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Yanshuo Chen

Publications and source records attributed to Yanshuo Chen.

12 recordsLinked to original sources
arXiv2026

Scale as a Modality: Multi-Scale Pixel-Space Diffusion Transformers

Latent diffusion models rely on pretrained autoencoders that introduce lossy compression and constrain spatial granularity. Pixel-space diffusion avoids this bottleneck and enables flexible tokenization at multiple spatial scales, yet existing approaches largely adopt two-level coarse-to-fine architectures with limited cross-scale interaction. We introduce MS-pDiT, a multi-scale pixel-space diffusion transformer that treats spatial scale as a modality. MS-pDiT tokenizes the same noisy image at multiple patch sizes, processes each scale in a dedicated transformer stream, and enables bidirectional information exchange through compacted MM-DiT-style joint attention, with attention cost independent of the finest patch size. This design establishes the number of scales as a new architectural scaling dimension. On ImageNet $256\times256$, increasing the number of scales from two to five consistently improves FID from 4.39 to 2.31, 2.26, and 2.19, while adding an intermediate scale substantially outperforms increasing depth under comparable parameter budgets. Further analysis highlights the importance of bidirectional cross-scale interaction and late introduction of fine-grained streams. MS-pDiT achieves FID scores of 1.43 and 1.44 on ImageNet $256\times256$ and $512\times512$, respectively, and naturally extends to text-to-image generation, achieving 0.86 on GenEval and 83.9 on DPG-Bench.

cs.CV↗
arXiv2026

Grounding Multimodal Reasoning with Evidence-Ablated Negatives

Reinforcement learning with verifiable rewards (RLVR) has become a powerful tool for improving multimodal reasoning. However, standard outcome supervision suffers from credit assignment ambiguity, as a model may receive positive rewards by exploiting language priors or dataset shortcuts rather than grounding its reasoning in the requisite visual evidence. This makes high-quality negative responses critical, since effective negatives should remain plausible under the current policy while exposing the shortcut that should be suppressed. In this paper, we propose EVAN, a multimodal reinforcement learning framework utilizing EVidence-Ablated Negatives to train LMMs against their own language-prior failures. EVAN first identifies highly visually dependent examples using a scaled image information gain metric and preserves data diversity with a mixed-ranking strategy. It then constructs evidence-ablated images by masking the most discriminative image patches, eliciting plausible but visually ungrounded responses from the current policy. During policy optimization, these negative responses are incorporated as bounded auxiliary signals under the clean image, penalizing shortcut learning while maintaining RL stability. Experiments across challenging multimodal reasoning benchmarks demonstrate that EVAN mitigates modality imbalance and improves over strong RLVR baselines. Our code is available at https://github.com/DawnLIU35/EVAN.git.

cs.CL↗
arXiv2026

MPQ: A Message-Passing View of Post-Training Quantization

Post-training quantization (PTQ) is a key technique for efficiently deploying large language models, as it compresses weights into low-bit representations without retraining. Existing PTQ solvers, including GPTQ, LDLQ, and block coordinate descent, commit each weight block to a single codeword before its neighbors are considered, leaving near-optimal alternatives unexplored. In this work, we cast row-wise PTQ as posterior inference over discrete codebooks, in which existing solvers correspond to a zero-temperature, hard-decision limit retaining only the top codeword per block. We propose Message-Passing Quantization (MPQ), which preserves soft posterior information across blocks during inference and commits to hard codewords only at the output stage. MPQ first uses vector approximate message passing to compute approximate blockwise posteriors, then refines a hard-decision initialization by exact block coordinate descent. Across 2-bit lattice and 3- and 4-bit scalar quantization on dense language models from Llama, Qwen, and Mistral families, MPQ improves perplexity and zero-shot accuracy over strong hard-decision baselines, and composes favorably with preprocessing techniques such as activation-aware scaling and incoherence processing. Our implementation is available at https://github.com/poseidonchan/MPQ.

cs.AI↗
arXiv2026

CloneOT: predicting clone-specific perturbation responses with lineage-supervised neural inverse optimal transport

Predicting single-cell perturbation responses requires mapping between two unpaired populations of cells measured before and after the perturbation. Optimal transport (OT) provides a principled framework for constructing such mappings by minimizing the transport cost, and neural OT methods (\textit{e.g.}, CellOT) have been employed for this prediction task. However, these methods rely on a fixed transport cost, typically the squared Euclidean distance. This cost may connect cells with the wrong responses. Lineage tracing provides the information needed to learn the cost, as heritable barcodes link the cells of the same clone before and after the perturbation. Here, we propose \CloneOT, a neural inverse OT method that learns both the transport cost and the transport map from partially lineage-traced single-cell datasets. \CloneOT\ represents the cost as a neural network. It learns the cost by minimizing the extra cost that the lineage adds to the optimal transport, so that the cheapest transport keeps the cells of each clone together. Our experiments demonstrate that \CloneOT\ recovers the correct transport on 2D datasets, while the squared Euclidean cost fails. Moreover, \CloneOT\ outperforms five baselines on 14 lineage-tracing perturbation scenarios of cancer cells, for both seen and unseen clones. Furthermore, we show that \CloneOT\ reveals the clone-specific transcriptional programs of drug-tolerant persister cells and forecasts the fate of each clone from its cells before treatment. Our implementation is available at https://github.com/poseidonchan/CloneOT.

