Rex Ying

Hiren Madhu, Ngoc Bui, Ali Maatouk et al.

Embedding geometry plays a fundamental role in retrieval quality, yet dense retrievers for retrieval-augmented generation (RAG) remain largely confined to Euclidean space. However, natural language exhibits hierarchical structure from broad topics to specific entities that Euclidean embeddings fail to preserve, causing semantically distant documents to appear spuriously similar and increasing hallucination risk. To address these limitations, we introduce hyperbolic dense retrieval, developing two model variants in the Lorentz model of hyperbolic space: HyTE-FH, a fully hyperbolic transformer, and HyTE-H, a hybrid architecture projecting pre-trained Euclidean embeddings into hyperbolic space. To prevent representational collapse during sequence aggregation, we introduce the Outward Einstein Midpoint, a geometry-aware pooling operator that provably preserves hierarchical structure. On MTEB, HyTE-FH outperforms equivalent Euclidean baselines, while on RAGBench, HyTE-H achieves up to 29% gains over Euclidean baselines in context relevance and answer relevance using substantially smaller models than current state-of-the-art retrievers. Our analysis also reveals that hyperbolic representations encode document specificity through norm-based separation, with over 20% radial increase from general to specific concepts, a property absent in Euclidean embeddings, underscoring the critical role of geometric inductive bias in faithful RAG systems.

Tianyu Fu, Chiyue Wei, Yu Wang et al. · tsinghua

We introduce DeSCo, a scalable neural deep subgraph counting pipeline, designed to accurately predict both the count and occurrence position of queries on target graphs post single training. Firstly, DeSCo uses a novel canonical partition and divides the large target graph into small neighborhood graphs, greatly reducing the count variation while guaranteeing no missing or double-counting. Secondly, neighborhood counting uses an expressive subgraph-based heterogeneous graph neural network to accurately count in each neighborhood. Finally, gossip propagation propagates neighborhood counts with learnable gates to harness the inductive biases of motif counts. DeSCo is evaluated on eight real-world datasets from various domains. It outperforms state-of-the-art neural methods with 137x improvement in the mean squared error of count prediction, while maintaining the polynomial runtime complexity. Our open source project is at https://github.com/fuvty/DeSCo.

Zhen Yang, Tinglin Huang, Ming Ding et al. · tsinghua

In-Batch contrastive learning is a state-of-the-art self-supervised method that brings semantically-similar instances close while pushing dissimilar instances apart within a mini-batch. Its key to success is the negative sharing strategy, in which every instance serves as a negative for the others within the mini-batch. Recent studies aim to improve performance by sampling hard negatives \textit{within the current mini-batch}, whose quality is bounded by the mini-batch itself. In this work, we propose to improve contrastive learning by sampling mini-batches from the input data. We present BatchSampler\footnote{The code is available at \url{https://github.com/THUDM/BatchSampler}} to sample mini-batches of hard-to-distinguish (i.e., hard and true negatives to each other) instances. To make each mini-batch have fewer false negatives, we design the proximity graph of randomly-selected instances. To form the mini-batch, we leverage random walk with restart on the proximity graph to help sample hard-to-distinguish instances. BatchSampler is a simple and general technique that can be directly plugged into existing contrastive learning models in vision, language, and graphs. Extensive experiments on datasets of three modalities show that BatchSampler can consistently improve the performance of powerful contrastive models, as shown by significant improvements of SimCLR on ImageNet-100, SimCSE on STS (language), and GraphCL and MVGRL on graph datasets.

Tailin Wu, Qinchen Wang, Yinan Zhang et al. · mit, stanford

Subsurface simulations use computational models to predict the flow of fluids (e.g., oil, water, gas) through porous media. These simulations are pivotal in industrial applications such as petroleum production, where fast and accurate models are needed for high-stake decision making, for example, for well placement optimization and field development planning. Classical finite difference numerical simulators require massive computational resources to model large-scale real-world reservoirs. Alternatively, streamline simulators and data-driven surrogate models are computationally more efficient by relying on approximate physics models, however they are insufficient to model complex reservoir dynamics at scale. Here we introduce Hybrid Graph Network Simulator (HGNS), which is a data-driven surrogate model for learning reservoir simulations of 3D subsurface fluid flows. To model complex reservoir dynamics at both local and global scale, HGNS consists of a subsurface graph neural network (SGNN) to model the evolution of fluid flows, and a 3D-U-Net to model the evolution of pressure. HGNS is able to scale to grids with millions of cells per time step, two orders of magnitude higher than previous surrogate models, and can accurately predict the fluid flow for tens of time steps (years into the future). Using an industry-standard subsurface flow dataset (SPE-10) with 1.1 million cells, we demonstrate that HGNS is able to reduce the inference time up to 18 times compared to standard subsurface simulators, and that it outperforms other learning-based models by reducing long-term prediction errors by up to 21%.

Simeng Han, Hailey Schoelkopf, Yilun Zhao et al. · salesforce

Large language models (LLMs) have achieved remarkable performance on a variety of natural language understanding tasks. However, existing benchmarks are inadequate in measuring the complex logical reasoning capabilities of a model. We present FOLIO, a human-annotated, logically complex and diverse dataset for reasoning in natural language (NL), equipped with first-order logic (FOL) annotations. FOLIO consists of 1,430 examples (unique conclusions), each paired with one of 487 sets of premises used to deductively reason for the validity of each conclusion. The logical correctness of the premises and conclusions is ensured by their FOL annotations, which are automatically verified by an FOL inference engine. In addition to the main NL reasoning task, NL-FOL pairs in FOLIO constitute a new NL-FOL translation dataset. Our experiments on FOLIO systematically evaluate the FOL reasoning ability of supervised fine-tuning on medium-sized language models. For both NL reasoning and NL-FOL translation, we benchmark multiple state-of-the-art language models. Our results show that a subset of FOLIO presents a challenge for one of the most capable {Large Language Model (LLM)} publicly available, GPT-4.

Zhen Xu, Lanning Wei, Huan Zhao et al. · tsinghua

Graph structured data is ubiquitous in daily life and scientific areas and has attracted increasing attention. Graph Neural Networks (GNNs) have been proved to be effective in modeling graph structured data and many variants of GNN architectures have been proposed. However, much human effort is often needed to tune the architecture depending on different datasets. Researchers naturally adopt Automated Machine Learning on Graph Learning, aiming to reduce the human effort and achieve generally top-performing GNNs, but their methods focus more on the architecture search. To understand GNN practitioners' automated solutions, we organized AutoGraph Challenge at KDD Cup 2020, emphasizing on automated graph neural networks for node classification. We received top solutions especially from industrial tech companies like Meituan, Alibaba and Twitter, which are already open sourced on Github. After detailed comparisons with solutions from academia, we quantify the gaps between academia and industry on modeling scope, effectiveness and efficiency, and show that (1) academia AutoML for Graph solutions focus on GNN architecture search while industrial solutions, especially the winning ones in the KDD Cup, tend to obtain an overall solution (2) by neural architecture search only, academia solutions achieve on average 97.3% accuracy of industrial solutions (3) academia solutions are cheap to obtain with several GPU hours while industrial solutions take a few months' labors. Academic solutions also contain much fewer parameters.

