we show that the worst-case generalization error scales as $\sqrt{\log d / n}$ with sample size $n$ and input dimension $d$, matching the $1/\sqrt{n}$ behavior of feed-forward networks. Under a spectral--homophily condition combining strong label homophily and bounded spectral expansion, we prove a stronger minimax lower bound of $d/\log n$ for transductive node prediction. We complement these results with a systematic empirical study on three large-scale benchmarks (ogbn\_arxiv, ogbn\_products\_50k, Reddit\_50k) and two controlled synthetic datasets representing the worst-case and structured regimes of our theory. All benchmark graphs we study fall in the slow-mixing, bottlenecked regime captured by our spectral-homophily condition, and ratio-based scaling tests show error decay consistent with the $d/\log n$ rate in real and structured settings, while the worst-case synthetic dataset follows the $\sqrt{\log d / n}$ curve. Together, these results indicate that practical GNN tasks often operate in the spectral-homophily regime, where our lower bound $d/\log n$ is tight and effective sample complexity is driven by graph topology rather than universal $1/\sqrt{n}$ behavior.

Poster
DOPPLER: Dual-Policy Learning for Device Assignment in Asynchronous Dataflow Graphs

Xinyu Yao, Daniel Bourgeois, Abhinav Jain, Yuxin Tang, Jiawen Yao, Zhimin Ding, Arlei Silva, Chris Jermaine

展开摘要

We study the problem of assigning operations in a dataflow graph to devices to minimize execution time in a work-conserving system, with emphasis on complex machine learning workloads. Prior learning-based approaches face three limitations: (1) reliance on bulk-synchronous frameworks that under-utilize devices, (2) learning a single placement policy without modeling the system dynamics, and (3) depending solely on reinforcement learning in pre-training while ignoring optimization during deployment. We propose Doppler, a three-stage framework with two policies—SEL for selecting operations and PLC for placing them on devices. Doppler consistently outperforms baselines by reducing execution time and improving sampling efficiency through faster per-episode training. Our results show that DOPPLER achieves up to 52.7% lower execution times than the best baseline.

Poster
A Graph Meta-Network for Learning on Kolmogorov–Arnold Networks

Guy Bar-Shalom, Ami Tavory, Itay Evron, Maya Bechler-Speicher, Ido Guy, Haggai Maron

展开摘要

Weight-space models learn directly from the parameters of neural networks, enabling tasks such as predicting their accuracy on new datasets. Naive methods -- like applying MLPs to flattened parameters -- perform poorly, making the design of better weight-space architectures a central challenge. While prior work leveraged permutation symmetries in standard networks to guide such designs, no analogous analysis or tailored architecture yet exists for Kolmogorov–Arnold Networks (KANs). In this work, we show that KANs share the same permutation symmetries as MLPs, and propose the KAN-graph, a graph representation of their computation. Building on this, we develop WS-KAN, the first weight-space architecture that learns on KANs, which naturally accounts for their symmetry. We analyze WS-KAN’s expressive power, showing it can replicate an input KAN’s forward pass - a standard approach for assessing expressiveness in weight-space architectures. We construct a comprehensive ``zoo'' of trained KANs spanning diverse tasks, which we use as benchmarks to empirically evaluate WS-KAN. Across all tasks, WS-KAN consistently outperforms structure-agnostic baselines, often by a substantial margin.

Poster
Explore-on-Graph: Incentivizing Autonomous Exploration of Large Language Models on Knowledge Graphs with Path-refined Reward Modeling

Shiqi Yan, Yubo Chen, Ruiqi Zhou, Zhengxi Yao, Shuai Chen, Tianyi Zhang, Shijie Zhang, Wei-Qiang Zhang, Yongfeng Huang, Haixin Duan, Yunqi Zhang

展开摘要

The reasoning process of Large Language Models (LLMs) is often plagued by hallucinations and missing facts in question-answering tasks. A promising solution is to ground LLMs' answers in verifiable knowledge sources, such as Knowledge Graphs (KGs). Prevailing KG-enhanced methods typically constrained LLM reasoning either by enforcing rules during generation or by imitating paths from a fixed set of demonstrations. However, they naturally confined the reasoning patterns of LLMs within the scope of prior experience or fine-tuning data, limiting their generalizability to out-of-distribution graph reasoning problems. To tackle this problem, in this paper, we propose Explore-on-Graph (EoG), a novel framework that encourages LLMs to autonomously explore a more diverse reasoning space on KGs. To incentivize exploration and discovery of novel reasoning paths, we propose to introduce reinforcement learning during training, whose reward is the correctness of the reasoning paths' final answers. To enhance the efficiency and meaningfulness of the exploration, we propose to incorporate path information as additional reward signals to refine the exploration process and reduce futile efforts. Extensive experiments on five KGQA benchmark datasets demonstrate that, to the best of our knowledge, our method achieves state-of-the-art performance, outperforming not only open-source but also even closed-source LLMs.

