arXiv subjects

Rex Ying

Publications and source records attributed to Rex Ying.

At least 73 records · Page 4Linked to original sources

arXiv2025

Experience Retrieval-Augmentation with Electronic Health Records Enables Accurate Discharge QA

To improve the reliability of Large Language Models (LLMs) in clinical applications, retrieval-augmented generation (RAG) is extensively applied to provide factual medical knowledge. However, beyond general medical knowledge from open-ended datasets, clinical case-based knowledge is also critical for effective medical reasoning, as it provides context grounded in real-world patient experiences.Motivated by this, we propose Experience Retrieval-Augmentation ExpRAG framework based on Electronic Health Record(EHR), aiming to offer the relevant context from other patients' discharge reports. ExpRAG performs retrieval through a coarse-to-fine process, utilizing an EHR-based report ranker to efficiently identify similar patients, followed by an experience retriever to extract task-relevant content for enhanced medical reasoning.To evaluate ExpRAG, we introduce DischargeQA, a clinical QA dataset with 1,280 discharge-related questions across diagnosis, medication, and instruction tasks. Each problem is generated using EHR data to ensure realistic and challenging scenarios. Experimental results demonstrate that ExpRAG consistently outperforms a text-based ranker, achieving an average relative improvement of 5.2%, highlighting the importance of case-based knowledge for medical reasoning.

cs.CL↗

arXiv2025

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

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.

cs.LG↗

arXiv2025

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

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.

cs.CV↗

arXiv2025

Long Sequence Modeling with Attention Tensorization: From Sequence to Tensor Learning

As the demand for processing extended textual data grows, the ability to handle long-range dependencies and maintain computational efficiency is more critical than ever. One of the key issues for long-sequence modeling using attention-based model is the mismatch between the limited-range modeling power of full attention and the long-range token dependency in the input sequence. In this work, we propose to scale up the attention receptive field by tensorizing long input sequences into compact tensor representations followed by attention on each transformed dimension. The resulting Tensorized Attention can be adopted as efficient transformer backbones to extend input context length with improved memory and time efficiency. We show that the proposed attention tensorization encodes token dependencies as a multi-hop attention process, and is equivalent to Kronecker decomposition of full attention. Extensive experiments show that tensorized attention can be used to adapt pretrained LLMs with improved efficiency. Notably, Llama-8B with tensorization is trained under 32,768 context length and can steadily extrapolate to 128k length during inference with $11\times$ speedup, compared to full attention with FlashAttention-2.

cs.CL↗

arXiv2025

Towards Non-Euclidean Foundation Models: Advancing AI Beyond Euclidean Frameworks

In the era of foundation models and Large Language Models (LLMs), Euclidean space is the de facto geometric setting of our machine learning architectures. However, recent literature has demonstrated that this choice comes with fundamental limitations. To that end, non-Euclidean learning is quickly gaining traction, particularly in web-related applications where complex relationships and structures are prevalent. Non-Euclidean spaces, such as hyperbolic, spherical, and mixed-curvature spaces, have been shown to provide more efficient and effective representations for data with intrinsic geometric properties, including web-related data like social network topology, query-document relationships, and user-item interactions. Integrating foundation models with non-Euclidean geometries has great potential to enhance their ability to capture and model the underlying structures, leading to better performance in search, recommendations, and content understanding. This workshop focuses on the intersection of Non-Euclidean Foundation Models and Geometric Learning (NEGEL), exploring its potential benefits, including the potential benefits for advancing web-related technologies, challenges, and future directions. Workshop page: [https://hyperboliclearning.github.io/events/www2025workshop](https://hyperboliclearning.github.io/events/www2025workshop)

cs.CG↗

arXiv2025

DYSTIL: Dynamic Strategy Induction with Large Language Models for Reinforcement Learning

Reinforcement learning from expert demonstrations has long remained a challenging research problem, and existing state-of-the-art methods using behavioral cloning plus further RL training often suffer from poor generalization, low sample efficiency, and poor model interpretability. Inspired by the strong reasoning abilities of large language models (LLMs), we propose a novel strategy-based reinforcement learning framework integrated with LLMs called DYnamic STrategy Induction with Llms for reinforcement learning (DYSTIL) to overcome these limitations. DYSTIL dynamically queries a strategy-generating LLM to induce textual strategies based on advantage estimations and expert demonstrations, and gradually internalizes induced strategies into the RL agent through policy optimization to improve its performance through boosting policy generalization and enhancing sample efficiency. It also provides a direct textual channel to observe and interpret the evolution of the policy's underlying strategies during training. We test DYSTIL over challenging RL environments from Minigrid and BabyAI, and empirically demonstrate that DYSTIL significantly outperforms state-of-the-art baseline methods by 17.75% in average success rate while also enjoying higher sample efficiency during the learning process.

