Yaowenqi Liu, BingXu Meng, Rui Pan, Yuxing Liu, Jerry Huang, Jiaxuan You, Tong Zhang. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

When exposed to complex queries containing multiple conditions, today's large language models (LLMs) tend to produce responses that only partially satisfy the query while neglecting certain conditions.We therefore introduce the concept of Intent Hallucination.In this phenomenon, LLMs either omit (neglecting to address certain parts) or misinterpret (responding to invented query parts) elements of the given query, leading to intent hallucinated generation.To systematically evaluate intent hallucination, we introduce FAITHQA, a novel benchmark for intent hallucination that contains 20,068 problems, covering both query-only and retrievalaugmented generation (RAG) setups with varying topics and difficulty.FAITHQA is the first hallucination benchmark that goes beyond factual verification, tailored to identify the fundamental cause of intent hallucination.By evaluating various LLMs on FAITHQA, we find that (1) intent hallucination is a common issue even for state-of-the-art models, and (2) the phenomenon stems from omission or misinterpretation of LLMs.To facilitate future research, we introduce an automatic LLM generation evaluation metric, CONSTRAINT SCORE, for detecting intent hallucination.Human evaluation results demonstrate that CONSTRAINT SCORE is closer to human performance for intent hallucination compared to baselines.

Evaluating consistency in Large Language Models (LLMs) is crucial for ensuring reliability, particularly in complex, multi-step interactions between humans and LLMs.Traditional self-consistency methods often miss subtle semantic changes in natural language and functional shifts in code or equations, which can accumulate over multiple transformations.To address this, we propose ConsistencyChecker, a tree-based evaluation framework designed to measure consistency through sequences of reversible transformations, including machine translation tasks and AI-assisted programming tasks.In our proposed framework, nodes represent distinct text states, while edges correspond to pairs of inverse operations.Dynamic and LLM-generated benchmarks ensure a fair assessment of the model's generalization ability and eliminate benchmark leakage.Consistency is quantified based on similarity across different depths of the transformation tree.Experiments on eight models from various families and sizes show that ConsistencyChecker can distinguish the performance of different models.Notably, our consistency scores, computed entirely without using WMT paired data, correlate strongly (r > 0.7) with WMT 2024 auto-ranking, demonstrating the validity of our benchmark-free approach.Our implementation is available at https://github.com

Retrieval-augmented generation (RAG) has revitalized Large Language Models (LLMs) by injecting non-parametric factual knowledge. Compared with long-context LLMs, RAG is considered an effective summarization tool in a more concise and lightweight manner, which can interact with LLMs multiple times using diverse queries to get comprehensive responses. However, the LLM-generated historical responses, which contain potentially insightful information, are largely neglected and discarded by existing approaches, leading to suboptimal results. In this paper, we propose \textit{graph of records} (\textbf{GoR}), which leverages historical responses generated by LLMs to enhance RAG for long-context global summarization. Inspired by the \textit{retrieve-then-generate} paradigm of RAG, we construct a graph by establishing an edge between the retrieved text chunks and the corresponding LLM-generated response. To further uncover the intricate correlations between them, GoR features a \textit{graph neural network} and an elaborately designed \textit{BERTScore}-based objective for self-supervised model training, enabling seamless supervision signal backpropagation between reference summaries and node embeddings. We comprehensively compare GoR with 12 baselines across four long-context summarization datasets, and the results indicate that our proposed method reaches the best performance (\textit{e.g.}, 15%, 8%, and 19% improvement over retrievers w.r.t. Rouge-L, Rouge-1, and Rouge-2 on the WCEP dataset). Extensive experiments further demonstrate the effectiveness of GoR.

Large Language Models (LLMs) have shown remarkable capabilities as autonomous agents; yet existing benchmarks either focus on single-agent tasks or are confined to narrow domains, failing to capture the dynamics of multi-agent coordination and competition. In this paper, we introduce MultiAgentBench, a comprehensive benchmark designed to evaluate LLM-based multi-agent systems across diverse, interactive scenarios. Our framework measures not only task completion but also the quality of collaboration and competition using novel, milestone-based key performance indicators. Moreover, we evaluate various coordination protocols (including star, chain, tree, and graph topologies) and innovative strategies such as group discussion and cognitive planning. Notably, gpt-4o-mini reaches the average highest task score, graph structure performs the best among coordination protocols in the research scenario,and cognitive planning improves milestone achievement rates by 3%. Code and datasets are publicavailable at https://github.com/ulab-uiuc/MARBLE.

