Justice Ou, Tinglin Huang, Yilun Zhao, Ziyang Yu, Peiqing Lu, Yifei Shen, Rex Ying. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

While large language models (LLMs) have become the de facto framework for literature-related tasks, they still struggle to function as domain-specific literature agents due to their inability to connect pieces of knowledge and reason across domain-specific contexts, terminologies, and nomenclatures. This challenge underscores the need for a tool that facilitates such domain-specific adaptation and enables rigorous benchmarking across literature tasks. To that end, we introduce LitBench, a benchmarking tool designed to enable the development and evaluation of domain-specific LLMs tailored to literature-related tasks. At its core, LitBench uses a data curation process that generates domain-specific literature sub-graphs and constructs training and evaluation datasets based on the textual attributes of the resulting nodes and edges. The tool is designed for flexibility, supporting the curation of literature graphs across any domain chosen by the user, whether high-level fields or specialized interdisciplinary areas. In addition to dataset curation, LitBench defines a comprehensive suite of literature tasks, ranging from node and edge level analyses to advanced applications such as related work generation. These tasks enable LLMs to internalize domain-specific knowledge and relationships embedded in the curated graph during training, while also supporting rigorous evaluation of model performance. Our results show that small domain-specific LLMs trained and evaluated on LitBench datasets achieve competitive performance compared to state-of-the-art models like GPT-4o and DeepSeek-R1. To enhance accessibility and ease of use, we open-source the tool along with an AI agent tool that streamlines data curation, model training, and evaluation.

Building on the success of text-to-image diffusion models (DPMs), image editing is an important application to enable human interaction with AI-generated content. Among various editing methods, editing within the prompt space gains more attention due to its capacity and simplicity of controlling semantics. However, since diffusion models are commonly pretrained on descriptive text captions, direct editing of words in text prompts usually leads to completely different generated images, violating the requirements for image editing. On the other hand, existing editing methods usually consider introducing spatial masks to preserve the identity of unedited regions, which are usually ignored by DPMs and therefore lead to inharmonic editing results. Targeting these two challenges, in this work, we propose to disentangle the comprehensive image-prompt interaction into several item-prompt interactions, with each item linked to a special learned prompt. The resulting framework, named D-Edit, is based on pretrained diffusion models with cross-attention layers disentangled and adopts a two-step optimization to build item-prompt associations. Versatile image editing can then be applied to specific items by manipulating the corresponding prompts. We demonstrate state-of-the-art results in four types of editing operations including image-based, text-based, mask-based editing, and item removal, covering most types of editing applications, all within a single unified framework. Notably, D-Edit is the first framework that can (1) achieve item editing through mask editing and (2) combine image and text-based editing. We demonstrate the quality and versatility of the editing results for a diverse collection of images through both qualitative and quantitative evaluations.

Recent advances in spatial transcriptomics (ST) and cost reductions have enabled large-scale multi-slice ST data generation, enhancing the statistical power to detect subtle biological signals. However, cross-slice inconsistencies and data quality variability present significant analytical challenges. To overcome these limitations, we developed MUSE, a computational framework designed for multislice joint embedding, spatial domain identification, and gene expression imputation. Specifically, MUSE integrates a two-module architecture to ensure robust cross-slice alignment and data harmonization. The alignment module models each slice as a graph and employs optimal transport to align cells across slices while preserving spatial continuity. The optimization module further refines integration by incorporating an alignment loss, allowing lower-quality data to leverage structural information from higher-quality slices. Additionally, MUSE generates virtual neighbors from aligned cells, enriching contextual information and mitigating data sparsity. These design principles enable seamless integration with existing single-slice methods, extending their applicability to multi-slice ST analysis. To comprehensively evaluate its performance, we applied MUSE to 12 real and 48 simulated datasets spanning a range of data qualities. Across all metrics, MUSE consistently outperformed existing methods in cross-slice consistency, spatial domain identification, and gene expression imputation. To promote accessibility and adoption, we provide MUSE as an open-source software package. As multi-slice ST datasets become increasingly prevalent, MUSE provides a robust and extensible framework designed to effectively integrate growing numbers of slices, thereby advancing the analysis of tissue architectures and spatial gene expression in complex biological systems.

Spatial transcriptomics (ST) has emerged as a powerful technology for bridging histology imaging with gene expression profiling. However, its application has been limited by low throughput and the need for specialized experimental facilities. Prior works sought to predict ST from whole-slide histology images to accelerate this process, but they suffer from two major limitations. First, they do not explicitly model cell-cell interaction as they factorize the joint distribution of whole-slide ST data and predict the gene expression of each spot independently. Second, their encoders struggle with memory constraints due to the large number of spots (often exceeding 10,000) in typical ST datasets. Herein, we propose STFlow, a flow matching generative model that considers cell-cell interaction by modeling the joint distribution of gene expression of an entire slide. It also employs an efficient slide-level encoder with local spatial attention, enabling whole-slide processing without excessive memory overhead. On the recently curated HEST-1k and STImage-1K4M benchmarks, STFlow substantially outperforms state-of-the-art baselines and achieves over 18% relative improvements over the pathology foundation models.