Kenza Amara, Rex Ying, Zitao Zhang et al. · eth-zurich

As one of the most popular machine learning models today, graph neural networks (GNNs) have attracted intense interest recently, and so does their explainability. Users are increasingly interested in a better understanding of GNN models and their outcomes. Unfortunately, today's evaluation frameworks for GNN explainability often rely on few inadequate synthetic datasets, leading to conclusions of limited scope due to a lack of complexity in the problem instances. As GNN models are deployed to more mission-critical applications, we are in dire need for a common evaluation protocol of explainability methods of GNNs. In this paper, we propose, to our best knowledge, the first systematic evaluation framework for GNN explainability, considering explainability on three different "user needs". We propose a unique metric that combines the fidelity measures and classifies explanations based on their quality of being sufficient or necessary. We scope ourselves to node classification tasks and compare the most representative techniques in the field of input-level explainability for GNNs. For the inadequate but widely used synthetic benchmarks, surprisingly shallow techniques such as personalized PageRank have the best performance for a minimum computation time. But when the graph structure is more complex and nodes have meaningful features, gradient-based methods are the best according to our evaluation criteria. However, none dominates the others on all evaluation dimensions and there is always a trade-off. We further apply our evaluation protocol in a case study for frauds explanation on eBay transaction graphs to reflect the production environment.

Songtao Liu, Zhengkai Tu, Minkai Xu et al.

Retrosynthetic planning aims to devise a complete multi-step synthetic route from starting materials to a target molecule. Current strategies use a decoupled approach of single-step retrosynthesis models and search algorithms, taking only the product as the input to predict the reactants for each planning step and ignoring valuable context information along the synthetic route. In this work, we propose a novel framework that utilizes context information for improved retrosynthetic planning. We view synthetic routes as reaction graphs and propose to incorporate context through three principled steps: encode molecules into embeddings, aggregate information over routes, and readout to predict reactants. Our approach is the first attempt to utilize in-context learning for retrosynthesis prediction in retrosynthetic planning. The entire framework can be efficiently optimized in an end-to-end fashion and produce more practical and accurate predictions. Comprehensive experiments demonstrate that by fusing in the context information over routes, our model significantly improves the performance of retrosynthetic planning over baselines that are not context-aware, especially for long synthetic routes. Code is available at https://github.com/SongtaoLiu0823/FusionRetro.

Chenqing Hua, Sitao Luan, Minkai Xu et al.

Molecule generation is a very important practical problem, with uses in drug discovery and material design, and AI methods promise to provide useful solutions. However, existing methods for molecule generation focus either on 2D graph structure or on 3D geometric structure, which is not sufficient to represent a complete molecule as 2D graph captures mainly topology while 3D geometry captures mainly spatial atom arrangements. Combining these representations is essential to better represent a molecule. In this paper, we present a new model for generating a comprehensive representation of molecules, including atom features, 2D discrete molecule structures, and 3D continuous molecule coordinates, by combining discrete and continuous diffusion processes. The use of diffusion processes allows for capturing the probabilistic nature of molecular processes and exploring the effect of different factors on molecular structures. Additionally, we propose a novel graph transformer architecture to denoise the diffusion process. The transformer adheres to 3D roto-translation equivariance constraints, allowing it to learn invariant atom and edge representations while preserving the equivariance of atom coordinates. This transformer can be used to learn molecular representations robust to geometric transformations. We evaluate the performance of our model through experiments and comparisons with existing methods, showing its ability to generate more stable and valid molecules. Our model is a promising approach for designing stable and diverse molecules and can be applied to a wide range of tasks in molecular modeling.

Ali Maatouk, Kenny Chirino Ampudia, Rex Ying et al.

The emergence of large language models (LLMs) has significantly impacted various fields, from natural language processing to sectors like medicine and finance. However, despite their rapid proliferation, the applications of LLMs in telecommunications remain limited, often relying on general-purpose models that lack domain-specific specialization. This lack of specialization results in underperformance, particularly when dealing with telecommunications-specific technical terminology and their associated mathematical representations. This paper addresses this gap by first creating and disseminating Tele-Data, a comprehensive dataset of telecommunications material curated from relevant sources, and Tele-Eval, a large-scale question-and-answer dataset tailored to the domain. Through extensive experiments, we explore the most effective training techniques for adapting LLMs to the telecommunications domain, ranging from examining the division of expertise across various telecommunications aspects to employing parameter-efficient techniques. We also investigate how models of different sizes behave during adaptation and analyze the impact of their training data on this behavior. Leveraging these findings, we develop and open-source Tele-LLMs, the first series of language models ranging from 1B to 8B parameters, specifically tailored for telecommunications. Our evaluations demonstrate that these models outperform their general-purpose counterparts on Tele-Eval and telecommunications-related literature tasks while retaining their previously acquired capabilities, thus avoiding the catastrophic forgetting phenomenon.

Beini Xie, Heng Chang, Ziwei Zhang et al. · tsinghua

Graph Neural Networks (GNNs) obtain tremendous success in modeling relational data. Still, they are prone to adversarial attacks, which are massive threats to applying GNNs to risk-sensitive domains. Existing defensive methods neither guarantee performance facing new data/tasks or adversarial attacks nor provide insights to understand GNN robustness from an architectural perspective. Neural Architecture Search (NAS) has the potential to solve this problem by automating GNN architecture designs. Nevertheless, current graph NAS approaches lack robust design and are vulnerable to adversarial attacks. To tackle these challenges, we propose a novel Robust Neural Architecture search framework for GNNs (G-RNA). Specifically, we design a robust search space for the message-passing mechanism by adding graph structure mask operations into the search space, which comprises various defensive operation candidates and allows us to search for defensive GNNs. Furthermore, we define a robustness metric to guide the search procedure, which helps to filter robust architectures. In this way, G-RNA helps understand GNN robustness from an architectural perspective and effectively searches for optimal adversarial robust GNNs. Extensive experimental results on benchmark datasets show that G-RNA significantly outperforms manually designed robust GNNs and vanilla graph NAS baselines by 12.1% to 23.4% under adversarial attacks.

Michal Pándy, Weikang Qiu, Gabriele Corso et al.

Searching for a path between two nodes in a graph is one of the most well-studied and fundamental problems in computer science. In numerous domains such as robotics, AI, or biology, practitioners develop search heuristics to accelerate their pathfinding algorithms. However, it is a laborious and complex process to hand-design heuristics based on the problem and the structure of a given use case. Here we present PHIL (Path Heuristic with Imitation Learning), a novel neural architecture and a training algorithm for discovering graph search and navigation heuristics from data by leveraging recent advances in imitation learning and graph representation learning. At training time, we aggregate datasets of search trajectories and ground-truth shortest path distances, which we use to train a specialized graph neural network-based heuristic function using backpropagation through steps of the pathfinding process. Our heuristic function learns graph embeddings useful for inferring node distances, runs in constant time independent of graph sizes, and can be easily incorporated in an algorithm such as A* at test time. Experiments show that PHIL reduces the number of explored nodes compared to state-of-the-art methods on benchmark datasets by 58.5\% on average, can be directly applied in diverse graphs ranging from biological networks to road networks, and allows for fast planning in time-critical robotics domains.

Yangtian Zhang, Zhe Wang, Arthur Gretton et al.

Non-monotonic sequence generation methods, such as masked diffusion models, provide a flexible alternative to left-to-right autoregressive modeling by allowing tokens to be generated in non-fixed and prescribed orders. Despite their practical advantages, most existing non-monotonic models are order-agnostic and rely on a fixed-length grid, limiting their ability to support variable-length generation and adaptive insertion order. In this work, we introduce a probabilistic framework for learning insertion order in variable-length insertion models. We formalize a bijective correspondence between insertion trajectories and permutations, which enables an exact reparameterization of the data likelihood as a sum over permutations. Building on this result, we propose the Insertion Process (IP), a stochastic generative model that jointly learns where to insert, what to insert, and when to terminate, trained via permutation-based variational inference. Unlike prior fixed-canvas approaches, IP natively supports variable-length generation and learns data-driven preferences over insertion orders. Experiments on goal-conditioned planning and molecular string generation demonstrate that learning insertion order improves both modeling quality and generalization in domains without a canonical left-to-right structure.