Graph Self-Supervised Learning (SSL) has emerged as a pivotal area of research in recent years. By engaging in pretext tasks to learn the intricate topological structures and properties of graphs using unlabeled data, these graph SSL models achieve enhanced performance, improved generalization, and heightened robustness. Despite the remarkable achievements of these graph SSL methods, their current implementation poses significant challenges for beginners and practitioners due to the complex nature of graph structures, inconsistent evaluation metrics, and concerns regarding reproducibility hinder further progress in this field. Recognizing the growing interest within the research community, there is an urgent need for a comprehensive, beginner-friendly, and accessible toolkit consisting of the most representative graph SSL algorithms. To address these challenges, we present a Graph SSL toolkit named PyG-SSL, which is built upon PyTorch and is compatible with various deep learning and scientific computing backends. Within the toolkit, we offer a unified framework encompassing dataset loading, hyper-parameter configuration, model training, and comprehensive performance evaluation for diverse downstream tasks. Moreover, we provide beginner-friendly tutorials and the best hyper-parameters of each graph SSL algorithm on different graph datasets, facilitating the reproduction of results. The GitHub repository of the library is https://github.com/iDEA-iSAIL-Lab-UIUC/pyg-ssl.

Diagrams play a central role in research papers for conveying ideas, yet they are often notoriously complex and labor-intensive to create.Although diagrams are presented as images, standard image generative models struggle to produce clear diagrams with well-defined structure.We argue that a promising direction is to generate demonstration diagrams directly in textual form as SVGs, which can leverage recent advances in large language models (LLMs).However, due to the complexity of components and the multimodal nature of diagrams, sufficiently discriminative and explainable metrics for evaluating the quality of LLM-generated diagrams remain lacking.In this paper, we propose DiagramEval, a novel evaluation metric designed to assess demonstration diagrams generated by LLMs.Specifically, DiagramEval conceptualizes diagrams as graphs, treating text elements as nodes and their connections as directed edges, and evaluates diagram quality using two new groups of metrics: node alignment and path alignment.For the first time, we effectively evaluate diagrams produced by stateof-the-art LLMs on recent research literature, quantitatively demonstrating the validity of our metrics.Furthermore, we show how the enhanced explainability of our proposed metrics offers valuable insights into the characteristics of LLM-generated diagrams.Code

Kunlun Zhu, Jiaxun Zhang, Ziheng Qi, Nuoxing Shang, Zijia Liu, Peixuan Han, Yue Su, Haofei Yu, Jiaxuan You. Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing. 2025.

The powerful capabilities of Large Language Models (LLMs) have led to their growing use in evaluating human-generated content, particularly in evaluating research ideas within academic settings. Existing solutions primarily rely on prompt-based LLM methods or fine-tuned lightweight language models for idea evaluation. However, these methods are often unstable and struggle to comprehend the complex semantic information embedded in the ideas, impeding their ability to perform high-quality evaluations. To address the above challenges, we propose $\texttt{GraphEval}$, a lightweight graph-based LLM framework for idea evaluation. Our insight is that a complex idea can be broken down into comprehensible viewpoint nodes using prompts from small LLMs. These viewpoint nodes can then be linked together through edges created from LLM-based relation extraction and/or BERT similarity scores. The created viewpoint-graph can be used to conveniently propagate scores across view-nodes to improve the robustness of the idea evaluations. In particular, we propose two lightweight graph-based methods for idea evaluation: (1) GraphEval-LP: a training-free label propagation algorithm that propagates evaluation scores from known view-nodes to unknown nodes; (2) GraphEval-GNN: a Graph Neural Networks (GNN) that is trained to predict the evaluation scores given the observed graph with minimal computation resources. Moreover, to overcome LLM's limitation in objectively assessing the novelty of ideas, we further propose a novelty detection model to GraphEval-GNN to enhance its capability in judging idea novelty. Experiments on two datasets show $\texttt{GraphEval}$ improves F1 scores by at least 14% with low computation and API costs. Additionally, $\texttt{GraphEval}$ can effectively detect plagiarized ideas.