Poster
HGNet: Scalable Foundation Model for Automated Knowledge Graph Generation from Scientific Literature

Devvrat Joshi, Islem Rekik

展开摘要

Automated knowledge graph (KG) construction is essential for navigating the rapidly expanding body of scientific literature. However, existing approaches face persistent challenges: they struggle to recognize long multi-word entities, often fail to generalize across domains, and typically overlook the hierarchical and logically constrained nature of scientific knowledge. While general-purpose large language models (LLMs) offer some adaptability, they are computationally expensive and yield inconsistent accuracy on specialized, domain-heavy tasks such as scientific knowledge graph construction. As a result, current KGs are shallow and inconsistent, limiting their utility for exploration and synthesis. We propose a two-stage framework for scalable, zero-shot scientific KG construction. The first stage, Z-NERD, introduces (i) Orthogonal Semantic Decomposition (OSD), which promotes domain-agnostic entity recognition by isolating semantic “turns” in text, and (ii) a Multi-Scale TCQK attention mechanism that captures coherent multi-word entities through n-gram–aware attention heads. The second stage, HGNet, performs relation extraction with hierarchy-aware message passing, explicitly modeling parent, child, and peer relations. To enforce global consistency, we introduce two complementary objectives: a Differentiable Hierarchy Loss to discourage cycles and shortcut edges, and a Continuum Abstraction Field (CAF) Loss that embeds abstraction levels along a learnable axis in Euclidean space. To the best of our knowledge, this is the first approach to formalize hierarchical abstraction as a continuous property within standard Euclidean embeddings, offering a simpler and more interpretable alternative to hyperbolic methods. To address data scarcity, we also release SPHERE, a large-scale, multi-domain benchmark for hierarchical relation extraction. Our framework establishes a new state of the art on benchmarks such as SciERC, SciER and SPHERE benchmarks, improving named entity recognition (NER) by 8.08\% and relation extraction (RE) by 5.99\% on the official out-of-distrubtion test sets. In zero-shot settings, the gains are even more pronounced, with improvements of 10.76\% for NER and 26.2\% for RE, marking a significant step toward reliable and scalable scientific knowledge graph construction.

Poster
Intrinsic Lorentz Neural Network

Xianglong Shi, Ziheng Chen, Yunhan Jiang, Nicu Sebe

展开摘要

Real-world data frequently exhibit latent hierarchical structures, which can be naturally represented by hyperbolic geometry. Although recent hyperbolic neural networks have demonstrated promising results, many existing architectures remain partially intrinsic, mixing Euclidean operations with hyperbolic ones or relying on extrinsic parameterizations. To address it, we propose the \emph{Intrinsic Lorentz Neural Network} (ILNN), a fully intrinsic hyperbolic architecture that conducts all computations within the Lorentz model. At its core, the network introduces a novel \emph{point-to-hyperplane} fully connected layer (FC), replacing traditional Euclidean affine logits with closed-form hyperbolic distances from features to learned Lorentz hyperplanes, thereby ensuring that the resulting geometric decision functions respect the inherent curvature. Around this fundamental layer, we design intrinsic modules: GyroLBN, a Lorentz batch normalization that couples gyro-centering with gyro-scaling, consistently outperforming both LBN and GyroBN while reducing training time. We additionally proposed a gyro-additive bias for the FC output, a Lorentz patch-concatenation operator that aligns the expected log-radius across feature blocks via a digamma-based scale, and a Lorentz dropout layer. Extensive experiments conducted on CIFAR-10/100 and two genomic benchmarks (TEB and GUE) illustrate that ILNN achieves state-of-the-art performance and computational cost among hyperbolic models and consistently surpasses strong Euclidean baselines.

