arXiv subjects

Yifei Shen

Publications and source records attributed to Yifei Shen.

At least 37 records · Page 2Linked to original sources

arXiv2026

UniG2U-Bench: Do Unified Models Advance Multimodal Understanding?

Unified multimodal models have recently demonstrated strong generative capabilities, yet whether and when generation improves understanding remains unclear. Existing benchmarks lack a systematic exploration of the specific tasks where generation facilitates understanding. To this end, we introduce UniG2U-Bench, a comprehensive benchmark categorizing generation-to-understanding (G2U) evaluation into 7 regimes and 30 subtasks, requiring varying degrees of implicit or explicit visual transformations. Extensive evaluation of over 30 models reveals three core findings: 1) Unified models generally underperform their base Vision-Language Models (VLMs), and Generate-then-Answer (GtA) inference typically degrades performance relative to direct inference. 2) Consistent enhancements emerge in spatial intelligence, visual illusions, or multi-round reasoning subtasks, where enhanced spatial and shape perception, as well as multi-step intermediate image states, prove beneficial. 3) Tasks with similar reasoning structures and models sharing architectures exhibit correlated behaviors, suggesting that generation-understanding coupling induces class-consistent inductive biases over tasks, pretraining data, and model architectures. These findings highlight the necessity for more diverse training data and novel paradigms to fully unlock the potential of unified multimodal modeling.

cs.CV↗

arXiv2026

OneVision-Encoder: Codec-Aligned Sparsity as a Foundational Principle for Multimodal Intelligence

Hypothesis. Artificial general intelligence is, at its core, a compression problem. Effective compression demands resonance: deep learning scales best when its architecture aligns with the fundamental structure of the data. These are the fundamental principles. Yet, modern vision architectures have strayed from these truths: visual signals are highly redundant, while discriminative information, the surprise, is sparse. Current models process dense pixel grids uniformly, wasting vast compute on static background rather than focusing on the predictive residuals that define motion and meaning. We argue that to solve visual understanding, we must align our architectures with the information-theoretic principles of video, i.e., Codecs. Method. OneVision-Encoder encodes video by compressing predictive visual structure into semantic meaning. By adopting Codec Patchification, OV-Encoder abandons uniform computation to focus exclusively on the 3.1%-25% of regions rich in signal entropy. To unify spatial and temporal reasoning under irregular token layouts, OneVision-Encoder employs a shared 3D RoPE and is trained with a large-scale cluster discrimination objective over more than one million semantic concepts, jointly capturing object permanence and motion dynamics. Evidence. The results validate our core hypothesis: efficiency and accuracy are not a trade-off; they are positively correlated. When integrated into LLM, it consistently outperforms strong vision backbones such as Qwen3-ViT and SigLIP2 across 16 image, video, and document understanding benchmarks, despite using substantially fewer visual tokens and pretraining data. Notably, on video understanding tasks, OV-Encoder achieves an average improvement of 4.1% over Qwen3-ViT. Codec-aligned, patch-level sparsity is a foundational principle, enabling OV-Encoder as a scalable engine for next-generation visual generalists.

cs.CV↗

arXiv2026

OLion: Approaching the Hadamard Ideal by Intersecting Spectral and $\ell_{\infty}$ Implicit Biases

Many optimizers can be interpreted as steepest-descent methods under norm-induced geometries, and thus inherit corresponding implicit biases. We introduce \nameA{} (\fullname{}), which combines spectral control from orthogonalized update directions with $\ell_\infty$-style coordinate control from sign updates. \nameA{} forms a Lion-style momentum direction, approximately orthogonalizes it via a few Newton--Schulz iterations, and then applies an entrywise sign, providing an efficient approximation to taking a maximal step over the intersection of the spectral and $\ell_\infty$ constraint sets (a scaled Hadamard-like set for matrix parameters). Despite the strong nonlinearity of orthogonalization and sign, we prove convergence under a mild, empirically verified diagonal-isotropy assumption. Across large-scale language and vision training, including GPT-2 and Llama pretraining, SiT image pretraining, and supervised fine-tuning, \nameA{} matches or outperforms AdamW and Muon under comparable tuning while using only momentum-level optimizer state, and it mitigates optimizer mismatch when fine-tuning AdamW-pretrained checkpoints.