The rapidly growing number and variety of Large Language Models (LLMs) present significant challenges in efficiently selecting the appropriate LLM for a given query, especially considering the trade-offs between performance and computational cost. Current LLM selection methods often struggle to generalize across new LLMs and different tasks because of their limited ability to leverage contextual interactions among tasks, queries, and LLMs, as well as their depen- dence on a transductive learning framework. To address these shortcomings, we introduce a novel inductive graph framework, named as GraphRouter, which fully utilizes the contextual information among tasks, queries, and LLMs to en- hance the LLM selection process. GraphRouter constructs a heterogeneous graph comprising task, query, and LLM nodes, with interactions represented as edges, which efficiently captures the contextual information between the query’s requirements and the LLM’s capabilities. Through an innovative edge prediction mechanism, GraphRouter is able to predict attributes (the effect and cost of LLM response) of potential edges, allowing for optimized recommendations that adapt to both existing and newly introduced LLMs without requiring retraining. Comprehensive experiments across three distinct effect-cost weight scenarios have shown that GraphRouter substantially surpasses existing routers, delivering a minimum performance improvement of 12.3%. In addition, it achieves enhanced generalization across new LLMs settings and supports diverse tasks with at least a 9.5% boost in effect and a significant reduction in computational demands. This work endeavors to apply a graph-based approach for the contextual and adaptive selection of LLMs, offering insights for real-world applications.

Large language models (LLMs) are increasingly employed for complex tasks that process multiple generation calls in a tree structure with shared prefixes of tokens, including few-shot prompting, multi-step reasoning, speculative decoding, etc. However, existing inference systems for tree-based applications are inefficient due to improper partitioning of queries and KV cache during attention calculation.This leads to two main issues: (1) a lack of memory access (IO) reuse for KV cache of shared prefixes, and (2) poor load balancing.As a result, there is redundant KV cache IO between GPU global memory and shared memory, along with low GPU utilization. To address these challenges, we propose DeFT(Decoding with Flash Tree-Attention), a hardware-efficient attention algorithm with prefix-aware and load-balanced KV cache partitions. DeFT reduces the number of read/write operations of KV cache during attention calculation through **KV-Guided Grouping**, a method that avoids repeatedly loading KV cache of shared prefixes in attention computation. Additionally, we propose **Flattened Tree KV Splitting**, a mechanism that ensures even distribution of the KV cache across partitions with little computation redundancy, enhancing GPU utilization during attention computations. By reducing 73-99% KV cache IO and nearly 100% IO for partial results during attention calculation, DeFT achieves up to 2.23/3.59$\times$ speedup in the end-to-end/attention latency across three practical tree-based workloads compared to state-of-the-art attention algorithms. Our code is available at https://github.com/LINs-lab/DeFT.

World models (WMs) demonstrate strong capabilities in prediction, generation, and planning tasks. Existing WMs primarily focus on unstructured data while cannot leverage the ubiquitous structured data, often represented as graphs, in the digital world. While multiple graph foundation models have been proposed, they focus on graph learning tasks and cannot extend to diverse multi-modal data and interdisciplinary tasks. To address these challenges, we propose the Graph World Model (GWM), a world model that supports both unstructured and graph-structured states with multi-modal information and represents diverse tasks as actions. The core of a GWM is a generic message-passing algorithm to aggregate structured information, either over a unified multi-modal token space by converting multi-modal data into text (GWM-T) or a unified multi-modal embedding space by modality-specific encoders (GWM-E). Notably, GWM introduces action nodes to support diverse tasks, where action nodes are linked to other nodes via direct reference or similarity computation. Extensive experiments on 6 tasks from diverse domains, including multi-modal generation and matching, recommendation, graph prediction, multi-agent, retrieval-augmented generation, and planning and optimization, show that the same GWM outperforms or matches domain-specific baselines’ performance, benefits from multi-hop structures, and demonstrate strong zero-shot/few-shot capabilities on unseen new tasks. Our codes for GWM is released at https://github.com/ulab-uiuc/GWM.

