Arrow Research search

Author name cluster

Rex Ying

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

34 papers
2 author rows

Possible papers

34

AAAI Conference 2025 Conference Paper

An Item Is Worth a Prompt: Versatile Image Editing with Disentangled Control

  • Aosong Feng
  • Weikang Qiu
  • Jinbin Bai
  • Zhen Dong
  • Kaicheng Zhou
  • Xiao Zhang
  • Rex Ying
  • Leandros Tassiulas

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.

PDF Details DOI

NeurIPS Conference 2025 Conference Paper

HELM: Hyperbolic Large Language Models via Mixture-of-Curvature Experts

  • Neil He
  • Rishabh Anand
  • Hiren Madhu
  • Ali Maatouk
  • Smita Krishnaswamy
  • Leandros Tassiulas
  • Menglin Yang
  • Rex Ying

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.

PDF Details

NeurIPS Conference 2025 Conference Paper

HiPoNet: A Multi-View Simplicial Complex Network for High Dimensional Point-Cloud and Single-Cell data

  • Siddharth Viswanath
  • Hiren Madhu
  • Dhananjay Bhaskar
  • Jake Kovalic
  • Dave Johnson
  • Christopher Tape
  • Ian Adelstein
  • Rex Ying

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.

PDF Details

NeurIPS Conference 2025 Conference Paper

Hyperbolic Fine-Tuning for Large Language Models

  • Menglin Yang
  • Ram B
  • Aosong Feng
  • Bo Xiong
  • Jiahong Liu
  • Irwin King
  • Rex Ying

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.

PDF Details

ICML Conference 2025 Conference Paper

Learning Along the Arrow of Time: Hyperbolic Geometry for Backward-Compatible Representation Learning

  • Ngoc Bui
  • Menglin Yang 0001
  • Runjin Chen
  • Leonardo Neves
  • Mingxuan Ju
  • Rex Ying
  • Neil Shah
  • Tong Zhao 0003

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.

Details

ICML Conference 2025 Conference Paper

MindLLM: A Subject-Agnostic and Versatile Model for fMRI-to-text Decoding

  • Weikang Qiu
  • Zheng Huang
  • Haoyu Hu
  • Aosong Feng
  • Yujun Yan
  • Rex Ying

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.

Details

NeurIPS Conference 2025 Conference Paper

Non-Markovian Discrete Diffusion with Causal Language Models

  • Yangtian Zhang
  • Sizhuang He
  • Daniel Levine
  • Lawrence Zhao
  • David Zhang
  • Syed Rizvi
  • Shiyang Zhang
  • Emanuele Zappala

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.

PDF Details

ICML Conference 2025 Conference Paper

Retrieval-Augmented Language Model for Knowledge-aware Protein Encoding

  • Jiasheng Zhang
  • Delvin Ce Zhang
  • Shuang Liang 0002
  • Zhengpin Li
  • Rex Ying
  • Jie Shao 0001

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.

Details

TMLR Journal 2025 Journal Article

RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design

  • Rishabh Anand
  • Chaitanya K. Joshi
  • Alex Morehead
  • Arian Rokkum Jamasb
  • Charles Harris
  • Simon V Mathis
  • Kieran Didi
  • Rex Ying

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

PDF Details

ICML Conference 2025 Conference Paper

Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching

  • Tinglin Huang 0001
  • Tianyu Liu 0005
  • Mehrtash Babadi
  • Wengong Jin
  • Rex Ying

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.

Details

NeurIPS Conference 2025 Conference Paper

TRACE: Grounding Time Series in Context for Multimodal Embedding and Retrieval

  • Jialin Chen
  • Ziyu Zhao
  • Gaukhar Nurbek
  • Aosong Feng
  • Ali Maatouk
  • Leandros Tassiulas
  • Yifeng Gao
  • Rex Ying

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.

PDF Details

NeurIPS Conference 2024 Conference Paper

DTGB: A Comprehensive Benchmark for Dynamic Text-Attributed Graphs

  • Jiasheng Zhang
  • Jialin Chen
  • Menglin Yang
  • Aosong Feng
  • Shuang Liang
  • Jie Shao
  • Rex Ying

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.

PDF Details DOI

ICML Conference 2024 Conference Paper

Explaining Graph Neural Networks via Structure-aware Interaction Index

  • Ngoc Bui
  • Hieu Trung Nguyen
  • Viet Anh Nguyen
  • Rex Ying

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.

Details

NeurIPS Conference 2024 Conference Paper

From Similarity to Superiority: Channel Clustering for Time Series Forecasting

  • Jialin Chen
  • Jan Eric Lenssen
  • Aosong Feng
  • Weihua Hu
  • Matthias Fey
  • Leandros Tassiulas
  • Jure Leskovec
  • Rex Ying

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.

PDF Details DOI

ICML Conference 2024 Conference Paper

Learning High-Order Relationships of Brain Regions

  • Weikang Qiu
  • Huangrui Chu
  • Selena Wang
  • Haolan Zuo
  • Xiaoxiao Li
  • Yize Zhao
  • Rex Ying

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.

Details

ICML Conference 2024 Conference Paper

Position: Relational Deep Learning - Graph Representation Learning on Relational Databases

  • Matthias Fey
  • Weihua Hu
  • Kexin Huang
  • Jan Eric Lenssen
  • Rishabh Ranjan
  • Joshua Robinson 0001
  • Rex Ying
  • Jiaxuan You

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.