Backward compatible representation learning enables updated models to integrate seamlessly with existing ones, avoiding to reprocess stored data. Despite recent advances, existing compatibility approaches in Euclidean space neglect the uncertainty in the old embedding models and force the new model to replicate outdated representations regardless of their quality, and thereby hindering the learning process. In this paper, we switch perspectives to hyperbolic geometry, where we treat time as a natural axis for capturing a model’s confidence and evolution. By lifting embeddings into hyperbolic space and constraining updated embeddings to lie within the entailment cone of the old ones, we maintain generational consistency across models while accounting for uncertainties in the representations. To further enhance compatibility, we introduce a robust contrastive alignment loss that dynamically adjusts alignment weights based on the uncertainty of the old embeddings. Experiments validate the superiority of the proposed method in achieving compatibility, paving the way for more resilient and adaptable machine learning systems.

Decoding functional magnetic resonance imaging (fMRI) signals into text has been a key challenge in the neuroscience community, with the potential to advance brain-computer interfaces and uncover deeper insights into brain mechanisms. However, existing approaches often struggle with suboptimal predictive performance, limited task variety, and poor generalization across subjects. In response to this, we propose MindLLM, a model designed for subject-agnostic and versatile fMRI-to-text decoding. MindLLM consists of an fMRI encoder and an off-the-shelf LLM. The fMRI encoder employs a neuroscience-informed attention mechanism, which is capable of accommodating subjects with varying input shapes and thus achieves high-performance subject-agnostic decoding. Moreover, we introduce Brain Instruction Tuning (BIT), a novel approach that enhances the model’s ability to capture diverse semantic representations from fMRI signals, facilitating more versatile decoding. We evaluate MindLLM on comprehensive fMRI-to-text benchmarks. Results demonstrate that our model outperforms the baselines, improving downstream tasks by $12.0%$, unseen subject generalization by $24.5%$, and novel task adaptation by $25.0%$. Furthermore, the attention patterns in MindLLM provide interpretable insights into its decision-making process.

Protein language models often struggle to capture biological functions due to their lack of factual knowledge (e.g., gene descriptions). Existing solutions leverage protein knowledge graphs (PKGs) as auxiliary pre-training objectives, but lack explicit integration of task-oriented knowledge, making them suffer from limited knowledge exploitation and catastrophic forgetting. The root cause is that they fail to align PKGs with task-specific data, forcing their knowledge modeling to adapt to the knowledge-isolated nature of downstream tasks. In this paper, we propose Knowledge-aware retrieval augmented protein language model (Kara), achieving the first task-oriented and explicit integration of PKGs and protein language models. With a knowledge retriever learning to predict linkages between PKG and task proteins, Kara unifies the knowledge integration of the pre-training and fine-tuning stages with a structure-based regularization, mitigating catastrophic forgetting. To ensure task-oriented integration, Kara uses contextualized virtual tokens to extract graph context as task-specific knowledge for new proteins. Experiments show that Kara outperforms existing knowledge-enhanced models in 6 representative tasks, achieving on average 5.1% improvements.

Hyperbolic neural networks have emerged as a powerful tool for modeling hierarchical data structures prevalent in real-world datasets. Notably, residual connections, which facilitate the direct flow of information across layers, have been instrumental in the success of deep neural networks. However, current methods for constructing hyperbolic residual networks suffer from limitations such as increased model complexity, numerical instability, and errors due to multiple mappings to and from the tangent space. To address these limitations, we introduce LResNet, a novel Lorentzian residual neural network based on the weighted Lorentzian centroid in the Lorentz model of hyperbolic geometry. Our method enables the efficient integration of residual connections in Lorentz hyperbolic neural networks while preserving their hierarchical representation capabilities. We demonstrate that our method can theoretically derive previous methods while offering improved stability, efficiency, and effectiveness. Extensive experiments on both graph and vision tasks showcase the superior performance and robustness of our method compared to state-of-the-art Euclidean and hyperbolic alternatives. Our findings highlight the potential of LResNet for building more expressive neural networks in hyperbolic embedding space as a generally applicable method to multiple architectures, including CNNs, GNNs, and graph Transformers.