Large Language Models (LLMs) have demonstrated remarkable potential in scientific domains, yet a fundamental question remains unanswered: Can we simulate human research communities with LLMs? Addressing this question can deepen our understanding of the processes behind idea brainstorming and inspire the automatic discovery of novel scientific insights. In this work, we propose ResearchTown, a multi-agent framework for research community simulation. Within this framework, the human research community is simplified as an agent-data graph, where researchers and papers are represented as agent-type and data-type nodes, respectively, and connected based on their collaboration relationships. We also introduce TextGNN, a text-based inference framework that models various research activities (e.g., paper reading, paper writing, and review writing) as special forms of a unified message-passing process on the agent-data graph. To evaluate the quality of the research community simulation, we present ResearchBench, a benchmark that uses a node-masking prediction task for scalable and objective assessment based on similarity. Our experiments reveal three key findings: (1) ResearchTown can provide a realistic simulation of collaborative research activities, including paper writing and review writing; (2) ResearchTown can maintain robust simulation with multiple researchers and diverse papers; (3) ResearchTown can generate interdisciplinary research ideas that potentially inspire pioneering research directions.

The rapid emergence of diverse large language models (LLMs) has spurred the development of LLM routers that assign user queries to the most suitable model. However, existing LLM routers typically perform a single-round, one-to-one mapping (\textit{i.e.}, assigning each query to a single model in isolation), which limits their capability to tackle complex tasks that demand the complementary strengths of multiple LLMs. In this paper, we present \textbf{Router-R1}, a reinforcement learning (RL)-based framework that formulates multi-LLM routing and aggregation as a sequential decision process. Router-R1 instantiates the router itself as a capable LLM, leveraging its reasoning ability to interleave "think" actions (internal deliberation) with "route" actions (dynamic model invocation), and integrates each response into its evolving context. To facilitate learning, we employ a lightweight rule-based reward comprising format rewards, final outcome rewards, and a novel cost reward for optimizing the balance between performance and cost, opening a pathway toward enhancing performance-cost trade-offs via RL. Router-R1 also conditions only on simple model descriptors such as pricing, latency, and example performance, enabling strong generalization to unseen model selection. Experiments on seven general and multi-hop QA benchmarks show that Router-R1 outperforms several strong baselines, achieving superior performance while maintaining robust generalization and cost management.

The advancement of large language models (LLMs) has extended their use to dynamic and interactive real-world applications, where models engage continuously with their environment and potentially enhance their performance over time.Most existing LLM benchmarks evaluate LLMs on i.i.d.tasks, overlooking their ability to learn iteratively from past experiences.Our paper bridges this evaluation gap by proposing a novel framework, LLM-Evolve, which extends established benchmarks to sequential problem-solving settings.LLM-Evolve evaluates LLMs over multiple rounds, providing feedback after each round to build a demonstration memory that the models can query in future tasks.We applied LLM-Evolve to the MMLU, GSM8K, and AgentBench benchmarks, testing 8 state-of-the-art open-source and closed-source models.Results show that LLMs can achieve performance improvements of up to 17% by learning from past interactions, with the quality of retrieval algorithms and feedback significantly influencing this capability.These insights advocate for more understanding and benchmarks for LLMs' performance in evolving interactive scenarios.

Structure prediction of large protein complexes (a.k.a., protein multimer mod- elling, PMM) can be achieved through the one-by-one assembly using provided dimer structures and predicted docking paths. However, existing PMM methods struggle with vast search spaces and generalization challenges: (1) The assembly of a N -chain multimer can be depicted using graph structured data, with each chain represented as a node and assembly actions as edges. Thus the assembly graph can be arbitrary acyclic undirected connected graph, leading to the com- binatorial optimization space of N^(N −2) for the PMM problem. (2) Knowledge transfer in the PMM task is non-trivial. The gradually limited data availability as the chain number increases necessitates PMM models that can generalize across multimers of various chains. To address these challenges, we propose GAPN, a Generative Adversarial Policy Network powered by domain-specific rewards and adversarial loss through policy gradient for automatic PMM prediction. Specifi- cally, GAPN learns to efficiently search through the immense assembly space and optimize the direct docking reward through policy gradient. Importantly, we de- sign a adversarial reward function to enhance the receptive field of our model. In this way, GAPN will simultaneously focus on a specific batch of multimers and the global assembly rules learned from multimers with varying chain numbers. Empirically, we have achieved both significant accuracy (measured by RMSD and TM-Score) and efficiency improvements compared to leading complex mod- eling software. GAPN outperforms the state-of-the-art method (MoLPC) with up to 27% improvement in TM-Score, with a speed-up of 600×.