Jindong Li, Ying Liu, Yali Fu et al.

LLMs are increasingly equipped with safety alignment mechanisms, yet recent studies demonstrate that they remain vulnerable to jailbreaking attacks that elicit harmful behaviors without explicit policy violations. While a growing body of work has explored automated jailbreak strategies, existing methods face several fundamental challenges, including the lack of systematic utilization of both successful and failed attack experiences, as well as the absence of principled mechanisms for composing and selecting reusable attack rules under diverse constraints. As a result, existing methods struggle to accumulate transferable knowledge over time and to reliably adapt attack strategies across different targets and evolving safety mechanisms. To address these issues, we propose a Self-Evolving Rule-Driven Training-Free Jailbreak (SRTJ) framework that systematically discovers, composes, and refines attack strategies through interaction and feedback, without updating model parameters. Specifically, SRTJ couples experience-driven attack generation with answer set programming (ASP)-based rule selection and constraint-aware composition, where iterative verifier feedback is leveraged to jointly refine successful strategies and analyze failure patterns. The resulting rule memory evolves in a hierarchical multi-level manner, explicitly organizing distilled attack knowledge into long-term, middle-term, and short-term rules, thereby capturing both stable transferable strategies and transient adaptive behaviors to effectively balance exploration and exploitation across attack attempts. Extensive experiments on mainstream jailbreak benchmark (HarmBench) demonstrate that SRTJ achieves strong and stable attack performance across different target LLMs, while exhibiting improved robustness and generalization compared to existing jailbreak methods. The code is available at https://github.com/TheSolkatt/SRTJ.

Xiaojie Gu, Sherry T. Tong, Aosong Feng et al.

Reasoning-focused large language models (LLMs) have advanced in many NLP tasks, yet their evaluation remains challenging: final answers alone do not expose the intermediate reasoning steps, making it difficult to determine whether a model truly reasons correctly and where failures occur, while existing multi-hop QA benchmarks lack step-level annotations for diagnosing reasoning failures. To address this gap, we propose Omanic, an open-domain multi-hop QA resource that provides decomposed sub-questions and intermediate answers as structural annotations for analyzing reasoning processes. It contains 10,296 machine-generated training examples (OmanicSynth) and 967 expert-reviewed human-annotated evaluation examples (OmanicBench). Systematic evaluations show that state-of-the-art LLMs achieve only 73.11% multiple-choice accuracy on OmanicBench, confirming its high difficulty. Stepwise analysis reveals that CoT's performance hinges on factual completeness, with its gains diminishing under knowledge gaps and errors amplifying in later hops. Additionally, supervised fine-tuning on OmanicSynth brings substantial transfer gains (7.41 average points) across six reasoning and math benchmarks, validating the dataset's quality and further supporting the effectiveness of OmanicSynth as supervision for reasoning-capability transfer. We release the data at https://huggingface.co/datasets/li-lab/Omanic and the code at https://github.com/XiaojieGu/Omanic.

Jialin Chen, Yuelin Wang, Cristian Bodnar et al. · cambridge

Graph convolutions have been a pivotal element in learning graph representations. However, recursively aggregating neighboring information with graph convolutions leads to indistinguishable node features in deep layers, which is known as the over-smoothing issue. The performance of graph neural networks decays fast as the number of stacked layers increases, and the Dirichlet energy associated with the graph decreases to zero as well. In this work, we introduce a framelet system into the analysis of Dirichlet energy and take a multi-scale perspective to leverage the Dirichlet energy and alleviate the over-smoothing issue. Specifically, we develop a Framelet Augmentation strategy by adjusting the update rules with positive and negative increments for low-pass and high-passes respectively. Based on that, we design the Energy Enhanced Convolution (EEConv), which is an effective and practical operation that is proved to strictly enhance Dirichlet energy. From a message-passing perspective, EEConv inherits multi-hop aggregation property from the framelet transform and takes into account all hops in the multi-scale representation, which benefits the node classification tasks over heterophilous graphs. Experiments show that deep GNNs with EEConv achieve state-of-the-art performance over various node classification datasets, especially for heterophilous graphs, while also lifting the Dirichlet energy as the network goes deeper.

Menglin Yang, Min Zhou, Rex Ying et al.

The non-Euclidean geometry of hyperbolic spaces has recently garnered considerable attention in the realm of representation learning. Current endeavors in hyperbolic representation largely presuppose that the underlying hierarchies can be automatically inferred and preserved through the adaptive optimization process. This assumption, however, is questionable and requires further validation. In this work, we first introduce a position-tracking mechanism to scrutinize existing prevalent \hlms, revealing that the learned representations are sub-optimal and unsatisfactory. To address this, we propose a simple yet effective method, hyperbolic informed embedding (HIE), by incorporating cost-free hierarchical information deduced from the hyperbolic distance of the node to origin (i.e., induced hyperbolic norm) to advance existing \hlms. The proposed method HIE is both task-agnostic and model-agnostic, enabling its seamless integration with a broad spectrum of models and tasks. Extensive experiments across various models and different tasks demonstrate the versatility and adaptability of the proposed method. Remarkably, our method achieves a remarkable improvement of up to 21.4\% compared to the competing baselines.

Shirley Wu, Jiaxuan You, Jure Leskovec et al.

Despite the success of automated machine learning (AutoML), which aims to find the best design, including the architecture of deep networks and hyper-parameters, conventional AutoML methods are computationally expensive and hardly provide insights into the relations of different model design choices. To tackle the challenges, we propose FALCON, an efficient sample-based method to search for the optimal model design. Our key insight is to model the design space of possible model designs as a design graph, where the nodes represent design choices, and the edges denote design similarities. FALCON features 1) a task-agnostic module, which performs message passing on the design graph via a Graph Neural Network (GNN), and 2) a task-specific module, which conducts label propagation of the known model performance information on the design graph. Both modules are combined to predict the design performances in the design space, navigating the search direction. We conduct extensive experiments on 27 node and graph classification tasks from various application domains, and an image classification task on the CIFAR-10 dataset. We empirically show that FALCON can efficiently obtain the well-performing designs for each task using only 30 explored nodes. Specifically, FALCON has a comparable time cost with the one-shot approaches while achieving an average improvement of 3.3% compared with the best baselines.

Sitao Luan, Chenqing Hua, Qincheng Lu et al.

Homophily principle, \ie{} nodes with the same labels or similar attributes are more likely to be connected, has been commonly believed to be the main reason for the superiority of Graph Neural Networks (GNNs) over traditional Neural Networks (NNs) on graph-structured data, especially on node-level tasks. However, recent work has identified a non-trivial set of datasets where GNN's performance compared to the NN's is not satisfactory. Heterophily, i.e. low homophily, has been considered the main cause of this empirical observation. People have begun to revisit and re-evaluate most existing graph models, including graph transformer and its variants, in the heterophily scenario across various kinds of graphs, e.g. heterogeneous graphs, temporal graphs and hypergraphs. Moreover, numerous graph-related applications are found to be closely related to the heterophily problem. In the past few years, considerable effort has been devoted to studying and addressing the heterophily issue. In this survey, we provide a comprehensive review of the latest progress on heterophilic graph learning, including an extensive summary of benchmark datasets and evaluation of homophily metrics on synthetic graphs, meticulous classification of the most updated supervised and unsupervised learning methods, thorough digestion of the theoretical analysis on homophily/heterophily, and broad exploration of the heterophily-related applications. Notably, through detailed experiments, we are the first to categorize benchmark heterophilic datasets into three sub-categories: malignant, benign and ambiguous heterophily. Malignant and ambiguous datasets are identified as the real challenging datasets to test the effectiveness of new models on the heterophily challenge. Finally, we propose several challenges and future directions for heterophilic graph representation learning.

