arXiv subjects

Rex Ying

Publications and source records attributed to Rex Ying.

At least 55 records · Page 3Linked to original sources

arXiv2026

Hyperbolic Fine-Tuning for Large Language Models

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.

cs.LG↗

arXiv2026

Personalized Safety Alignment for Text-to-Image Diffusion Models

Text-to-image diffusion models have revolutionized visual content generation, yet their deployment is hindered by a fundamental limitation: safety mechanisms enforce rigid, uniform standards that fail to reflect diverse user preferences shaped by age, culture, or personal beliefs. To address this, we propose Personalized Safety Alignment (PSA), a framework that transitions generative safety from static filtration to user-conditioned adaptation. We introduce Sage, a large-scale dataset capturing diverse safety boundaries across 1,000 simulated user profiles, covering complex risks often missed by traditional datasets. By integrating these profiles via a parameter-efficient cross-attention adapter, PSA dynamically modulates generation to align with individual sensitivities. Extensive experiments demonstrate that PSA achieves a calibrated safety-quality trade-off: under permissive profiles, it relaxes over-cautious constraints to enhance visual fidelity, while under restrictive profiles, it enforces state-of-the-art suppression, significantly outperforming static baselines. Furthermore, PSA exhibits superior instruction adherence compared to prompt-engineering methods, establishing personalization as a vital direction for creating adaptive, user-centered, and responsible generative AI. Our code, data, and models are publicly available at https://github.com/M-E-AGI-Lab/PSAlign.

cs.CV↗

arXiv2026

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

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.

cs.LG↗

arXiv2025

LitFM: A Retrieval Augmented Structure-aware Foundation Model For Citation Graphs

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. Here 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 to integrate graph structure by navigating citation graphs and extracting relevant literature, thereby enhancing model reliability. 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

cs.SI↗

arXiv2025

Position: Beyond Euclidean -- Foundation Models Should Embrace Non-Euclidean Geometries

In the era of foundation models and Large Language Models (LLMs), Euclidean space has been the de facto geometric setting for machine learning architectures. However, recent literature has demonstrated that this choice comes with fundamental limitations. At a large scale, real-world data often exhibits inherently non-Euclidean structures, such as multi-way relationships, hierarchies, symmetries, and non-isotropic scaling, in a variety of domains, such as languages, vision, and the natural sciences. It is challenging to effectively capture these structures within the constraints of Euclidean spaces. This position paper argues that moving beyond Euclidean geometry is not merely an optional enhancement but a necessity to maintain the scaling law for the next-generation of foundation models. By adopting these geometries, foundation models could more efficiently leverage the aforementioned structures. Task-aware adaptability that dynamically reconfigures embeddings to match the geometry of downstream applications could further enhance efficiency and expressivity. Our position is supported by a series of theoretical and empirical investigations of prevalent foundation models. Finally, we outline a roadmap for integrating non-Euclidean geometries into foundation models, including strategies for building geometric foundation models via fine-tuning, training from scratch, and hybrid approaches.

cs.LG↗

arXiv2025

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

Large language models (LLMs) have shown great success in text modeling 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. Recent studies have also shown that not respecting the 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 Hyperbolic space, known for its expansive, scale-free, and low-distortion properties. We thus introduce HELM, a family of HypErbolic Large Language Models, 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 Mixture-of-Curvature Experts model, 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, HELM-D. For HELM-MICE, we further develop hyperbolic Multi-Head Latent Attention (HMLA) for efficient, reduced-KV-cache training and inference. For both models, we develop essential hyperbolic equivalents of rotary positional encodings and RMS 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 HELM architectures -- up to 4% -- over popular Euclidean architectures used in LLaMA and DeepSeek, highlighting the efficacy and enhanced reasoning afforded by hyperbolic geometry in large-scale LM pretraining.

cs.LG↗

arXiv2025

Low-Rank Adaptation for Foundation Models: A Comprehensive Review

The rapid advancement of foundation modelslarge-scale neural networks trained on diverse, extensive datasetshas revolutionized artificial intelligence, enabling unprecedented advancements across domains such as natural language processing, computer vision, and scientific discovery. However, the substantial parameter count of these models, often reaching billions or trillions, poses significant challenges in adapting them to specific downstream tasks. Low-Rank Adaptation (LoRA) has emerged as a highly promising approach for mitigating these challenges, offering a parameter-efficient mechanism to fine-tune foundation models with minimal computational overhead. This survey provides the first comprehensive review of LoRA techniques beyond large Language Models to general foundation models, including recent techniques foundations, emerging frontiers and applications of low-rank adaptation across multiple domains. Finally, this survey discusses key challenges and future research directions in theoretical understanding, scalability, and robustness. This survey serves as a valuable resource for researchers and practitioners working with efficient foundation model adaptation.