Much of the world’s most valued data is stored in relational databases and data warehouses, where the data is organized into tables connected by primary-foreign key relations. However, building machine learning models using this data is both challenging and time consuming because no ML algorithm can directly learn from multiple connected tables. Current approaches can only learn from a single table, so data must first be manually joined and aggregated into this format, the laborious process known as feature engineering. Feature engineering is slow, error prone and leads to suboptimal models. Here we introduce Relational Deep Learning (RDL), a blueprint for end-to-end learning on relational databases. The key is to represent relational databases as a temporal, heterogeneous graphs, with a node for each row in each table, and edges specified by primary-foreign key links. Graph Neural Networks then learn representations that leverage all input data, without any manual feature engineering. We also introduce RelBench, and benchmark and testing suite, demonstrating strong initial results. Overall, we define a new research area that generalizes graph machine learning and broadens its applicability.

In this paper, we approach an overlooked yet critical task Graph2Image: generating images from multimodal attributed graphs (MMAGs). This task poses significant challenges due to the explosion in graph size, dependencies among graph entities, and the need for controllability in graph conditions. To address these challenges, we propose a graph context-conditioned diffusion model called InstructG2I. InstructG2I first exploits the graph structure and multimodal information to conduct informative neighbor sampling by combining personalized page rank and re-ranking based on vision-language features. Then, a graph QFormer encoder adaptively encodes the graph nodes into an auxiliary set of graph prompts to guide the denoising process of diffusion. Finally, we propose graph classifier-free guidance, enabling controllable generation by varying the strength of graph guidance and multiple connected edges to a node. Extensive experiments conducted on three datasets from different domains demonstrate the effectiveness and controllability of our approach. The code is available at https://github.com/PeterGriffinJin/InstructG2I.

Large language models (LLMs) typically utilize the top-k contexts from a retriever in retrieval-augmented generation (RAG). In this work, we propose a novel method called RankRAG, which instruction-tunes a single LLM for both context ranking and answer generation in RAG. In particular, the instruction-tuned LLMs work surprisingly well by adding a small fraction of ranking data into the training blend, and outperform existing expert ranking models, including the same LLM exclusively fine-tuned on a large amount of ranking data. For generation, we compare our model with many strong baselines, including ChatQA-1.5, an open-sourced model with the state-of-the-art performance on RAG benchmarks. Specifically, our Llama3-RankRAG-8B and Llama3-RankRAG-70B significantly outperform Llama3-ChatQA-1.5-8B and Llama3-ChatQA-1.5-70B, respectively, on nine general knowledge-intensive benchmarks for RAG. In addition, it also performs comparably to GPT-4 on five RAG benchmarks in the biomedical domain without instruction fine-tuning on biomedical data, demonstrating its superb capability for generalization to new domains.

Graph Neural Networks (GNNs) have been successfully applied to many real-world static graphs. However, the success of static graphs has not fully translated to dynamic graphs due to the limitations in model design, evaluation settings, and training strategies. Concretely, existing dynamic GNNs do not incorporate state-of-the-art designs from static GNNs, which limits their performance. Current evaluation settings for dynamic GNNs do not fully reflect the evolving nature of dynamic graphs. Finally, commonly used training methods for dynamic GNNs are not scalable. Here we propose ROLAND, an effective graph representation learning framework for real-world dynamic graphs. At its core, the ROLAND framework can help researchers easily repurpose any static GNN to dynamic graphs. Our insight is to view the node embeddings at different GNN layers as hierarchical node states and then recurrently update them over time. We then introduce a live-update evaluation setting for dynamic graphs that mimics real-world use cases, where GNNs are making predictions and being updated on a rolling basis. Finally, we propose a scalable and efficient training approach for dynamic GNNs via incremental training and meta-learning. We conduct experiments over eight different dynamic graph datasets on future link prediction tasks. Models built using the ROLAND framework achieve on average 62.7% relative mean reciprocal rank (MRR) improvement over state-of-the-art baselines under the standard evaluation settings on three datasets. We find state-of-the-art baselines experience out-of-memory errors for larger datasets, while ROLAND can easily scale to dynamic graphs with 56 million edges. After re-implementing these baselines using the ROLAND training strategy, ROLAND models still achieve on average 15.5% relative MRR improvement over the baselines.