Lige Zhang, Ali Maatouk, Jialin Chen et al.

Real-world time series exhibit complex and evolving dynamics, making accurate forecasting extremely challenging. Recent multi-modal forecasting methods leverage textual information such as news reports to improve prediction, but most rely on token-level fusion that mixes temporal patches with language tokens in a shared embedding space. However, such fusion can be ill-suited when high-quality time-text pairs are scarce and when time series exhibit substantial variation in scale and characteristics, thus complicating cross-modal alignment. In parallel, Mixture-of-Experts (MoE) architectures have proven effective for both time series modeling and multi-modal learning, yet many existing MoE-based modality integration methods still depend on token-level fusion. To address this, we propose Expert Modulation, a new paradigm for multi-modal time series prediction that conditions both routing and expert computation on textual signals, enabling direct and efficient cross-modal control over expert behavior. Through comprehensive theoretical analysis and experiments, our proposed method demonstrates substantial improvements in multi-modal time series prediction. The current code is available at https://github.com/BruceZhangReve/MoME

Aosong Feng, Irene Li, Yuang Jiang et al.

Efficient Transformers have been developed for long sequence modeling, due to their subquadratic memory and time complexity. Sparse Transformer is a popular approach to improving the efficiency of Transformers by restricting self-attention to locations specified by the predefined sparse patterns. However, leveraging sparsity may sacrifice expressiveness compared to full-attention, when important token correlations are multiple hops away. To combine advantages of both the efficiency of sparse transformer and the expressiveness of full-attention Transformer, we propose \textit{Diffuser}, a new state-of-the-art efficient Transformer. Diffuser incorporates all token interactions within one attention layer while maintaining low computation and memory costs. The key idea is to expand the receptive field of sparse attention using Attention Diffusion, which computes multi-hop token correlations based on all paths between corresponding disconnected tokens, besides attention among neighboring tokens. Theoretically, we show the expressiveness of Diffuser as a universal sequence approximator for sequence-to-sequence modeling, and investigate its ability to approximate full-attention by analyzing the graph expander property from the spectral perspective. Experimentally, we investigate the effectiveness of Diffuser with extensive evaluations, including language modeling, image modeling, and Long Range Arena (LRA). Evaluation results show that Diffuser achieves improvements by an average of 0.94% on text classification tasks and 2.30% on LRA, with 1.67$\times$ memory savings compared to state-of-the-art benchmarks, which demonstrates superior performance of Diffuser in both expressiveness and efficiency aspects.

Jiasheng Zhang, Rex Ying, Jie Shao

Temporal knowledge graphs (TKGs) are valuable resources for capturing evolving relationships among entities, yet they are often plagued by noise, necessitating robust anomaly detection mechanisms. Existing dynamic graph anomaly detection approaches struggle to capture the rich semantics introduced by node and edge categories within TKGs, while TKG embedding methods lack interpretability, undermining the credibility of anomaly detection. Moreover, these methods falter in adapting to pattern changes and semantic drifts resulting from knowledge updates. To tackle these challenges, we introduce AnoT, an efficient TKG summarization method tailored for interpretable online anomaly detection in TKGs. AnoT begins by summarizing a TKG into a novel rule graph, enabling flexible inference of complex patterns in TKGs. When new knowledge emerges, AnoT maps it onto a node in the rule graph and traverses the rule graph recursively to derive the anomaly score of the knowledge. The traversal yields reachable nodes that furnish interpretable evidence for the validity or the anomalous of the new knowledge. Overall, AnoT embodies a detector-updater-monitor architecture, encompassing a detector for offline TKG summarization and online scoring, an updater for real-time rule graph updates based on emerging knowledge, and a monitor for estimating the approximation error of the rule graph. Experimental results on four real-world datasets demonstrate that AnoT surpasses existing methods significantly in terms of accuracy and interoperability. All of the raw datasets and the implementation of AnoT are provided in https://github.com/zjs123/ANoT.

Junchi Yu, Ran He, Rex Ying

Large Language Models (LLMs) have achieved remarkable success in reasoning tasks with the development of prompting methods. However, existing prompting approaches cannot reuse insights of solving similar problems and suffer from accumulated errors in multi-step reasoning, since they prompt LLMs to reason \textit{from scratch}. To address these issues, we propose \textbf{\textit{Thought Propagation} (TP)}, which explores the analogous problems and leverages their solutions to enhance the complex reasoning ability of LLMs. These analogous problems are related to the input one, with reusable solutions and problem-solving strategies. Thus, it is promising to propagate insights of solving previous analogous problems to inspire new problem-solving. To achieve this, TP first prompts LLMs to propose and solve a set of analogous problems that are related to the input one. Then, TP reuses the results of analogous problems to directly yield a new solution or derive a knowledge-intensive plan for execution to amend the initial solution obtained from scratch. TP is compatible with existing prompting approaches, allowing plug-and-play generalization and enhancement in a wide range of tasks without much labor in task-specific prompt engineering. Experiments across three challenging tasks demonstrate TP enjoys a substantial improvement over the baselines by an average of 12\% absolute increase in finding the optimal solutions in Shortest-path Reasoning, 13\% improvement of human preference in Creative Writing, and 15\% enhancement in the task completion rate of LLM-Agent Planning.

Syed Asad Rizvi, Nazreen Pallikkavaliyaveetil, David Zhang et al.

Foundation models have achieved remarkable success across many domains, relying on pretraining over vast amounts of data. Graph-structured data often lacks the same scale as unstructured data, making the development of graph foundation models challenging. In this work, we propose Foundation-Informed Message Passing (FIMP), a Graph Neural Network (GNN) message-passing framework that leverages pretrained non-textual foundation models in graph-based tasks. We show that the self-attention layers of foundation models can effectively be repurposed on graphs to perform cross-node attention-based message-passing. Our model is evaluated on a real-world image network dataset and two biological applications (single-cell RNA sequencing data and fMRI brain activity recordings) in both finetuned and zero-shot settings. FIMP outperforms strong baselines, demonstrating that it can effectively leverage state-of-the-art foundation models in graph tasks.

Kenza Amara, Mennatallah El-Assady, Rex Ying

Diverse explainability methods of graph neural networks (GNN) have recently been developed to highlight the edges and nodes in the graph that contribute the most to the model predictions. However, it is not clear yet how to evaluate the correctness of those explanations, whether it is from a human or a model perspective. One unaddressed bottleneck in the current evaluation procedure is the problem of out-of-distribution explanations, whose distribution differs from those of the training data. This important issue affects existing evaluation metrics such as the popular faithfulness or fidelity score. In this paper, we show the limitations of faithfulness metrics. We propose GInX-Eval (Graph In-distribution eXplanation Evaluation), an evaluation procedure of graph explanations that overcomes the pitfalls of faithfulness and offers new insights on explainability methods. Using a fine-tuning strategy, the GInX score measures how informative removed edges are for the model and the EdgeRank score evaluates if explanatory edges are correctly ordered by their importance. GInX-Eval verifies if ground-truth explanations are instructive to the GNN model. In addition, it shows that many popular methods, including gradient-based methods, produce explanations that are not better than a random designation of edges as important subgraphs, challenging the findings of current works in the area. Results with GInX-Eval are consistent across multiple datasets and align with human evaluation.