Foundation models pre-trained on massive datasets, including large language models (LLMs), vision-language models (VLMs), and large multimodal models, have demonstrated remarkable success in diverse downstream tasks. However, recent studies have shown fundamental limitations of these models: (1) limited representational capacity(2) lower adaptability, and (3) diminishing scalability. These shortcomings raise a critical question: is Euclidean geometry truly the optimal inductive bias for all foundation models, or could incorporating alternative geometric spaces enable models to better align with the intrinsic structure of real-world data and improve reasoning processes? Hyperbolic spaces, a class of non-Euclidean manifolds characterized by exponential volume growth with respect to distance, offer a mathematically grounded solution. These spaces enable low-distortion embeddings of hierarchical structures (e.g., trees, taxonomies) and power-law distributions with substantially fewer dimensions compared to Euclidean counterparts. Recent advances have leveraged these properties to enhance foundation models, including improving LLMs' complex reasoning ability, VLMs' zero-shot generalization, and cross-modal semantic alignment, while maintaining parameter efficiency. This paper provides a comprehensive review of hyperbolic neural networks and their recent development for foundation models. We further outline key challenges and research directions to advance the field.

Generative models have shown great promise in collaborative filtering by capturing the underlying distribution of user interests and preferences. However, existing approaches struggle with inaccurate posterior approximations and misalignment with the discrete nature of recommendation data, limiting their expressiveness and real-world performance. To address these limitations, we propose FlowCF, a novel flow-based recommendation system leveraging flow matching for collaborative filtering. We tailor flow matching to the unique challenges in recommendation through two key innovations: (1) a behavior-guided prior that aligns with user behavior patterns to handle the sparse and heterogeneous user-item interactions, and (2) a discrete flow framework to preserve the binary nature of implicit feedback while maintaining the benefits of flow matching, such as stable training and efficient inference. Extensive experiments demonstrate that FlowCF achieves state-of-the-art recommendation accuracy across various datasets with the fastest inference speed, making it a compelling approach for real-world recommender systems. The code is available at https://github.com/chengkai-liu/FlowCF.

With the advent of large language models (LLMs), managing scientific literature via LLMs has become a promising direction of research. However, existing approaches often overlook the rich structural and semantic relevance among scientific literature, limiting their ability to discern the relationships between pieces of scientific knowledge, and suffer from various types of hallucinations. These methods also focus narrowly on individual downstream tasks, limiting their applicability across use cases. We propose LitFM, the first literature foundation model designed for a wide variety of practical downstream tasks on domain-specific literature, with a focus on citation information. At its core, LitFM contains a novel graph retriever that can provide accurate and diverse recommendations for LLM to integrate graph structure information and relevant literature. LitFM also leverages a knowledge-infused LLM, fine-tuned through a well-developed instruction paradigm. It enables LitFM to extract domain-specific knowledge from literature and reason relationships among them. By integrating citation graphs during both training and inference, LitFM can generalize to unseen papers and accurately assess their relevance within existing literature. Additionally, we introduce new large-scale literature citation benchmark datasets on three academic fields, featuring sentence-level citation information and local context. Extensive experiments validate the superiority of LitFM, achieving 28.1% improvement on retrieval task in precision, and an average improvement of 7.52% over state-of-the-art across six downstream literature-related tasks.

The ubiquity of dynamic data in domains such as weather, healthcare, and energy underscores a growing need for effective interpretation and retrieval of time-series data. These data are inherently tied to domain-specific contexts, such as clinical notes or weather narratives, making cross-modal retrieval essential not only for downstream tasks but also for developing robust time-series foundation models by retrieval-augmented generation (RAG). Despite the increasing demand, time-series retrieval remains largely underexplored. Existing methods often lack semantic grounding, struggle to align heterogeneous modalities, and have limited capacity for handling multi-channel signals. To address this gap, we propose TRACE, a generic multimodal retriever that grounds time-series embeddings in aligned textual context. TRACE enables fine-grained channel-level alignment and employs hard negative mining to facilitate semantically meaningful retrieval. It supports flexible cross-modal retrieval modes, including Text-to-Timeseries and Timeseries-to-Text, effectively linking linguistic descriptions with complex temporal patterns. By retrieving semantically relevant pairs, TRACE enriches downstream models with informative context, leading to improved predictive accuracy and interpretability. Beyond a static retrieval engine, TRACE also serves as a powerful standalone encoder, with lightweight task-specific tuning that refines context-aware representations while maintaining strong cross-modal alignment. These representations achieve state-of-the-art performance on downstream forecasting and classification tasks. Extensive experiments across multiple domains highlight its dual utility, as both an effective encoder for downstream applications and a general-purpose retriever to enhance time-series models.