Message passing Graph Neural Networks (GNNs) provide a powerful modeling framework for relational data. However, the expressive power of existing GNNs is upper-bounded by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test, which means GNNs that are not able to predict node clustering coefficients and shortest path distances, and cannot differentiate between different d-regular graphs. Here we develop a class of message passing GNNs, named Identity-aware Graph Neural Networks (ID-GNNs), with greater expressive power than the 1-WL test. ID-GNN offers a minimal but powerful solution to limitations of existing GNNs. ID-GNN extends existing GNN architectures by inductively considering nodes’ identities during message passing. To embed a given node, ID-GNN first extracts the ego network centered at the node, then conducts rounds of heterogeneous message passing, where different sets of parameters are applied to the center node than to other surrounding nodes in the ego network. We further propose a simplified but faster version of ID-GNN that injects node identity information as augmented node features. Alto- gether, both versions of ID-GNN represent general extensions of message passing GNNs, where experiments show that transforming existing GNNs to ID-GNNs yields on average 40% accuracy improvement on challenging node, edge, and graph property prediction tasks; 3% accuracy improvement on node and graph classification benchmarks; and 15% ROC AUC improvement on real-world link prediction tasks. Additionally, ID-GNNs demonstrate improved or comparable performance over other task-specific graph networks.

Commonsense knowledge graph (CKG) is a special type of knowledge graph (KG), where entities are composed of free-form text. Existing CKG completion methods focus on transductive learning setting, where all the entities are present during training. Here, we propose the first inductive learning setting for CKG completion, where unseen entities may appear at test time. We emphasize that the inductive learning setting is crucial for CKGs, because unseen entities are frequently introduced due to the fact that CKGs are dynamic and highly sparse. We propose InductivE as the first framework targeted at the inductive CKG completion task. InductivE first ensures the inductive learning capability by directly computing entity embeddings from raw entity attributes. Second, a graph neural network with novel densification process is proposed to further enhance unseen entity representation with neighboring structural information. Experimental results show that InductivE performs especially well on inductive scenarios where it achieves above 48% improvement over previous methods while also outperforms state-of-the-art baselines in transductive settings.

Neural networks are often represented as graphs of connections between neurons. However, despite their wide use, there is currently little understanding of the relationship between the graph structure of the neural network and its predictive performance. Here we systematically investigate how does the graph structure of neural networks affect their predictive performance. To this end, we develop a novel graph-based representation of neural networks called relational graph, where layers of neural network computation correspond to rounds of message exchange along the graph structure. Using this representation we show that: (1) a “sweet spot” of relational graphs leads to neural networks with significantly improved predictive performance; (2) neural network’s performance is approximately a smooth function of the clustering coefficient and average path length of its relational graph; (3) our findings are consistent across many different tasks and datasets; (4) the sweet spot can be identified efficiently; (5) top-performing neural networks have graph structure surprisingly similar to those of real biological neural networks. Our work opens new directions for the design of neural architectures and the understanding on neural networks in general.

Graph Neural Networks (GNNs) are based on repeated aggregations of information from nodes' neighbors in a graph. However, because nodes share many neighbors, a naive implementation leads to repeated and inefficient aggregations and represents significant computational overhead. Here we propose Hierarchically Aggregated computation Graphs(HAGs), a new GNN representation technique that explicitly avoids redundancy by managing intermediate aggregation results hierarchically and eliminates repeated computations and unnecessary data transfers in GNN training and inference. HAGs perform the same computations and give the same models/accuracy as traditional GNNs, but in a much shorter time dueto optimized computations. To identify redundant computations,we introduce an accurate cost function and use a novel search algorithm to find optimized HAGs. Experiments show that the HAG representation significantly outperforms the standard GNN by increasing the end-to-end training throughput by up to 2.8× and reducing the aggregations and data transfers in GNN training byup to 6.3× and 5.6×, with only 0.1% memory overhead. Overall,our results represent an important advancement in speeding-up and scaling-up GNNs without any loss in model predictive performance.