Tinglin Huang, Ziniu Hu, Rex Ying

The limited availability of annotations in small molecule datasets presents a challenge to machine learning models. To address this, one common strategy is to collaborate with additional auxiliary datasets. However, having more data does not always guarantee improvements. Negative transfer can occur when the knowledge in the target dataset differs or contradicts that of the auxiliary molecule datasets. In light of this, identifying the auxiliary molecule datasets that can benefit the target dataset when jointly trained remains a critical and unresolved problem. Through an empirical analysis, we observe that combining graph structure similarity and task similarity can serve as a more reliable indicator for identifying high-affinity auxiliary datasets. Motivated by this insight, we propose MolGroup, which separates the dataset affinity into task and structure affinity to predict the potential benefits of each auxiliary molecule dataset. MolGroup achieves this by utilizing a routing mechanism optimized through a bi-level optimization framework. Empowered by the meta gradient, the routing mechanism is optimized toward maximizing the target dataset's performance and quantifies the affinity as the gating score. As a result, MolGroup is capable of predicting the optimal combination of auxiliary datasets for each target dataset. Our extensive experiments demonstrate the efficiency and effectiveness of MolGroup, showing an average improvement of 4.41%/3.47% for GIN/Graphormer trained with the group of molecule datasets selected by MolGroup on 11 target molecule datasets.

Yue Huang, Lichao Sun, Haoran Wang et al.

Large language models (LLMs), exemplified by ChatGPT, have gained considerable attention for their excellent natural language processing capabilities. Nonetheless, these LLMs present many challenges, particularly in the realm of trustworthiness. Therefore, ensuring the trustworthiness of LLMs emerges as an important topic. This paper introduces TrustLLM, a comprehensive study of trustworthiness in LLMs, including principles for different dimensions of trustworthiness, established benchmark, evaluation, and analysis of trustworthiness for mainstream LLMs, and discussion of open challenges and future directions. Specifically, we first propose a set of principles for trustworthy LLMs that span eight different dimensions. Based on these principles, we further establish a benchmark across six dimensions including truthfulness, safety, fairness, robustness, privacy, and machine ethics. We then present a study evaluating 16 mainstream LLMs in TrustLLM, consisting of over 30 datasets. Our findings firstly show that in general trustworthiness and utility (i.e., functional effectiveness) are positively related. Secondly, our observations reveal that proprietary LLMs generally outperform most open-source counterparts in terms of trustworthiness, raising concerns about the potential risks of widely accessible open-source LLMs. However, a few open-source LLMs come very close to proprietary ones. Thirdly, it is important to note that some LLMs may be overly calibrated towards exhibiting trustworthiness, to the extent that they compromise their utility by mistakenly treating benign prompts as harmful and consequently not responding. Finally, we emphasize the importance of ensuring transparency not only in the models themselves but also in the technologies that underpin trustworthiness. Knowing the specific trustworthy technologies that have been employed is crucial for analyzing their effectiveness.

Songtao Liu, Rex Ying, Hanze Dong et al.

Graph Neural Networks (GNNs), which aggregate features from neighbors, are widely used for graph-structured data processing due to their powerful representation learning capabilities. It is generally believed that GNNs can implicitly remove the non-predictive noises. However, the analysis of implicit denoising effect in graph neural networks remains open. In this work, we conduct a comprehensive theoretical study and analyze when and why the implicit denoising happens in GNNs. Specifically, we study the convergence properties of noise matrix. Our theoretical analysis suggests that the implicit denoising largely depends on the connectivity, the graph size, and GNN architectures. Moreover, we formally define and propose the adversarial graph signal denoising (AGSD) problem by extending graph signal denoising problem. By solving such a problem, we derive a robust graph convolution, where the smoothness of the node representations and the implicit denoising effect can be enhanced. Extensive empirical evaluations verify our theoretical analyses and the effectiveness of our proposed model.

Menglin Yang, Harshit Verma, Delvin Ce Zhang et al.

Hyperbolic geometry have shown significant potential in modeling complex structured data, particularly those with underlying tree-like and hierarchical structures. Despite the impressive performance of various hyperbolic neural networks across numerous domains, research on adapting the Transformer to hyperbolic space remains limited. Previous attempts have mainly focused on modifying self-attention modules in the Transformer. However, these efforts have fallen short of developing a complete hyperbolic Transformer. This stems primarily from: (i) the absence of well-defined modules in hyperbolic space, including linear transformation layers, LayerNorm layers, activation functions, dropout operations, etc. (ii) the quadratic time complexity of the existing hyperbolic self-attention module w.r.t the number of input tokens, which hinders its scalability. To address these challenges, we propose, Hypformer, a novel hyperbolic Transformer based on the Lorentz model of hyperbolic geometry. In Hypformer, we introduce two foundational blocks that define the essential modules of the Transformer in hyperbolic space. Furthermore, we develop a linear self-attention mechanism in hyperbolic space, enabling hyperbolic Transformer to process billion-scale graph data and long-sequence inputs for the first time. Our experimental results confirm the effectiveness and efficiency of Hypformer across various datasets, demonstrating its potential as an effective and scalable solution for large-scale data representation and large models.

Jialin Chen, Rex Ying

Temporal graphs are widely used to model dynamic systems with time-varying interactions. In real-world scenarios, the underlying mechanisms of generating future interactions in dynamic systems are typically governed by a set of recurring substructures within the graph, known as temporal motifs. Despite the success and prevalence of current temporal graph neural networks (TGNN), it remains uncertain which temporal motifs are recognized as the significant indications that trigger a certain prediction from the model, which is a critical challenge for advancing the explainability and trustworthiness of current TGNNs. To address this challenge, we propose a novel approach, called Temporal Motifs Explainer (TempME), which uncovers the most pivotal temporal motifs guiding the prediction of TGNNs. Derived from the information bottleneck principle, TempME extracts the most interaction-related motifs while minimizing the amount of contained information to preserve the sparsity and succinctness of the explanation. Events in the explanations generated by TempME are verified to be more spatiotemporally correlated than those of existing approaches, providing more understandable insights. Extensive experiments validate the superiority of TempME, with up to 8.21% increase in terms of explanation accuracy across six real-world datasets and up to 22.96% increase in boosting the prediction Average Precision of current TGNNs.

Yifei Zhang, Hao Zhu, Menglin Yang et al.

Learning generalizable self-supervised graph representations for downstream tasks is challenging. To this end, Contrastive Learning (CL) has emerged as a leading approach. The embeddings of CL are arranged on a hypersphere where similarity is measured by the cosine distance. However, many real-world graphs, especially of hierarchical nature, cannot be embedded well in the Euclidean space. Although the hyperbolic embedding is suitable for hierarchical representation learning, naively applying CL to the hyperbolic space may result in the so-called dimension collapse, i.e., features will concentrate mostly within few density regions, leading to poor utilization of the whole feature space. Thus, we propose a novel contrastive learning framework to learn high-quality graph embeddings in hyperbolic space. Specifically, we design the alignment metric that effectively captures the hierarchical data-invariant information, as well as we propose a substitute of the uniformity metric to prevent the so-called dimensional collapse. We show that in the hyperbolic space one has to address the leaf- and height-level uniformity related to properties of trees. In the ambient space of the hyperbolic manifold these notions translate into imposing an isotropic ring density towards boundaries of Poincaré ball. Our experiments support the efficacy of our method.

Tianyu Liu, Yuge Wang, Rex Ying et al.