q-bio.GN↗
arXiv2026

Learning from Self-Debate: Preparing Reasoning Models for Multi-Agent Debate

The reasoning abilities of large language models (LLMs) have been substantially improved by reinforcement learning with verifiable rewards (RLVR). At test time, collaborative reasoning through Multi-Agent Debate (MAD) has emerged as a promising approach for enhancing LLM performance. However, current RLVR methods typically train LLMs to solve problems in isolation, without explicitly preparing them to synthesize and benefit from different rationales that arise during debate. In this work, we propose Self-Debate Reinforcement Learning(SDRL), a training framework where models learn from self-debate, equipping a single LLM with both strong standalone problem-solving ability and the capability to process diverse reasoning trajectories in MAD. Given a prompt, SDRL first samples multiple candidate solutions, then constructs a debate context with diverse reasoning paths and generates second-turn responses conditioned on this context. Finally, SDRL jointly optimizes both the initial and debate-conditioned responses, yielding a model that is effective as both a standalone solver and a debate participant. Experiments across multiple base models and reasoning benchmarks show that SDRL consistently improves MAD performance across diverse debate protocols and agent configurations, while simultaneously strengthening single-model reasoning.

cs.CL↗
arXiv2026

Multi-Crit: Benchmarking Multimodal Judges on Pluralistic Criteria-Following

Large multimodal models (LMMs) are increasingly adopted as judges in multimodal evaluation systems due to their strong instruction following and consistency with human preferences. However, their ability to follow diverse, fine-grained evaluation criteria remains underexplored. We develop Multi-Crit, a benchmark for evaluating multimodal judges on their capacity to follow pluralistic criteria and produce reliable criterion-level judgments. Covering both open-ended generation and verifiable reasoning tasks, Multi-Crit is built through a rigorous data curation pipeline that gathers challenging response pairs with multi-criterion human annotations. It further introduces three novel metrics for systematically assessing pluralistic adherence, criterion-switching flexibility, and the ability to recognize criterion-level preference conflicts. Comprehensive analysis of 25 LMMs reveals that 1) proprietary models still struggle to maintain consistent adherence to pluralistic criteria--especially in open-ended evaluation; 2) open-source models lag further behind in flexibly following diverse criteria; and 3) critic fine-tuning with holistic judgment signals enhances visual grounding but fails to generalize to pluralistic criterion-level judgment. Additional analyses on reasoning fine-tuning, test-time scaling, and boundary consistency between open-source and proprietary models further probe the limits of current multimodal judges. As a pioneering study, Multi-Crit lays the foundation for building reliable and steerable multimodal AI evaluation.

cs.CV↗
arXiv2025

Modality-Balancing Preference Optimization of Large Multimodal Models by Adversarial Negative Mining

The task adaptation and alignment of Large Multimodal Models (LMMs) have been significantly advanced by instruction tuning and further strengthened by recent preference optimization. Yet, most LMMs still suffer from severe modality imbalance during reasoning, i.e., outweighing language prior biases over visual inputs, which bottlenecks their generalization to downstream tasks and causes hallucinations. However, existing preference optimization approaches for LMMs do not focus on restraining the internal biases of their Large Language Model (LLM) backbones when curating the training data. Moreover, they heavily rely on offline data and lack the capacity to explore diverse responses adaptive to dynamic distributional shifts during training. Meanwhile, Group Relative Policy Optimization (GRPO), a recent method using online-generated data and verified rewards to improve reasoning capabilities, remains largely underexplored in LMM alignment. In this paper, we propose a novel preference learning framework, Modality-Balancing Preference Optimization (MBPO), to address the modality imbalance in LMMs. MBPO constructs a more effective offline preference dataset by generating hard negatives, i.e., rejected responses misled by LLM biases due to limited usage of visual information, through adversarial perturbation of input images. Moreover, MBPO leverages the easy-to-verify nature of close-ended tasks to generate online responses with verified rewards. GRPO is then employed to train the model with offline-online hybrid data. Extensive experiments demonstrate that MBPO can enhance LMM performance on challenging vision-language tasks and effectively reduce hallucinations.

cs.LG↗
arXiv2025

Towards Copyright Protection for Knowledge Bases of Retrieval-augmented Language Models via Reasoning