Machine learning with missing data has been approached in many different ways, including feature imputation where missing feature values are estimated based on observed values and label prediction where downstream labels are learned directly from incomplete data. However, existing imputation models tend to have strong prior assumptions and cannot learn from downstream tasks, while models targeting label predictions often involve heuristics and can encounter scalability issues. Here we propose GRAPE, a framework for feature imputation as well as label prediction. GRAPE tackles the missing data problem using graph representation, where the observations and features are viewed as two types of nodes in a bipartite graph, and the observed feature values as edges. Under the GRAPE framework, the feature imputation is formulated as an edge-level prediction task and the label prediction as a node-level prediction task. These tasks are then solved with Graph Neural Networks. Experimental results on nine benchmark datasets show that GRAPE yields 20% lower mean absolute error for imputation tasks and 10% lower for label prediction tasks, compared with existing state-of-the-art methods.

The rapid evolution of Graph Neural Networks (GNNs) has led to a growing number of new architectures as well as novel applications. However, current research focuses on proposing and evaluating specific architectural designs of GNNs, such as GCN, GIN, or GAT, as opposed to studying the more general design space of GNNs that consists of a Cartesian product of different design dimensions, such as the number of layers or the type of the aggregation function. Additionally, GNN designs are often specialized to a single task, yet few efforts have been made to understand how to quickly find the best GNN design for a novel task or a novel dataset. Here we define and systematically study the architectural design space for GNNs which consists of 315,000 different designs over 32 different predictive tasks. Our approach features three key innovations: (1) A general GNN design space; (2) a GNN task space with a similarity metric, so that for a given novel task/dataset, we can quickly identify/transfer the best performing architecture; (3) an efficient and effective design space evaluation method which allows insights to be distilled from a huge number of model-task combinations. Our key results include: (1) A comprehensive set of guidelines for designing well-performing GNNs; (2) while best GNN designs for different tasks vary significantly, the GNN task space allows for transferring the best designs across different tasks; (3) models discovered using our design space achieve state-of-the-art performance. Overall, our work offers a principled and scalable approach to transition from studying individual GNN designs for specific tasks, to systematically studying the GNN design space and the task space. Finally, we release GraphGym, a powerful platform for exploring different GNN designs and tasks. GraphGym features modularized GNN implementation, standardized GNN evaluation, and reproducible and scalable experiment management.

Learning node embeddings that capture a node’s position within the broader graph structure is crucial for many prediction tasks on graphs. However, existing Graph Neural Network (GNN) architectures have limited power in capturing the position/location of a given node with respect to all other nodes of the graph. Here we propose Position-aware Graph Neural Networks (P-GNNs), a new class of GNNs for computing position-aware node embeddings. P-GNN first samples sets of anchor nodes, computes the distance of a given target node to each anchor-set, and then learns a non-linear distance-weighted aggregation scheme over the anchor-sets. This way P-GNNs can capture positions/locations of nodes with respect to the anchor nodes. P-GNNs have several advantages: they are inductive, scalable, and can incorporate node feature information. We apply P-GNNs to multiple prediction tasks including link prediction and community detection. We show that P-GNNs consistently outperform state of the art GNNs, with up to 66% improvement in terms of the ROC AUC score.

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models, and explaining predictions made by GNNs remains unsolved. Here we propose GNNExplainer, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GNNExplainer identifies a compact subgraph structure and a small subset of node features that have a crucial role in GNN's prediction. Further, GNNExplainer can generate consistent and concise explanations for an entire class of instances. We formulate GNNExplainer as an optimization task that maximizes the mutual information between a GNN's prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms baselines by 17.1% on average. GNNExplainer provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.

The Boolean Satisfiability (SAT) problem is the canonical NP-complete problem and is fundamental to computer science, with a wide array of applications in planning, verification, and theorem proving. Developing and evaluating practical SAT solvers relies on extensive empirical testing on a set of real-world benchmark formulas. However, the availability of such real-world SAT formulas is limited. While these benchmark formulas can be augmented with synthetically generated ones, existing approaches for doing so are heavily hand-crafted and fail to simultaneously capture a wide range of characteristics exhibited by real-world SAT instances. In this work, we present G2SAT, the first deep generative framework that learns to generate SAT formulas from a given set of input formulas. Our key insight is that SAT formulas can be transformed into latent bipartite graph representations which we model using a specialized deep generative neural network. We show that G2SAT can generate SAT formulas that closely resemble given real-world SAT instances, as measured by both graph metrics and SAT solver behavior. Further, we show that our synthetic SAT formulas could be used to improve SAT solver performance on real-world benchmarks, which opens up new opportunities for the continued development of SAT solvers and a deeper understanding of their performance.