Discovering genes with similar functions across diverse biomedical contexts poses a significant challenge in gene representation learning due to data heterogeneity. In this study, we resolve this problem by introducing a novel model called Multimodal Similarity Learning Graph Neural Network, which combines Multimodal Machine Learning and Deep Graph Neural Networks to learn gene representations from single-cell sequencing and spatial transcriptomic data. Leveraging 82 training datasets from 10 tissues, three sequencing techniques, and three species, we create informative graph structures for model training and gene representations generation, while incorporating regularization with weighted similarity learning and contrastive learning to learn cross-data gene-gene relationships. This novel design ensures that we can offer gene representations containing functional similarity across different contexts in a joint space. Comprehensive benchmarking analysis shows our model's capacity to effectively capture gene function similarity across multiple modalities, outperforming state-of-the-art methods in gene representation learning by up to 97.5%. Moreover, we employ bioinformatics tools in conjunction with gene representations to uncover pathway enrichment, regulation causal networks, and functions of disease-associated or dosage-sensitive genes. Therefore, our model efficiently produces unified gene representations for the analysis of gene functions, tissue functions, diseases, and species evolution.

Jialin Chen, Aosong Feng, Harshit Verma et al.

Financial markets are characterized by extreme non-stationarity, low signal-to-noise ratios, and strong dependence on external information such as news, company fundamentals, and macroeconomic signals. Yet, existing approaches either abstract time-series into text or decouple forecasting from language-based reasoning, leading to a fundamental mismatch between qualitative reasoning and quantitative outcomes. To address this, we introduce StockR1, a time-series-enhanced LLM that unifies stock forecasting and financial reasoning through a verifiable forecast action. Based on a tool-call design, the model first emits a forecast action, which is a structured and interpretable representation of its qualitative market outlook. It then invokes a time-series decoder conditioned on this action to generate distributional future trajectories, leading to more informed question answering and financial reasoning. We optimize the full pipeline with reinforcement learning, where rewards jointly reflect answer validity, forecast accuracy, and consistency between generated actions and observed time-series dynamics. In addition, rewards are reweighted by a sample-level uncertainty scalar, encouraging the model to accommodate varying uncertainty in market dynamics. We evaluate StockR1 on financial question answering and stock forecasting over a large-scale 10-year benchmark. Our method consistently outperforms time-series baselines and general-purpose LLMs, improving reasoning accuracy by 17.7% (4B) and 25.9% (8B). These findings demonstrate that structuring the forecast actions establishes a powerful synergy between language reasoning and temporal prediction, enabling LLMs to reason through verifiable, interpretable, and numerically grounded decisions.

Jialin Chen, Shirley Wu, Abhijit Gupta et al.

The widespread deployment of Graph Neural Networks (GNNs) sparks significant interest in their explainability, which plays a vital role in model auditing and ensuring trustworthy graph learning. The objective of GNN explainability is to discern the underlying graph structures that have the most significant impact on model predictions. Ensuring that explanations generated are reliable necessitates consideration of the in-distribution property, particularly due to the vulnerability of GNNs to out-of-distribution data. Unfortunately, prevailing explainability methods tend to constrain the generated explanations to the structure of the original graph, thereby downplaying the significance of the in-distribution property and resulting in explanations that lack reliability. To address these challenges, we propose D4Explainer, a novel approach that provides in-distribution GNN explanations for both counterfactual and model-level explanation scenarios. The proposed D4Explainer incorporates generative graph distribution learning into the optimization objective, which accomplishes two goals: 1) generate a collection of diverse counterfactual graphs that conform to the in-distribution property for a given instance, and 2) identify the most discriminative graph patterns that contribute to a specific class prediction, thus serving as model-level explanations. It is worth mentioning that D4Explainer is the first unified framework that combines both counterfactual and model-level explanations. Empirical evaluations conducted on synthetic and real-world datasets provide compelling evidence of the state-of-the-art performance achieved by D4Explainer in terms of explanation accuracy, faithfulness, diversity, and robustness.

Charles Xu, Laney Goldman, Valentina Guo et al.

Graph neural networks (GNNs) have emerged as a powerful tool for tasks such as node classification and graph classification. However, much less work has been done on signal classification, where the data consists of many functions (referred to as signals) defined on the vertices of a single graph. These tasks require networks designed differently from those designed for traditional GNN tasks. Indeed, traditional GNNs rely on localized low-pass filters, and signals of interest may have intricate multi-frequency behavior and exhibit long range interactions. This motivates us to introduce the BLIS-Net (Bi-Lipschitz Scattering Net), a novel GNN that builds on the previously introduced geometric scattering transform. Our network is able to capture both local and global signal structure and is able to capture both low-frequency and high-frequency information. We make several crucial changes to the original geometric scattering architecture which we prove increase the ability of our network to capture information about the input signal and show that BLIS-Net achieves superior performance on both synthetic and real-world data sets based on traffic flow and fMRI data.

Leyao Wang, Yanan He, Peng Chen et al.

Deep research agents increasingly automate complex information-seeking tasks, producing evidence-grounded reports via multi-step reasoning, tool use, and synthesis. Their growing role demands scalable, reliable evaluation, positioning LLM-as-judge as a supervision paradigm for assessing factual accuracy, evidence use, and reasoning quality. Yet the reliability of these judges for deep research agents remains poorly understood, posing a critical meta-evaluation problem: before deploying LLM judges to supervise research agents, we must first evaluate the judges themselves. Existing meta-evaluations fall short in two ways: (1) reliance on coarse, subjective human-preference agreement; (2) focus on instruction-following or verifiable tasks, leaving open-ended agent executions unexplored. To address these gaps, we introduce REFLECT (REliable Fine-grained LLM judge Evaluation via Controlled inTervention), a meta-evaluation benchmark targeting fine-grained failure detection in agentic environments. REFLECT defines a detailed taxonomy of process- and outcome-level failure modes, instantiated by performing controlled and localized interventions on quality-screened agent execution traces. This yields verifiable, comprehensive, and fine-grained instances for validating the judge models. Our experiments show that current LLM judges remain unreliable: even the best-performing models achieve overall accuracies below 55% across reasoning, tool-use, and report-quality failures, with especially poor performance on evidence verification. Together, our taxonomy and findings expose systematic judge limitations, reveal tradeoffs in cost and reliability, and offer actionable guidance for building more reliable evaluation pipelines for deep research agents.

Jialin Chen, Kenza Amara, Junchi Yu et al.

Graph Neural Networks (GNNs) achieve state-of-the-art performance in various graph-related tasks. However, the black-box nature often limits their interpretability and trustworthiness. Numerous explainability methods have been proposed to uncover the decision-making logic of GNNs, by generating underlying explanatory substructures. In this paper, we conduct a comprehensive review of the existing explanation methods for GNNs from the perspective of graph generation. Specifically, we propose a unified optimization objective for generative explanation methods, comprising two sub-objectives: Attribution and Information constraints. We further demonstrate their specific manifestations in various generative model architectures and different explanation scenarios. With the unified objective of the explanation problem, we reveal the shared characteristics and distinctions among current methods, laying the foundation for future methodological advancements. Empirical results demonstrate the advantages and limitations of different explainability approaches in terms of explanation performance, efficiency, and generalizability.

Jindong Li, Yali Fu, Li Fan et al.

Large Language Models (LLMs) have demonstrated strong generalization across a wide range of tasks. Reasoning with LLMs is central to solving multi-step problems and complex decision-making. To support efficient reasoning, recent studies have shifted attention from explicit chain-of-thought prompting toward implicit reasoning, where reasoning occurs silently via latent structures without emitting intermediate textual steps. Implicit reasoning brings advantages such as lower generation cost, faster inference, and better alignment with internal computation. Although prior surveys have discussed latent representations in the context of reasoning, a dedicated and mechanism-level examination of how reasoning unfolds internally within LLMs remains absent. This survey fills that gap by introducing a taxonomy centered on execution paradigms, shifting the focus from representational forms to computational strategies. We organize existing methods into three execution paradigms based on \textbf{\textit{how and where internal computation unfolds}}: latent optimization, signal-guided control, and layer-recurrent execution. We also review structural, behavioral and representation-based evidence that supports the presence of implicit reasoning in LLMs. We further provide a structured overview of the evaluation metrics and benchmarks used in existing works to assess the effectiveness and reliability of implicit reasoning. We maintain a continuously updated project at: https://github.com/digailab/awesome-llm-implicit-reasoning.