Poster
Experience-based Knowledge Correction for Robust Planning in Minecraft

Seungjoon Lee, Suhwan Kim, Minhyeon Oh, Youngsik Yoon, Jungseul Ok

展开摘要

Large Language Model (LLM)-based planning has advanced embodied agents in long-horizon environments such as Minecraft, where acquiring latent knowledge of goal (or item) dependencies and feasible actions is critical. However, LLMs often begin with flawed priors and fail to correct them through prompting, even with feedback. We present XENON (eXpErience-based kNOwledge correctioN), an agent that algorithmically revises knowledge from experience, enabling robustness to flawed priors and sparse binary feedback. XENON integrates two mechanisms: Adaptive Dependency Graph, which corrects item dependencies using past successes, and Failure-aware Action Memory, which corrects action knowledge using past failures. Together, these components allow XENON to acquire complex dependencies despite limited guidance. Experiments across multiple Minecraft benchmarks show that XENON outperforms prior agents in both knowledge learning and long-horizon planning. Remarkably, with only a 7B open-weight LLM, XENON surpasses agents that rely on much larger proprietary models.

Poster
One for Two: A Unified Framework for Imbalanced Graph Classification via Dynamic Balanced Prototype

Guanjun Wang, Binwu Wang, Jiaming Ma, Zhengyang Zhou, Pengkun Wang, Xu Wang, Yang Wang

展开摘要

Graph Neural Networks (GNNs) have advanced graph classification, yet they remain vulnerable to graph-level imbalance, encompassing class imbalance and topological imbalance. To address both types of imbalance in a unified manner, we propose UniImb, a Unified framework for Imbalanced graph classification. Specifically, UniImb first captures multi-scale topological features and enhances data diversity via learnable personalized graph perturbations. It then employs a dynamic balanced prototype module to learn representative prototypes from graph instances, improving the quality of graph representations. Concurrently, a prototype load-balancing optimization term mitigates dominance by majority samples to equalize sample influence during training. We justify these design choices theoretically using the Information Bottleneck principle. Extensive experiments on 19 datasets-including a large-scale imbalanced air pollution graph dataset AirGraph released by us and 23 baselines demonstrate that UniImb has achieved dominant performance across various imbalanced scenarios. Our code is available at GitHub.

Oral
Actions Speak Louder than Prompts: A Large-Scale Study of LLMs for Graph Inference

Ben Finkelshtein, Silviu Cucerzan, Sujay Kumar Jauhar, Ryen W White

展开摘要

Large language models (LLMs) are increasingly leveraged for text-rich graph machine learning tasks, with node classification standing out due to its high-impact application domains such as fraud detection and recommendation systems. Yet, despite a surge of interest, the field lacks a principled understanding of the capabilities of LLMs in processing graph data. In this work, we conduct a large-scale, controlled evaluation across the key axes of variability: the LLM-graph interaction mode, comparing prompting, tool-use, and code generation; dataset domains, spanning citation, web-link, e-commerce, and social networks; homophilic vs. heterophilic regimes; short- vs. long-text features; LLM sizes and reasoning capabilities. We further analyze dependencies by independently truncating features, deleting edges, and removing labels to quantify reliance on input types. Our findings provide actionable guidance for both research and practice. (1) Code generation mode achieves the strongest overall performance, with especially large gains on long-text or high-degree graphs where prompting quickly exceeds the token budget. (2) All interaction strategies remain effective on heterophilic graphs, challenging the assumption that LLM-based methods collapse under low homophily. (3) Code generation mode is able to flexibly shift its reliance to the most informative input type, whether that be structure, features, or labels. Together, these results establish a clear picture of the strengths and limitations of current LLM–graph interaction modes and point to design principles for future methods.