cs.LG↗

arXiv2026

Patient-Similarity Cohort Reasoning in Clinical Text-to-SQL

Real-world clinical text-to-SQL requires reasoning over heterogeneous EHR tables, temporal windows, and patient-similarity cohorts to produce executable queries. We introduce CLINSQL, a benchmark of 633 expert-annotated tasks on MIMIC-IV v3.1 that demands multi-table joins, clinically meaningful filters, and executable SQL. Solving CLINSQL entails navigating schema metadata and clinical coding systems, handling long contexts, and composing multi-step queries beyond traditional text-to-SQL. We evaluate 22 proprietary and open-source models under Chain-of-Thought self-refinement and use rubric-based SQL analysis with execution checks that prioritize critical clinical requirements. Despite recent advances, performance remains far from clinical reliability: on the test set, GPT-5-mini attains 74.7% execution score, DeepSeek-R1 leads open-source at 69.2% and Gemini-2.5-Pro drops from 85.5% on Easy to 67.2% on Hard. Progress on CLINSQL marks tangible advances toward clinically reliable text-to-SQL for real-world EHR analytics.

cs.CL↗

arXiv2025

Toward Relative Positional Encoding in Spiking Transformers

Spiking neural networks (SNNs) are bio-inspired networks that mimic how neurons in the brain communicate through discrete spikes, which have great potential in various tasks due to their energy efficiency and temporal processing capabilities. SNNs with self-attention mechanisms (spiking Transformers) have recently shown great advancements in various tasks, and inspired by traditional Transformers, several studies have demonstrated that spiking absolute positional encoding can help capture sequential relationships for input data, enhancing the capabilities of spiking Transformers for tasks such as sequential modeling and image classification. However, how to incorporate relative positional information into SNNs remains a challenge. In this paper, we introduce several strategies to approximate relative positional encoding in spiking Transformers while preserving the binary nature of spikes. Firstly, we formally prove that encoding relative distances with Gray Code ensures that the binary representations of positional indices maintain a constant Hamming distance whenever their decimal values differ by a power of two, and we propose Gray-PE based on this property. In addition, we propose another RPE method called Log-PE, which combines the logarithmic form of the relative distance matrix directly into the spiking attention map. Furthermore, we extend our RPE methods to a two-dimensional form, making them suitable for processing image patches. We evaluate our RPE methods on various tasks, including time series forecasting, text classification, and patch-based image classification, and the experimental results demonstrate a satisfying performance gain by incorporating our RPE methods across many architectures. Our results provide fresh perspectives on designing spiking Transformers to advance their sequential modeling capability, thereby expanding their applicability across various domains.

cs.NE↗

arXiv2025

Large Multi-modal Models Can Interpret Features in Large Multi-modal Models

Recent advances in Large Multimodal Models (LMMs) lead to significant breakthroughs in both academia and industry. One question that arises is how we, as humans, can understand their internal neural representations. This paper takes an initial step towards addressing this question by presenting a versatile framework to identify and interpret the semantics within LMMs. Specifically, 1) we first apply a Sparse Autoencoder(SAE) to disentangle the representations into human understandable features. 2) We then present an automatic interpretation framework to interpreted the open-semantic features learned in SAE by the LMMs themselves. We employ this framework to analyze the LLaVA-NeXT-8B model using the LLaVA-OV-72B model, demonstrating that these features can effectively steer the model's behavior. Our results contribute to a deeper understanding of why LMMs excel in specific tasks, including EQ tests, and illuminate the nature of their mistakes along with potential strategies for their rectification. These findings offer new insights into the internal mechanisms of LMMs and suggest parallels with the cognitive processes of the human brain.

cs.CV↗

arXiv2025

SciVer: Evaluating Foundation Models for Multimodal Scientific Claim Verification