Frontier large language models (LLMs) have shown great success in text modeling and generation tasks across domains. However, natural language exhibits inherent semantic hierarchies and nuanced geometric structure, which current LLMs do not capture completely owing to their reliance on Euclidean operations such as dot-products and norms. Furthermore, recent studies have shown that not respecting the underlying geometry of token embeddings leads to training instabilities and degradation of generative capabilities. These findings suggest that shifting to non-Euclidean geometries can better align language models with the underlying geometry of text. We thus propose to operate fully in $\textit{Hyperbolic space}$, known for its expansive, scale-free, and low-distortion properties. To this end, we introduce $\textbf{HELM}$, a family of $\textbf{H}$yp$\textbf{E}$rbolic Large $\textbf{L}$anguage $\textbf{M}$odels, offering a geometric rethinking of the Transformer-based LLM that addresses the representational inflexibility, missing set of necessary operations, and poor scalability of existing hyperbolic LMs. We additionally introduce a $\textbf{Mi}$xture-of-$\textbf{C}$urvature $\textbf{E}$xperts model, $\textbf{HELM-MiCE}$, where each expert operates in a distinct curvature space to encode more fine-grained geometric structure from text, as well as a dense model, $\textbf{HELM-D}$. For $\textbf{HELM-MiCE}$, we further develop hyperbolic Multi-Head Latent Attention ($\textbf{HMLA}$) for efficient, reduced-KV-cache training and inference. For both models, we further develop essential hyperbolic equivalents of rotary positional encodings and root mean square normalization. We are the first to train fully hyperbolic LLMs at billion-parameter scale, and evaluate them on well-known benchmarks such as MMLU and ARC, spanning STEM problem-solving, general knowledge, and commonsense reasoning. Our results show consistent gains from our $\textbf{HELM}$ architectures – up to 4\% – over popular Euclidean architectures used in LLaMA and DeepSeek with superior semantic hierarchy modeling capabilities, highlighting the efficacy and enhanced reasoning afforded by hyperbolic geometry in large-scale language model pretraining.

In this paper, we propose HiPoNet, an end-to-end differentiable neural network for regression, classification, and representation learning on high-dimensional point clouds. Our work is motivated by single-cell data which can have very high-dimensionality --exceeding the capabilities of existing methods for point clouds which are mostly tailored for 3D data. Moreover, modern single-cell and spatial experiments now yield entire cohorts of datasets (i.e., one data set for every patient), necessitating models that can process large, high-dimensional point-clouds at scale. Most current approaches build a single nearest-neighbor graph, discarding important geometric and topological information. In contrast, HiPoNet models the point-cloud as a set of higher-order simplicial complexes, with each particular complex being created using a reweighting of features. This method thus generates multiple constructs corresponding to different views of high-dimensional data, which in biology offers the possibility of disentangling distinct cellular processes. It then employs simplicial wavelet transforms to extract multiscale features, capturing both local and global topology from each view. We show that geometric and topological information is preserved in this framework both theoretically and empirically. We showcase the utility of HiPoNet on point-cloud level tasks, involving classification and regression of entire point-clouds in data cohorts. Experimentally, we find that HiPoNet outperforms other point-cloud and graph-based models on single-cell data. We also apply HiPoNet to spatial transcriptomics datasets using spatial coordinates as one of the views. Overall, HiPoNet offers a robust and scalable solution for high-dimensional data analysis.

Large language models (LLMs) have demonstrated remarkable performance across various tasks. However, it remains an open question whether the default Euclidean space is the most suitable choice for LLMs. In this study, we investigate the geometric characteristics of LLMs, focusing specifically on tokens and their embeddings. Our findings reveal that token frequency follows a power-law distribution, where high-frequency tokens (e.g., the, that ) constitute the minority, while low-frequency tokens (e.g., apple, dog) constitute the majority. Furthermore, high-frequency tokens cluster near the origin, whereas low-frequency tokens are positioned farther away in the embedding space. Additionally, token embeddings exhibit hyperbolic characteristics, indicating a latent tree-like structure within the embedding space. Motivated by these observations, we propose **HypLoRA**, an efficient fine-tuning approach that operates in hyperbolic space to exploit these underlying hierarchical structures better. HypLoRA performs low-rank adaptation directly in hyperbolic space, thereby preserving hyperbolic modeling capabilities throughout the fine-tuning process. Extensive experiments across various base models and reasoning benchmarks, specifically arithmetic and commonsense reasoning tasks, demonstrate that HypLoRA substantially improves LLM performance.

Discrete diffusion models offer a flexible, controllable approach to structured sequence generation, yet they still lag behind causal language models in expressive power. A key limitation lies in their reliance on the Markovian assumption, which restricts each step to condition only on the current state, leading to potential uncorrectable error accumulation. In this paper, We introduce CaDDi, a discrete diffusion model that conditions on the entire generative trajectory, thereby lifting the Markov constraint and allowing the model to revisit and improve past states. By unifying sequential (causal) and temporal (diffusion) reasoning in a single non‑Markovian transformer, CaDDi also treats standard causal language models as a special case and permits the direct reuse of pretrained LLM weights with no architectural changes. Empirically, CaDDi outperforms state‑of‑the‑art discrete diffusion baselines on natural‑language benchmarks, substantially narrowing the remaining gap to large autoregressive transformers.