cs.LG↗

arXiv2025

Tele-LLMs: A Series of Specialized Large Language Models for Telecommunications

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

cs.IT↗

arXiv2025

HyperCore: The Core Framework for Building Hyperbolic Foundation Models with Comprehensive Modules

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

cs.LG↗

arXiv2025

Beyond Feature Importance: Feature Interactions in Predicting Post-Stroke Rigidity with Graph Explainable AI

This study addresses the challenge of predicting post-stroke rigidity by emphasizing feature interactions through graph-based explainable AI. Post-stroke rigidity, characterized by increased muscle tone and stiffness, significantly affects survivors' mobility and quality of life. Despite its prevalence, early prediction remains limited, delaying intervention. We analyze 519K stroke hospitalization records from the Healthcare Cost and Utilization Project dataset, where 43% of patients exhibited rigidity. We compare traditional approaches such as Logistic Regression, XGBoost, and Transformer with graph-based models like Graphormer and Graph Attention Network. These graph models inherently capture feature interactions and incorporate intrinsic or post-hoc explainability. Our results show that graph-based methods outperform others (AUROC 0.75), identifying key predictors such as NIH Stroke Scale and APR-DRG mortality risk scores. They also uncover interactions missed by conventional models. This research provides a novel application of graph-based XAI in stroke prognosis, with potential to guide early identification and personalized rehabilitation strategies.

cs.LG↗

arXiv2025

Mixture-of-Personas Language Models for Population Simulation

Advances in Large Language Models (LLMs) paved the way for their emerging applications in various domains, such as human behavior simulations, where LLMs could augment human-generated data in social science research and machine learning model training. However, pretrained LLMs often fail to capture the behavioral diversity of target populations due to the inherent variability across individuals and groups. To address this, we propose \textit{Mixture of Personas} (MoP), a \textit{probabilistic} prompting method that aligns the LLM responses with the target population. MoP is a contextual mixture model, where each component is an LM agent characterized by a persona and an exemplar representing subpopulation behaviors. The persona and exemplar are randomly chosen according to the learned mixing weights to elicit diverse LLM responses during simulation. MoP is flexible, requires no model finetuning, and is transferable across base models. Experiments for synthetic data generation show that MoP outperforms competing methods in alignment and diversity metrics.

cs.LG↗

arXiv2025

Large-Scale AI in Telecom: Charting the Roadmap for Innovation, Scalability, and Enhanced Digital Experiences

This white paper discusses the role of large-scale AI in the telecommunications industry, with a specific focus on the potential of generative AI to revolutionize network functions and user experiences, especially in the context of 6G systems. It highlights the development and deployment of Large Telecom Models (LTMs), which are tailored AI models designed to address the complex challenges faced by modern telecom networks. The paper covers a wide range of topics, from the architecture and deployment strategies of LTMs to their applications in network management, resource allocation, and optimization. It also explores the regulatory, ethical, and standardization considerations for LTMs, offering insights into their future integration into telecom infrastructure. The goal is to provide a comprehensive roadmap for the adoption of LTMs to enhance scalability, performance, and user-centric innovation in telecom networks.

cs.NI↗

arXiv2025

Understanding and Mitigating Hyperbolic Dimensional Collapse in Graph Contrastive Learning

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

cs.LG↗

arXiv2025

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

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.

cs.CV↗

arXiv2025

Lorentzian Residual Neural Networks

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.

cs.LG↗

arXiv2024

Reaction-conditioned De Novo Enzyme Design with GENzyme

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

q-bio.BM↗

arXiv2024

From Similarity to Superiority: Channel Clustering for Time Series Forecasting

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 Channel Clustering Module (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.

cs.LG↗

arXiv2024

DTGB: A Comprehensive Benchmark for Dynamic Text-Attributed Graphs

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.

cs.AI↗

arXiv2024

Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer

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.

q-bio.BM↗