Recommender systems that can learn from cross-session data to dynamically predict the next item a user will choose are crucial for online platforms. However, existing approaches often use out-of-the-box sequence models which are limited by speed and memory consumption, are often infeasible for production environments, and usually do not incorporate cross-session information, which is crucial for effective recommendations. Here we propose Hierarchical Temporal Convolutional Networks (HierTCN), a hierarchical deep learning architecture that makes dynamic recommendations based on users' sequential multi-session interactions with items. HierTCN is designed for web-scale systems with billions of items and hundreds of millions of users. It consists of two levels of models: The high-level model uses Recurrent Neural Networks (RNN) to aggregate users' evolving long-term interests across different sessions, while the low-level model is implemented with Temporal Convolutional Networks (TCN), utilizing both the long-term interests and the short-term interactions within sessions to predict the next interaction. We conduct extensive experiments on a public XING dataset and a large-scale Pinterest dataset that contains 6 million users with 1.6 billion interactions. We show that HierTCN is 2.5x faster than RNN-based models and uses 90% less data memory compared to TCN-based models. We further develop an effective data caching scheme and a queue-based mini-batch generator, enabling our model to be trained within 24 hours on a single GPU. Our model consistently outperforms state-of-the-art dynamic recommendation methods, with up to 18% improvement in recall and 10% in mean reciprocal rank.

Modeling and generating graphs is fundamental for studying networks in biology, engineering, and social sciences. However, modeling complex distributions over graphs and then efficiently sampling from these distributions is challenging due to the non-unique, high-dimensional nature of graphs and the complex, non-local dependencies that exist between edges in a given graph. Here we propose GraphRNN, a deep autoregressive model that addresses the above challenges and approximates any distribution of graphs with minimal assumptions about their structure. GraphRNN learns to generate graphs by training on a representative set of graphs and decomposes the graph generation process into a sequence of node and edge formations, conditioned on the graph structure generated so far. In order to quantitatively evaluate the performance of GraphRNN, we introduce a benchmark suite of datasets, baselines and novel evaluation metrics based on Maximum Mean Discrepancy, which measure distances between sets of graphs. Our experiments show that GraphRNN significantly outperforms all baselines, learning to generate diverse graphs that match the structural characteristics of a target set, while also scaling to graphs 50 times larger than previous deep models.

Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10% accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark datasets.

Generating novel graph structures that optimize given objectives while obeying some given underlying rules is fundamental for chemistry, biology and social science research. This is especially important in the task of molecular graph generation, whose goal is to discover novel molecules with desired properties such as drug-likeness and synthetic accessibility, while obeying physical laws such as chemical valency. However, designing models that finds molecules that optimize desired properties while incorporating highly complex and non-differentiable rules remains to be a challenging task. Here we propose Graph Convolutional Policy Network (GCPN), a general graph convolutional network based model for goal-directed graph generation through reinforcement learning. The model is trained to optimize domain-specific rewards and adversarial loss through policy gradient, and acts in an environment that incorporates domain-specific rules. Experimental results show that GCPN can achieve 61% improvement on chemical property optimization over state-of-the-art baselines while resembling known molecules, and achieve 184% improvement on the constrained property optimization task.

Agricultural monitoring, especially in developing countries, can help prevent famine and support humanitarian efforts. A central challenge is yield estimation, i.e., predicting crop yields before harvest. We introduce a scalable, accurate, and inexpensive method to predict crop yields using publicly available remote sensing data. Our approach improves existing techniques in three ways. First, we forego hand-crafted features traditionally used in the remote sensing community and propose an approach based on modern representation learning ideas. We also introduce a novel dimensionality reduction technique that allows us to train a Convolutional Neural Network or Long-short Term Memory network and automatically learn useful features even when labeled training data are scarce. Finally, we incorporate a Gaussian Process component to explicitly model the spatio-temporal structure of the data and further improve accuracy. We evaluate our approach on county-level soybean yield prediction in the U.S. and show that it outperforms competing techniques.