Neil He, Menglin Yang, Rex Ying

Hyperbolic neural networks have emerged as a powerful tool for modeling hierarchical data across diverse modalities. Recent studies show that token distributions in foundation models exhibit scale-free properties, suggesting that hyperbolic space is a more suitable ambient space than Euclidean space for many pre-training and downstream tasks. However, existing tools lack essential components for building hyperbolic foundation models, making it difficult to leverage recent advancements. We introduce HyperCore, a comprehensive open-source framework that provides core modules for constructing hyperbolic foundation models across multiple modalities. HyperCore's modules can be effortlessly combined to develop novel hyperbolic foundation models, eliminating the need to extensively modify Euclidean modules from scratch and possible redundant research efforts. To demonstrate its versatility, we build and test the first fully hyperbolic vision transformers (LViT) with a fine-tuning pipeline, the first fully hyperbolic multimodal CLIP model (L-CLIP), and a hybrid Graph RAG with a hyperbolic graph encoder. Our experiments demonstrate that LViT outperforms its Euclidean counterpart. Additionally, we benchmark and reproduce experiments across hyperbolic GNNs, CNNs, Transformers, and vision Transformers to highlight HyperCore's advantages.

Chenqing Hua, Jiarui Lu, Yong Liu et al.

The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interaction prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \textsc{GENzyme}, a \textit{de novo} enzyme design model that takes a catalytic reaction as input and generates the catalytic pocket, full enzyme structure, and enzyme-substrate binding complex. \textsc{GENzyme} is an end-to-end, three-staged model that integrates (1) a catalytic pocket generation and sequence co-design module, (2) a pocket inpainting and enzyme inverse folding module, and (3) a binding and screening module to optimize and predict enzyme-substrate complexes. The entire design process is driven by the catalytic reaction being targeted. This reaction-first approach allows for more accurate and biologically relevant enzyme design, potentially surpassing structure-based and binding-focused models in creating enzymes capable of catalyzing specific reactions. We provide \textsc{GENzyme} code at https://github.com/WillHua127/GENzyme.

Buze Zhang, Jinkai Tao, Zilang Zeng et al.

Large Language Models (LLMs) have achieved remarkable progress, with Parameter-Efficient Fine-Tuning (PEFT) emerging as a key technique for downstream task adaptation. However, existing PEFT methods mainly operate in Euclidean space, fundamentally limiting their capacity to capture complex geometric structures inherent in language data. While alternative geometric spaces, like hyperbolic geometries for hierarchical data and spherical manifolds for circular patterns, offer theoretical advantages, forcing representations into a single manifold type ultimately limits expressiveness, even when curvature parameters are learnable. To address this, we propose Mixture of Space (MoS), a unified framework that leverages multiple geometric spaces simultaneously to learn richer, curvature-aware representations. Building on this scheme, we develop MoSLoRA, which extends Low-Rank Adaptation (LoRA) with heterogeneous geometric experts, enabling models to dynamically select or combine appropriate geometric spaces based on input context. Furthermore, to address the computational overhead of frequent manifold switching, we develop a lightweight routing mechanism. Moreover, we provide empirical insights into how curvature optimization impacts training stability and model performance. Our experiments across diverse benchmarks demonstrate that MoSLoRA consistently outperforms strong baselines, achieving up to 5.6% improvement on MATH500 and 15.9% on MAWPS.

Qiyao Ma, Menglin Yang, Mingxuan Ju et al.

Modern recommender systems often create information cocoons, restricting users' exposure to diverse content. A key challenge lies in balancing content exploration and exploitation while allowing users to adjust their recommendation preferences. Intuitively, this balance can be modeled as a tree-structured representation, where depth search facilitates exploitation and breadth search enables exploration. However, existing approaches face two fundamental limitations: Euclidean methods struggle to capture hierarchical structures, while hyperbolic methods, despite their superior hierarchical modeling, lack semantic understanding of user and item profiles and fail to provide a principled mechanism for balancing exploration and exploitation. To address these challenges, we propose HERec, a hyperbolic graph-LLM framework that effectively balances exploration and exploitation in recommender systems. Our framework introduces two key innovations: (1) a semantic-enhanced hierarchical mechanism that aligns rich textual descriptions processed by large language models (LLMs) with collaborative information directly in hyperbolic space, allowing for more nuanced updates that respect the underlying hierarchical structure in user-item profiles; (2) an automatic hierarchical representation by optimizing Dasgupta's cost, which discovers hierarchical structures without requiring predefined hyperparameters, enabling user-adjustable exploration-exploitation trade-offs. Extensive experiments demonstrate that HERec consistently outperforms both Euclidean and hyperbolic baselines, achieving up to 5.49% improvement in utility metrics and 11.39% increase in diversity metrics, effectively mitigating information cocoons. We open-source our model implementation at https://github.com/Martin-qyma/HERec.

Tinglin Huang, Bo Chen, Xiao Zhang et al.

Interpreting and following human instructions is a critical capability of large language models (LLMs) in automatic programming. However, synthesizing large-scale instruction-paired coding data remains largely unexplored and is particularly challenging when ensuring logical compatibility among multiple constraints. In this study, we propose IFCodeEvolve, an actor-schema co-evolution framework for instruction following coding data generation. By representing instructions as parametric function schema, we construct a library that covers the vast instruction space via dynamic constraint instantiation. Building upon this, Monte Carlo Tree Search (MCTS) sampler is applied to efficiently navigate this space, utilizing actor model feedback as a dynamic termination signal. Furthermore, to progressively explore challenging problems, we introduce a co-evolving paradigm that iteratively advances both the actor model and the schema library, via schema composition and mutation, based on sampler statistics. Empirical results demonstrate that IFCodeEvolve significantly boosts base model performance, with our 32B model achieving parity with proprietary SOTA models. Additionally, we contribute IFCodeBench, a comprehensive human-verified benchmark equipped with solutions and robust AST-based verification.

Ngoc Bui, Hieu Trung Nguyen, Arman Cohan et al.

The key-value (KV) cache is a major bottleneck in long-context inference, where memory and computation grow with sequence length. Existing KV eviction methods reduce this cost but typically degrade performance relative to full-cache inference. Our key insight is that full-cache attention is not always optimal: in long contexts, irrelevant tokens can dilute attention away from useful evidence, so selective, learnable eviction can improve generation rather than merely approximate the full cache. We introduce a global retention-based KV eviction method that learns each token's future utility under a unified memory budget. Lightweight retention gates assign utility scores to cached KV entries, and a shared final scoring projection calibrates these scores across all layers and heads. This enables a single global eviction policy in which tokens from different layers, heads, and modalities compete directly for cache capacity. We further provide theoretical analysis showing that preferentially retaining useful tokens reduces attention dilution, and we justify geometric retention as a query-agnostic proxy for future utility. Across diverse long-context language and vision-language reasoning, and multi-turn dialogue benchmarks, our method substantially reduces KV memory while matching or surpassing full-cache inference. These results suggest that learned, globally calibrated KV eviction is not only a compression technique, but also a mechanism for improving long-context reasoning.

Yijun Pan, Weikang Qiu, Qiyao Ma et al.