We introduce SciVer, the first benchmark specifically designed to evaluate the ability of foundation models to verify claims within a multimodal scientific context. SciVer consists of 3,000 expert-annotated examples over 1,113 scientific papers, covering four subsets, each representing a common reasoning type in multimodal scientific claim verification. To enable fine-grained evaluation, each example includes expert-annotated supporting evidence. We assess the performance of 21 state-of-the-art multimodal foundation models, including o4-mini, Gemini-2.5-Flash, Llama-3.2-Vision, and Qwen2.5-VL. Our experiment reveals a substantial performance gap between these models and human experts on SciVer. Through an in-depth analysis of retrieval-augmented generation (RAG), and human-conducted error evaluations, we identify critical limitations in current open-source models, offering key insights to advance models' comprehension and reasoning in multimodal scientific literature tasks.

cs.CL↗

arXiv2025

Edge-Spreading Raptor-Like LDPC Codes for 6G Wireless Systems

Next-generation channel coding has stringent demands on throughput, energy consumption, and error rate performance while maintaining key features of 5G New Radio (NR) standard codes such as rate compatibility, which is a significant challenge. Due to excellent capacity-achieving performance, spatially-coupled low-density parity-check (SC-LDPC) codes are considered a promising candidate for next-generation channel coding. In this paper, we propose an SC-LDPC code family called edge-spreading Raptor-like (ESRL) codes. Unlike other SC-LDPC codes that adopt the structure of existing rate-compatible LDPC block codes before coupling, ESRL codes maximize the possible locations of edge placement and focus on constructing an optimal coupled matrix. Moreover, a new graph representation called the unified graph is introduced. This graph offers a global perspective on ESRL codes and identifies the optimal edge reallocation to optimize the spreading strategy. We conduct comprehensive comparisons of ESRL codes and 5G-NR LDPC codes. Simulation results demonstrate that when all decoding parameters and complexity are the same, ESRL codes have obvious advantages in error rate performance and throughput compared to 5G-NR LDPC codes in some specific scenarios (low and high number of iterations), making them a promising solution towards next-generation channel coding.

cs.IT↗

arXiv2025

TRAIL: Transferable Robust Adversarial Images via Latent diffusion

Adversarial attacks exploiting unrestricted natural perturbations present severe security risks to deep learning systems, yet their transferability across models remains limited due to distribution mismatches between generated adversarial features and real-world data. While recent works utilize pre-trained diffusion models as adversarial priors, they still encounter challenges due to the distribution shift between the distribution of ideal adversarial samples and the natural image distribution learned by the diffusion model. To address the challenge, we propose Transferable Robust Adversarial Images via Latent Diffusion (TRAIL), a test-time adaptation framework that enables the model to generate images from a distribution of images with adversarial features and closely resembles the target images. To mitigate the distribution shift, during attacks, TRAIL updates the diffusion U-Net's weights by combining adversarial objectives (to mislead victim models) and perceptual constraints (to preserve image realism). The adapted model then generates adversarial samples through iterative noise injection and denoising guided by these objectives. Experiments demonstrate that TRAIL significantly outperforms state-of-the-art methods in cross-model attack transferability, validating that distribution-aligned adversarial feature synthesis is critical for practical black-box attacks.

cs.CV↗

arXiv2025

When Do LLMs Help With Node Classification? A Comprehensive Analysis

Node classification is a fundamental task in graph analysis, with broad applications across various fields. Recent breakthroughs in Large Language Models (LLMs) have enabled LLM-based approaches for this task. Although many studies demonstrate the impressive performance of LLM-based methods, the lack of clear design guidelines may hinder their practical application. In this work, we aim to establish such guidelines through a fair and systematic comparison of these algorithms. As a first step, we developed LLMNodeBed, a comprehensive codebase and testbed for node classification using LLMs. It includes 10 homophilic datasets, 4 heterophilic datasets, 8 LLM-based algorithms, 8 classic baselines, and 3 learning paradigms. Subsequently, we conducted extensive experiments, training and evaluating over 2,700 models, to determine the key settings (e.g., learning paradigms and homophily) and components (e.g., model size and prompt) that affect performance. Our findings uncover 8 insights, e.g., (1) LLM-based methods can significantly outperform traditional methods in a semi-supervised setting, while the advantage is marginal in a supervised setting; (2) Graph Foundation Models can beat open-source LLMs but still fall short of strong LLMs like GPT-4o in a zero-shot setting. We hope that the release of LLMNodeBed, along with our insights, will facilitate reproducible research and inspire future studies in this field. Codes and datasets are released at \href{https://llmnodebed.github.io/}{\texttt{https://llmnodebed.github.io/}}.