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.

Simeng Han, Hailey Schoelkopf, Yilun Zhao, Zhenting Qi, Martin Riddell, Wenfei Zhou, James Coady, David Peng, Yujie Qiao, Luke Benson, Lucy Sun, Alexander Wardle-Solano, Hannah Szabó, Ekaterina Zubova, Matthew Burtell, Jonathan Fan, Yixin Liu, Brian Wong, Malcolm Sailor, Ansong Ni, Linyong Nan, Jungo Kasai, Tao Yu, Rui Zhang, Alexander Fabbri, Wojciech Maciej Kryscinski, Semih Yavuz, Ye Liu, Xi Victoria Lin, Shafiq Joty, Yingbo Zhou, Caiming Xiong, Rex Ying, Arman Cohan, Dragomir Radev. Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing. 2024.

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.

The Shapley value is a prominent tool for interpreting black-box machine learning models thanks to its strong theoretical foundation. However, for models with structured inputs, such as graph neural networks, existing Shapley-based explainability approaches either focus solely on node-wise importance or neglect the graph structure when perturbing the input instance. This paper introduces the Myerson-Taylor interaction index that internalizes the graph structure into attributing the node values and the interaction values among nodes. Unlike the Shapley-based methods, the Myerson-Taylor index decomposes coalitions into components satisfying a pre-chosen connectivity criterion. We prove that the Myerson-Taylor index is the unique one that satisfies a system of five natural axioms accounting for graph structure and high-order interaction among nodes. Leveraging these properties, we propose Myerson-Taylor Structure-Aware Graph Explainer (MAGE), a novel explainer that uses the second-order Myerson-Taylor index to identify the most important motifs influencing the model prediction, both positively and negatively. Extensive experiments on various graph datasets and models demonstrate that our method consistently provides superior subgraph explanations compared to state-of-the-art methods.

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.

Large language models (LLMs) have gained considerable attention for their excellent natural language processing capabilities. Nonetheless, these LLMs present many challenges, particularly in the realm of trustworthiness. 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 capability (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, suggesting that open-source models can achieve high levels of trustworthiness without additional mechanisms like moderator, offering valuable insights for developers in this field. 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. Besides these observations, we’ve uncovered key insights into the multifaceted trustworthiness in LLMs. We emphasize the importance of ensuring transparency not only in the models themselves but also in the technologies that underpin trustworthiness. We advocate that the establishment of an AI alliance between industry, academia, the open-source community to foster collaboration is imperative to advance the trustworthiness of LLMs.

Discovering reliable and informative relationships among brain regions from functional magnetic resonance imaging (fMRI) signals is essential in phenotypic predictions in neuroscience. Most of the current methods fail to accurately characterize those interactions because they only focus on pairwise connections and overlook the high-order relationships of brain regions. We propose that these high-order relationships should be *maximally informative and minimally redundant* (MIMR). However, identifying such high-order relationships is challenging and under-explored due to the exponential search space and the absence of a tractable objective. In response to this gap, we propose a novel method named HyBRiD, which aims to extract MIMR high-order relationships from fMRI data. HyBRiD employs a Constructor to identify hyperedge structures, and a Weighter to compute a weight for each hyperedge, which avoids searching in exponential space. HyBRiD achieves the MIMR objective through an innovative information bottleneck framework named multi-head drop-bottleneck with theoretical guarantees. Our comprehensive experiments demonstrate the effectiveness of our model. Our model outperforms the state-of-the-art predictive model by an average of 11.2%, regarding the quality of hyperedges measured by CPM, a standard protocol for studying brain connections.

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 \method across various datasets, demonstrating its potential as an effective and scalable solution for large-scale data representation and large models.

Time series forecasting has attracted significant attention in recent decades. Previous studies have demonstrated that the Channel-Independent (CI) strategy improves forecasting performance by treating different channels individually, while it leads to poor generalization on unseen instances and ignores potentially necessary interactions between channels. Conversely, the Channel-Dependent (CD) strategy mixes all channels with even irrelevant and indiscriminate information, which, however, results in oversmoothing issues and limits forecasting accuracy. There is a lack of channel strategy that effectively balances individual channel treatment for improved forecasting performance without overlooking essential interactions between channels. Motivated by our observation of a correlation between the time series model's performance boost against channel mixing and the intrinsic similarity on a pair of channels, we developed a novel and adaptable \textbf{C}hannel \textbf{C}lustering \textbf{M}odule (CCM). CCM dynamically groups channels characterized by intrinsic similarities and leverages cluster information instead of individual channel identities, combining the best of CD and CI worlds. Extensive experiments on real-world datasets demonstrate that CCM can (1) boost the performance of CI and CD models by an average margin of 2.4% and 7.2% on long-term and short-term forecasting, respectively; (2) enable zero-shot forecasting with mainstream time series forecasting models; (3) uncover intrinsic time series patterns among channels and improve interpretability of complex time series models.