Modern recommender systems must adapt to dynamic, need-specific objectives for diverse recommendation scenarios, yet most traditional recommenders are optimized for a single static target and struggle to reconfigure behavior on demand. Recent advances in reinforcement-learning-based post-training have unlocked strong instruction-following and reasoning capabilities in LLMs, suggesting a principled route for aligning them to complex recommendation goals. Motivated by this, we study closed-set autoregressive ranking, where an LLM generates a permutation over a fixed candidate set conditioned on user context and an explicit need instruction. However, applying RL to this setting faces two key obstacles: (i) sequence-level rewards yield coarse credit assignment that fails to provide fine-grained training signals, and (ii) interaction feedback is sparse and noisy, which together lead to inefficient and unstable updates. We propose FlexRec, a post-training RL framework that addresses both issues with (1) a causally grounded item-level reward based on counterfactual swaps within the remaining candidate pool, and (2) critic-guided, uncertainty-aware scaling that explicitly models reward uncertainty and down-weights low-confidence rewards to stabilize learning under sparse supervision. Across diverse recommendation scenarios and objectives, FlexRec achieves substantial gains: it improves NDCG@5 by up to \textbf{59\%} and Recall@5 by up to \textbf{109.4\%} in need-specific ranking, and further achieves up to \textbf{24.1\%} Recall@5 improvement under generalization settings, outperforming strong traditional recommenders and LLM-based baselines.

Rishabh Anand, Chaitanya K. Joshi, Alex Morehead et al.

We introduce RNA-FrameFlow, the first generative model for 3D RNA backbone design. We build upon SE(3) flow matching for protein backbone generation and establish protocols for data preparation and evaluation to address unique challenges posed by RNA modeling. We formulate RNA structures as a set of rigid-body frames and associated loss functions which account for larger, more conformationally flexible RNA backbones (13 atoms per nucleotide) vs. proteins (4 atoms per residue). Toward tackling the lack of diversity in 3D RNA datasets, we explore training with structural clustering and cropping augmentations. Additionally, we define a suite of evaluation metrics to measure whether the generated RNA structures are globally self-consistent (via inverse folding followed by forward folding) and locally recover RNA-specific structural descriptors. The most performant version of RNA-FrameFlow generates locally realistic RNA backbones of 40-150 nucleotides, over 40% of which pass our validity criteria as measured by a self-consistency TM-score >= 0.45, at which two RNAs have the same global fold. Open-source code: https://github.com/rish-16/rna-backbone-design

Jiasheng Zhang, Jialin Chen, Menglin Yang et al.

Dynamic text-attributed graphs (DyTAGs) are prevalent in various real-world scenarios, where each node and edge are associated with text descriptions, and both the graph structure and text descriptions evolve over time. Despite their broad applicability, there is a notable scarcity of benchmark datasets tailored to DyTAGs, which hinders the potential advancement in many research fields. To address this gap, we introduce Dynamic Text-attributed Graph Benchmark (DTGB), a collection of large-scale, time-evolving graphs from diverse domains, with nodes and edges enriched by dynamically changing text attributes and categories. To facilitate the use of DTGB, we design standardized evaluation procedures based on four real-world use cases: future link prediction, destination node retrieval, edge classification, and textual relation generation. These tasks require models to understand both dynamic graph structures and natural language, highlighting the unique challenges posed by DyTAGs. Moreover, we conduct extensive benchmark experiments on DTGB, evaluating 7 popular dynamic graph learning algorithms and their variants of adapting to text attributes with LLM embeddings, along with 6 powerful large language models (LLMs). Our results show the limitations of existing models in handling DyTAGs. Our analysis also demonstrates the utility of DTGB in investigating the incorporation of structural and textual dynamics. The proposed DTGB fosters research on DyTAGs and their broad applications. It offers a comprehensive benchmark for evaluating and advancing models to handle the interplay between dynamic graph structures and natural language. The dataset and source code are available at https://github.com/zjs123/DTGB.

Songtao Liu, Rex Ying, Hanze Dong et al.

Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggregated for learning representations of nodes with few neighbors. To address this, we propose a simple and efficient data augmentation strategy, local augmentation, to learn the distribution of the node features of the neighbors conditioned on the central node's feature and enhance GNN's expressive power with generated features. Local augmentation is a general framework that can be applied to any GNN model in a plug-and-play manner. It samples feature vectors associated with each node from the learned conditional distribution as additional input for the backbone model at each training iteration. Extensive experiments and analyses show that local augmentation consistently yields performance improvement when applied to various GNN architectures across a diverse set of benchmarks. For example, experiments show that plugging in local augmentation to GCN and GAT improves by an average of 3.4\% and 1.6\% in terms of test accuracy on Cora, Citeseer, and Pubmed. Besides, our experimental results on large graphs (OGB) show that our model consistently improves performance over backbones. Code is available at https://github.com/SongtaoLiu0823/LAGNN.

Ngoc Bui, Shubham Sharma, Simran Lamba et al.

Memory and computation remain core bottlenecks in long-horizon LLM inference due to the quadratic cost of self-attention and the ever-growing key-value (KV) cache. Existing strategies for memory-bounded inference, such as quantization, offloading, or heuristic KV eviction, either incur high orchestration costs or rely on unreliable attention-based proxies of importance. We propose TRIM-KV, a novel approach that learns each token's intrinsic importance at creation time via a lightweight retention gate. Each gate predicts a scalar retention score that decays over time, reflecting the long-term utility of the token for a specific layer and head. Tokens with low scores are evicted when the memory budget is exceeded, ensuring that the cache always contains the most critical tokens. TRIM-KV is trained efficiently through distillation from a frozen LLM combined with a capacity loss, requiring only gate fine-tuning and adding negligible inference overhead. Across mathematical reasoning (GSM8K, MATH-500, AIME24), procedural generation (LongProc), conversational long-memory benchmarks (LongMemEval), and long-context understanding (LongBench and SCBench), TRIM-KV consistently outperforms strong eviction and learnable retrieval baselines, especially in low-memory regimes. Remarkably, it even surpasses full-cache models in some settings, showing that selective retention can serve as a form of regularization, suppressing noise from uninformative tokens. Qualitative analyses further reveal that learned retention scores align with human intuition, naturally recovering heuristics such as sink tokens, sliding windows, and gist compression without explicit design. Beyond efficiency, retention scores provide insights into layer- and head-specific roles, suggesting a new path toward LLM interpretability.

Matthias Fey, Weihua Hu, Kexin Huang et al.

Much of the world's most valued data is stored in relational databases and data warehouses, where the data is organized into many tables connected by primary-foreign key relations. However, building machine learning models using this data is both challenging and time consuming. The core problem is that no machine learning method is capable of learning on multiple tables interconnected by primary-foreign key relations. Current methods can only learn from a single table, so the data must first be manually joined and aggregated into a single training table, the process known as feature engineering. Feature engineering is slow, error prone and leads to suboptimal models. Here we introduce an end-to-end deep representation learning approach to directly learn on data laid out across multiple tables. We name our approach Relational Deep Learning (RDL). The core idea is to view relational databases as a temporal, heterogeneous graph, with a node for each row in each table, and edges specified by primary-foreign key links. Message Passing Graph Neural Networks can then automatically learn across the graph to extract representations that leverage all input data, without any manual feature engineering. Relational Deep Learning leads to more accurate models that can be built much faster. To facilitate research in this area, we develop RelBench, a set of benchmark datasets and an implementation of Relational Deep Learning. The data covers a wide spectrum, from discussions on Stack Exchange to book reviews on the Amazon Product Catalog. Overall, we define a new research area that generalizes graph machine learning and broadens its applicability to a wide set of AI use cases.