cs.LG↗

arXiv2025

Non-Markovian Discrete Diffusion with Causal Language Models

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 (Causal Discrete Diffusion Model), 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.

cs.LG↗

arXiv2025

RephQA: Evaluating Readability of Large Language Models in Public Health Question Answering

Large Language Models (LLMs) hold promise in addressing complex medical problems. However, while most prior studies focus on improving accuracy and reasoning abilities, a significant bottleneck in developing effective healthcare agents lies in the readability of LLM-generated responses, specifically, their ability to answer public health problems clearly and simply to people without medical backgrounds. In this work, we introduce RephQA, a benchmark for evaluating the readability of LLMs in public health question answering (QA). It contains 533 expert-reviewed QA pairs from 27 sources across 13 topics, and includes a proxy multiple-choice task to assess informativeness, along with two readability metrics: Flesch-Kincaid grade level and professional score. Evaluation of 25 LLMs reveals that most fail to meet readability standards, highlighting a gap between reasoning and effective communication. To address this, we explore four readability-enhancing strategies-standard prompting, chain-of-thought prompting, Group Relative Policy Optimization (GRPO), and a token-adapted variant. Token-adapted GRPO achieves the best results, advancing the development of more practical and user-friendly public health agents. These results represent a step toward building more practical agents for public health.

cs.CL↗

arXiv2025

GRIL: Knowledge Graph Retrieval-Integrated Learning with Large Language Models

Retrieval-Augmented Generation (RAG) has significantly mitigated the hallucinations of Large Language Models (LLMs) by grounding the generation with external knowledge. Recent extensions of RAG to graph-based retrieval offer a promising direction, leveraging the structural knowledge for multi-hop reasoning. However, existing graph RAG typically decouples retrieval and reasoning processes, which prevents the retriever from adapting to the reasoning needs of the LLM. They also struggle with scalability when performing multi-hop expansion over large-scale graphs, or depend heavily on annotated ground-truth entities, which are often unavailable in open-domain settings. To address these challenges, we propose a novel graph retriever trained end-to-end with LLM, which features an attention-based growing and pruning mechanism, adaptively navigating multi-hop relevant entities while filtering out noise. Within the extracted subgraph, structural knowledge and semantic features are encoded via soft tokens and the verbalized graph, respectively, which are infused into the LLM together, thereby enhancing its reasoning capability and facilitating interactive joint training of the graph retriever and the LLM reasoner. Experimental results across three QA benchmarks show that our approach consistently achieves state-of-the-art performance, validating the strength of joint graph-LLM optimization for complex reasoning tasks. Notably, our framework eliminates the need for predefined ground-truth entities by directly optimizing the retriever using LLM logits as implicit feedback, making it especially effective in open-domain settings.

cs.LG↗

arXiv2025

Flow Matching for Collaborative Filtering

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.

cs.IR↗

arXiv2025

Implicit Reasoning in Large Language Models: A Comprehensive Survey

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

cs.CL↗

arXiv2025

Hypformer: Exploring Efficient Transformer Fully in Hyperbolic Space

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

cs.LG↗

arXiv2025

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

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

q-bio.BM↗

arXiv2025

SANDWICH: Towards an Offline, Differentiable, Fully-Trainable Wireless Neural Ray-Tracing Surrogate

Wireless ray-tracing (RT) is emerging as a key tool for three-dimensional (3D) wireless channel modeling, driven by advances in graphical rendering. Current approaches struggle to accurately model beyond 5G (B5G) network signaling, which often operates at higher frequencies and is more susceptible to environmental conditions and changes. Existing online learning solutions require real-time environmental supervision during training, which is both costly and incompatible with GPU-based processing. In response, we propose a novel approach that redefines ray trajectory generation as a sequential decision-making problem, leveraging generative models to jointly learn the optical, physical, and signal properties within each designated environment. Our work introduces the Scene-Aware Neural Decision Wireless Channel Raytracing Hierarchy (SANDWICH), an innovative offline, fully differentiable approach that can be trained entirely on GPUs. SANDWICH offers superior performance compared to existing online learning methods, outperforms the baseline by 4e^-2 radian in RT accuracy, and only fades 0.5 dB away from toplined channel gain estimation.

cs.NI↗

arXiv2025

Hyperbolic Deep Learning for Foundation Models: A Survey

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.

cs.LG↗

arXiv2025

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

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.

q-bio.NC↗

arXiv2025

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

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 model and force the new model to reconstruct outdated representations regardless of their quality, thereby hindering the learning process of the new model. In this paper, we propose to 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.

cs.LG↗