Nucleic acid-based drugs like aptamers have recently demonstrated great therapeutic potential. However, experimental platforms for aptamer screening are costly, and the scarcity of labeled data presents a challenge for supervised methods to learn protein-aptamer binding. To this end, we develop an unsupervised learning approach based on the predicted pairwise contact map between a protein and a nucleic acid and demonstrate its effectiveness in protein-aptamer binding prediction. Our model is based on FAFormer, a novel equivariant transformer architecture that seamlessly integrates frame averaging (FA) within each transformer block. This integration allows our model to infuse geometric information into node features while preserving the spatial semantics of coordinates, leading to greater expressive power than standard FA models. Our results show that FAFormer outperforms existing equivariant models in contact map prediction across three protein complex datasets, with over 10% relative improvement. Moreover, we curate five real-world protein-aptamer interaction datasets and show that the contact map predicted by FAFormer serves as a strong binding indicator for aptamer screening.

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.

Subgraph counting is the problem of counting the occurrences of a given query graph in a large target graph. Large-scale subgraph counting is useful in various domains, such as motif analysis for social network and loop counting for money laundering detection. Recently, to address the exponential runtime complexity of scalable subgraph counting, neural methods are proposed. However, existing approaches fall short in three aspects. Firstly, the subgraph counts vary from zero to millions for different graphs, posing a much larger challenge than regular graph regression tasks. Secondly, current scalable graph neural networks have limited expressive power and fail to efficiently distinguish graphs for count prediction. Furthermore, existing neural approaches cannot predict query occurrence positions.

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.

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 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 1.67x memory savings compared to state-of-the-art benchmarks, which demonstrates superior performance of Diffuser in both expressiveness and efficiency aspects.

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.

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 hyperbolic models, 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 the origin (i.e., induced hyperbolic norm) to advance existing hyperbolic models. 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.

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.

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 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\footnoteThe code is available at 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.

Connectivity across documents often exhibits a hierarchical network structure. Hyperbolic Graph Neural Networks (HGNNs) have shown promise in preserving network hierarchy. However, they do not model the notion of topics, thus document representations lack semantic interpretability. On the other hand, a corpus of documents usually has high variability in degrees of topic specificity. For example, some documents contain general content (e.g., sports), while others focus on specific themes (e.g., basketball and swimming). Topic models indeed model latent topics for semantic interpretability, but most assume a flat topic structure and ignore such semantic hierarchy. Given these two challenges, we propose a Hyperbolic Graph Topic Modeling Network to integrate both network hierarchy across linked documents and semantic hierarchy within texts into a unified HGNN framework. Specifically, we construct a two-layer document graph. Intra- and cross-layer encoding captures network hierarchy. We design a topic tree for text decoding to preserve semantic hierarchy and learn interpretable topics. Supervised and unsupervised experiments verify the effectiveness of our model.

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 $\textbf{100.4}$%. Moreover, we employ bioinformatics tools in conjunction with gene representations to uncover pathway enrichment, regulation causal networks, and functions of disease-associated genes. Therefore, our model efficiently produces unified gene representations for the analysis of gene functions, tissue functions, diseases, and species evolution.

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.

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 **Temp**oral **M**otifs **E**xplainer (**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.

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.

With the growing demand for the right to be forgotten, there is an increasing need for machine learning models to forget sensitive data and its impact. To address this, the paradigm of selective forgetting (a.k.a machine unlearning) has been extensively studied, which aims to remove the impact of requested data from a well-trained model without retraining from scratch. Despite its significant success, limited attention has been given to the security vulnerabilities of the unlearning system concerning malicious data update requests. Motivated by this, in this paper, we explore the possibility and feasibility of malicious data update requests during the unlearning process. Specifically, we first propose a new class of malicious selective forgetting attacks, which involves a static scenario where all the malicious data update requests are provided by the adversary at once. Additionally, considering the sequential setting where the data update requests arrive sequentially, we also design a novel framework for sequential forgetting attacks, which is formulated as a stochastic optimal control problem. We also propose novel optimization algorithms that can find the effective malicious data update requests. We perform theoretical analyses for the proposed selective forgetting attacks, and extensive experimental results validate the effectiveness of our proposed selective forgetting attacks. The source code is available in the supplementary material.

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 representations of the neighbors conditioned on the central node’s representation 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.

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.

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.