Details

ICML Conference 2024 Conference Paper

Position: TrustLLM: Trustworthiness in Large Language Models

  • Yue Huang 0001
  • Lichao Sun 0001
  • Haoran Wang 0005
  • Siyuan Wu 0001
  • Qihui Zhang
  • Yuan Li
  • Chujie Gao
  • Yixin Huang

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.

Details

NeurIPS Conference 2024 Conference Paper

Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer

  • Tinglin Huang
  • Zhenqiao Song
  • Rex Ying
  • Wengong Jin

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.

PDF Details DOI

ICLR Conference 2024 Conference Paper

Thought Propagation: an Analogical Approach to Complex Reasoning with Large Language Models

  • Junchi Yu
  • Ran He 0001
  • 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.

Details

NeurIPS Conference 2023 Conference Paper

D4Explainer: In-distribution Explanations of Graph Neural Network via Discrete Denoising Diffusion

  • Jialin Chen
  • Shirley Wu
  • Abhijit Gupta
  • Rex Ying

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.

PDF Details

AAAI Conference 2023 Conference Paper

Diffuser: Efficient Transformers with Multi-Hop Attention Diffusion for Long Sequences

  • Aosong Feng
  • Irene Li
  • Yuang Jiang
  • Rex Ying

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.

PDF Details DOI

ICML Conference 2023 Conference Paper

FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning

  • Songtao Liu
  • Zhengkai Tu
  • Minkai Xu
  • Zuobai Zhang
  • Lu Lin 0001
  • Rex Ying
  • Jian Tang 0005
  • Peilin Zhao

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.

Details

ICML Conference 2023 Conference Paper

Hyperbolic Representation Learning: Revisiting and Advancing

  • Menglin Yang 0001
  • Min Zhou 0006
  • Rex Ying
  • Yankai Chen 0001
  • Irwin King

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.

Details

NeurIPS Conference 2023 Conference Paper

Learning to Group Auxiliary Datasets for Molecule

  • 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.

PDF Details

NeurIPS Conference 2023 Conference Paper

MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data

  • Tianyu Liu
  • Yuge Wang
  • Rex Ying
  • Hongyu Zhao

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.

PDF Details

NeurIPS Conference 2023 Conference Paper

Static and Sequential Malicious Attacks in the Context of Selective Forgetting

  • Chenxu Zhao
  • Wei Qian
  • Rex Ying
  • Mengdi Huai

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.

PDF Details

NeurIPS Conference 2023 Conference Paper

TempME: Towards the Explainability of Temporal Graph Neural Networks via Motif Discovery

  • 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 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.

PDF Details

ICML Conference 2022 Conference Paper

Local Augmentation for Graph Neural Networks

  • Songtao Liu
  • Rex Ying
  • Hanze Dong
  • Lanqing Li
  • Tingyang Xu
  • Yu Rong 0001
  • Peilin Zhao
  • Junzhou Huang

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.

Details

AAAI Conference 2021 Conference Paper

Identity-aware Graph Neural Networks

  • Jiaxuan You
  • Jonathan M Gomes-Selman
  • Rex Ying
  • Jure Leskovec

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. Altogether, 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.

PDF Details

IJCAI Conference 2021 Conference Paper

Multi-hop Attention Graph Neural Networks

  • Guangtao Wang
  • Rex Ying
  • Jing Huang
  • Jure Leskovec

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.

PDF Details DOI

ICML Conference 2020 Conference Paper

Learning to Simulate Complex Physics with Graph Networks

  • Alvaro Sanchez-Gonzalez
  • Jonathan Godwin
  • Tobias Pfaff
  • Rex Ying
  • Jure Leskovec
  • Peter W. Battaglia

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.

Details

ICLR Conference 2020 Conference Paper

Neural Execution of Graph Algorithms

  • Petar Velickovic
  • Rex Ying
  • Matilde Padovano
  • Raia Hadsell
  • Charles Blundell

Graph Neural Networks (GNNs) are a powerful representational tool for solving problems on graph-structured inputs. In almost all cases so far, however, they have been applied to directly recovering a final solution from raw inputs, without explicit guidance on how to structure their problem-solving. Here, instead, we focus on learning in the space of algorithms: we train several state-of-the-art GNN architectures to imitate individual steps of classical graph algorithms, parallel (breadth-first search, Bellman-Ford) as well as sequential (Prim's algorithm). As graph algorithms usually rely on making discrete decisions within neighbourhoods, we hypothesise that maximisation-based message passing neural networks are best-suited for such objectives, and validate this claim empirically. We also demonstrate how learning in the space of algorithms can yield new opportunities for positive transfer between tasks---showing how learning a shortest-path algorithm can be substantially improved when simultaneously learning a reachability algorithm.

Details

ICML Conference 2019 Conference Paper

Position-aware Graph Neural Networks

  • Jiaxuan You
  • Rex Ying
  • Jure Leskovec

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.

Details

ICML Conference 2018 Conference Paper

GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models

  • Jiaxuan You
  • Rex Ying
  • Xiang Ren 0001
  • William L. Hamilton
  • Jure Leskovec

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.

Details