Oral
FSD-CAP: Fractional Subgraph Diffusion with Class-Aware Propagation for Graph Feature Imputation

Xin Qiao, Shijie Sun, Anqi Dong, Cong Hua, Xia Zhao, Longfei Zhang, Guangming Zhu, zhang liang

展开摘要

Imputing missing node features in graphs is challenging, particularly under high missing rates. Existing methods based on latent representations or global diffusion often fail to produce reliable estimates, and may propagate errors across the graph. We propose FSD-CAP, a two-stage framework designed to improve imputation quality under extreme sparsity. In the first stage, a graph-distance-guided subgraph expansion localizes the diffusion process. A fractional diffusion operator adjusts propagation sharpness based on local structure. In the second stage, imputed features are refined using class-aware propagation, which incorporates pseudo-labels and neighborhood entropy to promote consistency. We evaluated FSD-CAP on multiple datasets. With 99.5% of features missing across five benchmark datasets, FSD-CAP achieves average accuracies of 80.06% (structural) and 81.01% (uniform) in node classification, close to the 81.31% achieved by a standard GCN with full features. For link prediction under the same setting, it reaches AUC scores of 91.65% (structural) and 92.41% (uniform), compared to 95.06% for the fully observed case. Furthermore, FSD-CAP demonstrates superior performance on both large-scale and heterophily datasets when compared to other models. Code conducting all experiments can be found at https://anonymous.4open.science/r/FSD-CAP-50E8.

Poster
Non-Clashing Teaching in Graphs: Algorithms, Complexity, and Bounds

Sujoy Bhore, Liana Khazaliya, Fionn Mc Inerney

展开摘要

Kirkpatrick et al. [ALT 2019] and Fallat et al. [JMLR 2023] introduced non-clashing teaching and proved that it is the most efficient batch machine teaching model satisfying the collusion-avoidance benchmark established in the seminal work of Goldman and Mathias [COLT 1993]. Recently, (positive) non-clashing teaching was thoroughly studied for balls in graphs, yielding numerous algorithmic and combinatorial results. In particular, Chalopin et al. [COLT 2024] and Ganian et al. [ICLR 2025] gave an almost complete picture of the complexity landscape of the positive variant, showing that it is tractable only for restricted graph classes due to the non-trivial nature of the problem and concept class. In this work, we consider (positive) non-clashing teaching for closed neighborhoods in graphs. This concept class is not only extensively studied in various related contexts, but it also exhibits broad generality, as any finite binary concept class can be equivalently represented by a set of closed neighborhoods in a graph. In comparison to the works on balls in graphs, we provide improved algorithmic results, notably including FPT algorithms for more general classes of parameters, and we complement these results by deriving stronger lower bounds. Lastly, we obtain combinatorial upper bounds for wider classes of graphs.

Poster
ACE: Attribution-Controlled Knowledge Editing for Multi-hop Factual Recall

Jiayu Yang, Yuxuan Fan, Songning Lai, Shengen Wu, Jiaqi Tang, Chun Kang, Zhijiang Guo, Yutao Yue

展开摘要

LLMs require efficient knowledge editing (KE) to update factual information, yet existing methods exhibit significant performance decay in multi-hop factual recall. This failure is particularly acute when edits involve intermediate implicit subjects within reasoning chains. Through causal analysis, we reveal that this limitation stems from an oversight of how chained knowledge is dynamically represented and utilized at the neuron level. We discover that during multi-hop reasoning, implicit subjects function as query neurons, which sequentially activate corresponding value neurons across transformer layers to accumulate information toward the final answer—a dynamic prior KE work has overlooked. Guided by this insight, we propose ACE (Attribution-Controlled Knowledge Editing), a framework that leverages neuron-level attribution to identify and edit these critical query-value (Q-V) pathways. Ace provides a mechanistically grounded solution for multi-hop KE, empirically outperforming state-of-the-art methods by 9.44% on GPT-J and 37.46% on Qwen3-8B. Our analysis further reveals more fine-grained activation patterns in Qwen3 and demonstrates that the semantic interpretability of value neurons is orchestrated by query-driven accumulation. These findings establish a new pathway for advancing KE capabilities based on the principled understanding of internal reasoning mechanisms.

Poster
LRIM: a Physics-Based Benchmark for Provably Evaluating Long-Range Capabilities in Graph Learning

Joël Mathys, Henrik Christiansen, Federico Errica, Takashi Maruyama, Francesco Alesiani