Self-attention mechanism in graph neural networks (GNNs) led to state-of-the-art performance on many graph representation learning tasks. Currently, at every layer, attention is computed between connected pairs of nodes and depends solely on the representation of the two nodes. However, such attention mechanism does not account for nodes that are not directly connected but provide important network context. Here we propose Multi-hop Attention Graph Neural Network (MAGNA), a principled way to incorporate multi-hop context information into every layer of attention computation. MAGNA diffuses the attention scores across the network, which increases the receptive field for every layer of the GNN. Unlike previous approaches, MAGNA uses a diffusion prior on attention values, to efficiently account for all paths between the pair of disconnected nodes. We demonstrate in theory and experiments that MAGNA captures large-scale structural information in every layer, and has a low-pass effect that eliminates noisy high-frequency information from graph data. Experimental results on node classification as well as the knowledge graph completion benchmarks show that MAGNA achieves state-of-the-art results: MAGNA achieves up to 5.7% relative error reduction over the previous state-of-the-art on Cora, Citeseer, and Pubmed. MAGNA also obtains the best performance on a large-scale Open Graph Benchmark dataset. On knowledge graph completion MAGNA advances state-of-the-art on WN18RR and FB15k-237 across four different performance metrics.

Abusive behavior in online retail websites and communities threatens the experience of regular community members. Such behavior often takes place within a complex, dynamic, and large-scale network of users interacting with items. Detecting abuse is challenging due to the scarcity of labeled abuse instances and complexity of combining temporal and network patterns while operating at a massive scale. Previous approaches to dynamic graph modeling either do not scale, do not effectively generalize from a few labeled instances, or compromise performance for scalability. Here we present BiDyn, a general method to detect abusive behavior in dynamic bipartite networks at scale, while generalizing from limited training labels. BiDyn develops an efficient hybrid RNN-GNN architecture trained via a novel stacked ensemble training scheme. We also propose a novel pre-training framework for dynamic graphs that helps to achieve superior performance at scale. Our approach outperforms recent large-scale dynamic graph baselines in an abuse classification task by up to 14% AUROC while requiring 10x less memory per training batch in both open and proprietary datasets.

Xiaochen Hou, Peng Qi, Guangtao Wang, Rex Ying, Jing Huang, Xiaodong He, Bowen Zhou. Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2021.

Hierarchical relations are prevalent and indispensable for organizing human knowledge captured by a knowledge graph (KG). The key property of hierarchical relations is that they induce a partial ordering over the entities, which needs to be modeled in order to allow for hierarchical reasoning. However, current KG embeddings can model only a single global hierarchy (single global partial ordering) and fail to model multiple heterogeneous hierarchies that exist in a single KG. Here we present ConE (Cone Embedding), a KG embedding model that is able to simultaneously model multiple hierarchical as well as non-hierarchical relations in a knowledge graph. ConE embeds entities into hyperbolic cones and models relations as transformations between the cones. In particular, ConE uses cone containment constraints in different subspaces of the hyperbolic embedding space to capture multiple heterogeneous hierarchies. Experiments on standard knowledge graph benchmarks show that ConE obtains state-of-the-art performance on hierarchical reasoning tasks as well as knowledge graph completion task on hierarchical graphs. In particular, our approach yields new state-of-the-art Hits@1 of 45.3% on WN18RR and 16.1% on DDB14 (0.231 MRR). As for hierarchical reasoning task, our approach outperforms previous best results by an average of 20% across the three datasets.

The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research. However, popular machine learning approaches, based on continuous Euclidean spaces, have struggled with the discrete combinatorial formulation of the edit distance that models evolution and the hierarchical relationship that characterises real-world datasets. We present Neural Distance Embeddings (NeuroSEED), a general framework to embed sequences in geometric vector spaces, and illustrate the effectiveness of the hyperbolic space that captures the hierarchical structure and provides an average 38% reduction in embedding RMSE against the best competing geometry. The capacity of the framework and the significance of these improvements are then demonstrated devising supervised and unsupervised NeuroSEED approaches to multiple core tasks in bioinformatics. Benchmarked with common baselines, the proposed approaches display significant accuracy and/or runtime improvements on real-world datasets. As an example for hierarchical clustering, the proposed pretrained and from-scratch methods match the quality of competing baselines with 30x and 15x runtime reduction, respectively.

Here we present a machine learning framework and model implementation that can learn to simulate a wide variety of challenging physical domains, involving fluids, rigid solids, and deformable materials interacting with one another. Our framework—which we term "Graph Network-based Simulators" (GNS)—represents the state of a physical system with particles, expressed as nodes in a graph, and computes dynamics via learned message-passing. Our results show that our model can generalize from single-timestep predictions with thousands of particles during training, to different initial conditions, thousands of timesteps, and at least an order of magnitude more particles at test time. Our model was robust to hyperparameter choices across various evaluation metrics: the main determinants of long-term performance were the number of message-passing steps, and mitigating the accumulation of error by corrupting the training data with noise. Our GNS framework advances the state-of-the-art in learned physical simulation, and holds promise for solving a wide range of complex forward and inverse problems.