cs.LG↗

arXiv2025

Towards Graph Foundation Models: Training on Knowledge Graphs Enables Transferability to General Graphs

Inspired by the success of large language models, there is a trend toward developing graph foundation models to conduct diverse downstream tasks in various domains. However, current models often require extra fine-tuning to apply their learned structural and semantic representations to new graphs, which limits their versatility. Recent breakthroughs in zero-shot inductive reasoning on knowledge graphs (KGs), offer us a new perspective on extending KG reasoning to general graph applications. In this paper, we introduce SCR, a unified graph reasoning framework designed to train on knowledge graphs and effectively generalize across a wide range of graph tasks and domains. We begin by designing the task-specific KG structures to establish a unified topology for different task formats. Then we propose semantic-conditioned message passing, a novel mechanism addressing the inherent semantic isolation in traditional KG reasoning, by jointly modeling structural and semantic invariance patterns in graph representations. To demonstrate the effectiveness, we evaluate the inductive reasoning capability of SCR using 38 diverse graph datasets, covering node-level, link-level, and graph-level tasks across multiple domains. Our results show substantial performance gains over existing foundation models and supervised baselines, highlighting the efficacy and adaptability of our approach.

cs.LG↗

arXiv2025

What Makes a Good Diffusion Planner for Decision Making?

Diffusion models have recently shown significant potential in solving decision-making problems, particularly in generating behavior plans -- also known as diffusion planning. While numerous studies have demonstrated the impressive performance of diffusion planning, the mechanisms behind the key components of a good diffusion planner remain unclear and the design choices are highly inconsistent in existing studies. In this work, we address this issue through systematic empirical experiments on diffusion planning in an offline reinforcement learning (RL) setting, providing practical insights into the essential components of diffusion planning. We trained and evaluated over 6,000 diffusion models, identifying the critical components such as guided sampling, network architecture, action generation and planning strategy. We revealed that some design choices opposite to the common practice in previous work in diffusion planning actually lead to better performance, e.g., unconditional sampling with selection can be better than guided sampling and Transformer outperforms U-Net as denoising network. Based on these insights, we suggest a simple yet strong diffusion planning baseline that achieves state-of-the-art results on standard offline RL benchmarks.

cs.LG↗

arXiv2025

Integral formulas and Teodorescu transform for generalized partial-slice monogenic functions

The theory of generalized partial-slice monogenic functions is considered as a syhthesis of the classical Clifford analysis and the theory of slice monogenic functions. In this paper, we investigate the Cauchy integral formula and the Plemelj formula for generalized partial-slice monogenic functions. Further, we study some properties of the Teodorescu transform in this context. A norm estimation for the Teodorescu transform is discussed as well.

math.CV↗

arXiv2025

Habitizing Diffusion Planning for Efficient and Effective Decision Making

Diffusion models have shown great promise in decision-making, also known as diffusion planning. However, the slow inference speeds limit their potential for broader real-world applications. Here, we introduce Habi, a general framework that transforms powerful but slow diffusion planning models into fast decision-making models, which mimics the cognitive process in the brain that costly goal-directed behavior gradually transitions to efficient habitual behavior with repetitive practice. Even using a laptop CPU, the habitized model can achieve an average 800+ Hz decision-making frequency (faster than previous diffusion planners by orders of magnitude) on standard offline reinforcement learning benchmarks D4RL, while maintaining comparable or even higher performance compared to its corresponding diffusion planner. Our work proposes a fresh perspective of leveraging powerful diffusion models for real-world decision-making tasks. We also provide robust evaluations and analysis, offering insights from both biological and engineering perspectives for efficient and effective decision-making.