展开摘要

Accurately modeling long-range dependencies in graph-structured data is critical for many real-world applications. However, incorporating long-range interactions beyond the nodes' immediate neighborhood in a $\textit{scalable}$ manner remains an open challenge for graph machine learning models. Existing benchmarks for evaluating long-range capabilities either cannot $\textit{guarantee}$ that their tasks actually depend on long-range information or are rather limited. Therefore, claims of long-range modeling improvements based on said performance remain questionable. We introduce the Long-Range Ising Model Graph Benchmark, a physics-based benchmark utilizing the well-studied Ising model whose ground truth $\textit{provably}$ depends on long-range dependencies. Our benchmark consists of ten datasets that scale from 256 to 65k nodes per graph, and provide controllable long-range dependencies through tunable parameters, allowing precise control over the hardness and ``long-rangedness". We provide model-agnostic evidence that local information is insufficient, further validating the design choices of our benchmark. Via experiments on classical message-passing architectures and graph transformers, we show that both perform far from the optimum, especially those with scalable complexity. Our goal is that our benchmark will foster the development of scalable methodologies that effectively model long-range interactions in graphs.

Poster
Exposing Weaknesses of Large Reasoning Models through Graph Algorithm Problems

Qifan Zhang, Jianhao Ruan, Aochuan Chen, Kang ZENG, Nuo Chen, Jing Tang, Jia Li

展开摘要

Large Reasoning Models (LRMs) have advanced rapidly, yet existing benchmarks on mathematics, code, and common-sense reasoning remain limited: they lack long-context evaluation, offer insufficient challenge, and provide answers that are difficult to verify programmatically. We introduce GrAlgoBench, a benchmark designed to evaluate LRMs through graph algorithm problems. Such problems are particularly well-suited for probing reasoning abilities: they demand long-context reasoning, allow fine-grained control of difficulty levels, and enable standardized programmatic evaluation. Across nine tasks, our systematic experiments reveal two major weaknesses of current LRMs. First, accuracy deteriorates sharply with longer contexts input—falling below 50% once graphs exceed 120 nodes—driven by frequent execution errors, weak memory, and redundant reasoning. Second, LRMs suffer from an "over-thinking" phenomenon, primarily driven by extensive yet largely ineffective self-verification, which inflates reasoning traces without improving correctness. By exposing these limitations, GrAlgoBench establishes graph algorithm problems as a rigorous, multidimensional, and practically relevant testbed for advancing the study of reasoning in LRMs. Code is available at https://anonymous.4open.science/r/GrAlgoBench-7D17.

Poster
Distilling and Adapting: A Topology-Aware Framework for Zero-Shot Interaction Prediction in Multiplex Biological Networks

Alana Deng, Sugitha Janarthanan, Yan Sun, Zihao Jing, Pingzhao Hu

展开摘要

Multiplex Biological Networks (MBNs), which represent multiple interaction types between entities, are crucial for understanding complex biological systems. Yet, existing methods often inadequately model multiplexity, struggle to integrate structural and sequence information, and face difficulties in zero-shot prediction for unseen entities with no prior neighbourhood information. To address these limitations, we propose a novel framework for zero-shot interaction prediction in MBNs by leveraging context-aware representation learning and knowledge distillation. Our approach leverages domain-specific foundation models to generate enriched embeddings, introduces a topology-aware graph tokenizer to capture multiplexity and higher-order connectivity, and employs contrastive learning to align embeddings across modalities. A teacher–student distillation strategy further enables robust zero-shot generalization. Experimental results demonstrate that our framework outperforms state-of-the-art methods in interaction prediction for MBNs, providing a powerful tool for exploring various biological interactions and advancing personalized therapeutics.

Poster
LLMs Struggle to Balance Reasoning and World Knowledge in Causal Narrative Understanding

Khurram Yamin, Shantanu Gupta, Gaurav Rohit Ghosal, Zachary Chase Lipton, Bryan Wilder

展开摘要

The ability to robustly identify causal relationships is essential for autonomous decision-making and adaptation to novel scenarios. However, accurately inferring causal structure requires integrating both world knowledge and abstract logical reasoning. In this work, we investigate the interaction between these two capabilities through the representative task of causal reasoning over narratives. Through controlled synthetic, semi-synthetic and real-world experiments, we find that state-of-the-art large language models (LLMs) often rely on superficial heuristics—for example, inferring causality from event order or recalling memorized world knowledge without attending to context. Furthermore, we show that simple reformulations of the task can elicit more robust reasoning behavior. Our evaluation spans a range of causal structures, from linear chains to complex graphs involving colliders and forks. These findings uncover systematic patterns in how LLMs perform causal reasoning and lay the groundwork for developing methods that better align LLM behavior with principled causal inference.

Poster