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.

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 convolutional neural networks (GCNs) embed nodes in a graph into Euclidean space, which has been shown to incur a large distortion when embedding real-world graphs with scale-free or hierarchical structure. Hyperbolic geometry offers an exciting alternative, as it enables embeddings with much smaller distortion. However, extending GCNs to hyperbolic geometry presents several unique challenges because it is not clear how to define neural network operations, such as feature transformation and aggregation, in hyperbolic space. Furthermore, since input features are often Euclidean, it is unclear how to transform the features into hyperbolic embeddings with the right amount of curvature. Here we propose Hyperbolic Graph Convolutional Neural Network (HGCN), the first inductive hyperbolic GCN that leverages both the expressiveness of GCNs and hyperbolic geometry to learn inductive node representations for hierarchical and scale-free graphs. We derive GCNs operations in the hyperboloid model of hyperbolic space and map Euclidean input features to embeddings in hyperbolic spaces with different trainable curvature at each layer. Experiments demonstrate that HGCN learns embeddings that preserve hierarchical structure, and leads to improved performance when compared to Euclidean analogs, even with very low dimensional embeddings: compared to state-of-the-art GCNs, HGCN achieves an error reduction of up to 63.1% in ROC AUC for link prediction and of up to 47.5% in F1 score for node classification, also improving state-of-the art on the Pubmed dataset.

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.

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.

Recent advancements in deep neural networks for graph-structured data have led to state-of-the-art performance on recommender system benchmarks. However, making these methods practical and scalable to web-scale recommendation tasks with billions of items and hundreds of millions of users remains an unsolved challenge. Here we describe a large-scale deep recommendation engine that we developed and deployed at Pinterest. We develop a data-efficient Graph Convolutional Network (GCN) algorithm, which combines efficient random walks and graph convolutions to generate embeddings of nodes (i.e., items) that incorporate both graph structure as well as node feature information. Compared to prior GCN approaches, we develop a novel method based on highly efficient random walks to structure the convolutions and design a novel training strategy that relies on harder-and-harder training examples to improve robustness and convergence of the model. We also develop an efficient MapReduce model inference algorithm to generate embeddings using a trained model. Overall, we can train on and embed graphs that are four orders of magnitude larger than typical GCN implementations. We show how GCN embeddings can be used to make high-quality recommendations in various settings at Pinterest, which has a massive underlying graph with 3 billion nodes representing pins and boards, and 17 billion edges. According to offline metrics, user studies, as well as A/B tests, our approach generates higher-quality recommendations than comparable deep learning based systems. To our knowledge, this is by far the largest application of deep graph embeddings to date and paves the way for a new generation of web-scale recommender systems based on graph convolutional architectures.

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.

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

We present the first subquadratic algorithms for computing similarity between a pair of point sequences in R^d, for any fixed d > 1, using dynamic time warping (DTW) and edit distance, assuming that the point sequences are drawn from certain natural families of curves. In particular, our algorithms compute (1 + eps)-approximations of DTW and ED in near-linear time for point sequences drawn from k-packed or k-bounded curves, and subquadratic time for backbone sequences. Roughly speaking, a curve is k-packed if the length of its intersection with any ball of radius r is at most kr, and it is k-bounded if the sub-curve between two curve points does not go too far from the two points compared to the distance between the two points. In backbone sequences, consecutive points are spaced at approximately equal distances apart, and no two points lie very close together. Recent results suggest that a subquadratic algorithm for DTW or ED is unlikely for an arbitrary pair of point sequences even for d = 1. The commonly used dynamic programming algorithms for these distance measures reduce the problem to computing a minimum-weight path in a grid graph. Our algorithms work by constructing a small set of rectangular regions that cover the grid vertices. The weights of vertices inside each rectangle are roughly the same, and we develop efficient procedures to compute the approximate minimum-weight paths through these rectangles.

Dynamic time warping (DTW) is a widely used curve similarity measure. We present a simple and efficient (1 + ε)- approximation algorithm for DTW between a pair of point sequences, say, P and Q, each of which is sampled from a curve. We prove that the running time of the algorithm is O([EQUATION]n log σ) for a pair of k-packed curves with a total of n points, assuming that the spreads of P and Q are bounded by σ. The spread of a point set is the ratio of the maximum to the minimum pairwise distance, and a curve is called K- packed if the length of its intersection with any disk of radius r is at most Kr. Although an algorithm with similar asymptotic time complexity was presented in [1], our algorithm is considerably simpler and more efficient in practice.