cs.LG↗

arXiv2025

Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes grow. Moreover, existing GFMs are constrained by rigid output formats, limiting their applicability to various genomic tasks. In this work, we revisit the transformer-based auto-regressive models and introduce Omni-DNA, a family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. Our approach consists of two stages: (i) pretraining on DNA sequences with next token prediction objective, and (ii) expanding the multi-modal task-specific tokens and finetuning for multiple downstream tasks simultaneously. When evaluated on the Nucleotide Transformer and GB benchmarks, Omni-DNA achieves state-of-the-art performance on 18 out of 26 tasks. Through multi-task finetuning, Omni-DNA addresses 10 acetylation and methylation tasks at once, surpassing models trained on each task individually. Finally, we design two complex genomic tasks, DNA2Function and Needle-in-DNA, which map DNA sequences to textual functional descriptions and images, respectively, indicating Omni-DNA's cross-modal capabilities to broaden the scope of genomic applications. All the models are available through https://huggingface.co/collections/zehui127

q-bio.GN↗

arXiv2025

Revisiting the Graph Reasoning Ability of Large Language Models: Case Studies in Translation, Connectivity and Shortest Path

Large Language Models (LLMs) have achieved great success in various reasoning tasks. In this work, we focus on the graph reasoning ability of LLMs. Although theoretical studies proved that LLMs are capable of handling graph reasoning tasks, empirical evaluations reveal numerous failures. To deepen our understanding on this discrepancy, we revisit the ability of LLMs on three fundamental graph tasks: graph description translation, graph connectivity, and the shortest-path problem. Our findings suggest that LLMs can fail to understand graph structures through text descriptions and exhibit varying performance for all these three fundamental tasks. Meanwhile, we perform a real-world investigation on knowledge graphs and make consistent observations with our findings. The codes and datasets are available.

cs.CL↗

arXiv2024

ALPINE: Unveiling the Planning Capability of Autoregressive Learning in Language Models

Planning is a crucial element of both human intelligence and contemporary large language models (LLMs). In this paper, we initiate a theoretical investigation into the emergence of planning capabilities in Transformer-based LLMs via their next-word prediction mechanisms. We model planning as a network path-finding task, where the objective is to generate a valid path from a specified source node to a designated target node. Our mathematical characterization shows that Transformer architectures can execute path-finding by embedding the adjacency and reachability matrices within their weights. Furthermore, our theoretical analysis of gradient-based learning dynamics reveals that LLMs can learn both the adjacency and a limited form of the reachability matrices. These theoretical insights are then validated through experiments, which demonstrate that Transformer architectures indeed learn the adjacency and an incomplete reachability matrices, consistent with our theoretical predictions. When applying our methodology to the real-world planning benchmark Blocksworld, our observations remain consistent. Additionally, our analyses uncover a fundamental limitation of current Transformer architectures in path-finding: these architectures cannot identify reachability relationships through transitivity, which leads to failures in generating paths when concatenation is required. These findings provide new insights into how the internal mechanisms of autoregressive learning facilitate intelligent planning and deepen our understanding of how future LLMs might achieve more advanced and general planning-and-reasoning capabilities across diverse applications.

cs.LG↗

arXiv2024

Can Graph Learning Improve Planning in LLM-based Agents?

Task planning in language agents is emerging as an important research topic alongside the development of large language models (LLMs). It aims to break down complex user requests in natural language into solvable sub-tasks, thereby fulfilling the original requests. In this context, the sub-tasks can be naturally viewed as a graph, where the nodes represent the sub-tasks, and the edges denote the dependencies among them. Consequently, task planning is a decision-making problem that involves selecting a connected path or subgraph within the corresponding graph and invoking it. In this paper, we explore graph learning-based methods for task planning, a direction that is orthogonal to the prevalent focus on prompt design. Our interest in graph learning stems from a theoretical discovery: the biases of attention and auto-regressive loss impede LLMs' ability to effectively navigate decision-making on graphs, which is adeptly addressed by graph neural networks (GNNs). This theoretical insight led us to integrate GNNs with LLMs to enhance overall performance. Extensive experiments demonstrate that GNN-based methods surpass existing solutions even without training, and minimal training can further enhance their performance. The performance gain increases with a larger task graph size.

cs.LG↗