Large language models (LLMs) are increasingly integrated into real-world personalized applications through retrieval-augmented generation (RAG) mechanisms to supplement their responses with domain-specific knowledge. However, the valuable and often proprietary nature of the knowledge bases used in RAG introduces the risk of unauthorized usage by adversaries. Existing methods that can be generalized as watermarking techniques to protect these knowledge bases typically involve poisoning or backdoor attacks. However, these methods require altering the LLM's results of verification samples, inevitably making these watermarks susceptible to anomaly detection and even introducing new security risks. To address these challenges, we propose \name{} for `harmless' copyright protection of knowledge bases. Instead of manipulating LLM's final output, \name{} implants distinct yet benign verification behaviors in the space of chain-of-thought (CoT) reasoning, maintaining the correctness of the final answer. Our method has three main stages: (1) Generating CoTs: For each verification question, we generate two `innocent' CoTs, including a target CoT for building watermark behaviors; (2) Optimizing Watermark Phrases and Target CoTs: Inspired by our theoretical analysis, we optimize them to minimize retrieval errors under the \emph{black-box} and \emph{text-only} setting of suspicious LLM, ensuring that only watermarked verification queries can retrieve their correspondingly target CoTs contained in the knowledge base; (3) Ownership Verification: We exploit a pairwise Wilcoxon test to verify whether a suspicious LLM is augmented with the protected knowledge base by comparing its responses to watermarked and benign verification queries. Our experiments on diverse benchmarks demonstrate that \name{} effectively protects knowledge bases and its resistance to adaptive attacks.

cs.CR↗
arXiv2025

Fast and scalable Wasserstein-1 neural optimal transport solver for single-cell perturbation prediction

\textbf{Motivation:} Predicting single-cell perturbation responses requires mapping between two unpaired single-cell data distributions. Optimal transport (OT) theory provides a principled framework for constructing such mappings by minimizing transport cost. Recently, Wasserstein-2 ($W_2$) neural optimal transport solvers (\textit{e.g.}, CellOT) have been employed for this prediction task. However, $W_2$ OT relies on the general Kantorovich dual formulation, which involves optimizing over two conjugate functions, leading to a complex min-max optimization problem that converges slowly. \\ \textbf{Results:} To address these challenges, we propose a novel solver based on the Wasserstein-1 ($W_1$) dual formulation. Unlike $W_2$, the $W_1$ dual simplifies the optimization to a maximization problem over a single 1-Lipschitz function, thus eliminating the need for time-consuming min-max optimization. While solving the $W_1$ dual only reveals the transport direction and does not directly provide a unique optimal transport map, we incorporate an additional step using adversarial training to determine an appropriate transport step size, effectively recovering the transport map. Our experiments demonstrate that the proposed $W_1$ neural optimal transport solver can mimic the $W_2$ OT solvers in finding a unique and ``monotonic" map on 2D datasets. Moreover, the $W_1$ OT solver achieves performance on par with or surpasses $W_2$ OT solvers on real single-cell perturbation datasets. Furthermore, we show that $W_1$ OT solver achieves $25 \sim 45\times$ speedup, scales better on high dimensional transportation task, and can be directly applied on single-cell RNA-seq dataset with highly variable genes. \\ \textbf{Availability and Implementation:} Our implementation and experiments are open-sourced at https://github.com/poseidonchan/w1ot.

cs.LG↗
arXiv2024

A Watermark for Order-Agnostic Language Models

Statistical watermarking techniques are well-established for sequentially decoded language models (LMs). However, these techniques cannot be directly applied to order-agnostic LMs, as the tokens in order-agnostic LMs are not generated sequentially. In this work, we introduce Pattern-mark, a pattern-based watermarking framework specifically designed for order-agnostic LMs. We develop a Markov-chain-based watermark generator that produces watermark key sequences with high-frequency key patterns. Correspondingly, we propose a statistical pattern-based detection algorithm that recovers the key sequence during detection and conducts statistical tests based on the count of high-frequency patterns. Our extensive evaluations on order-agnostic LMs, such as ProteinMPNN and CMLM, demonstrate Pattern-mark's enhanced detection efficiency, generation quality, and robustness, positioning it as a superior watermarking technique for order-agnostic LMs.

cs.CL↗
arXiv2024

Distortion-free Watermarks are not Truly Distortion-free under Watermark Key Collisions

Language model (LM) watermarking techniques inject a statistical signal into LM-generated content by substituting the random sampling process with pseudo-random sampling, using watermark keys as the random seed. Among these statistical watermarking approaches, distortion-free watermarks are particularly crucial because they embed watermarks into LM-generated content without compromising generation quality. However, one notable limitation of pseudo-random sampling compared to true-random sampling is that, under the same watermark keys (i.e., key collision), the results of pseudo-random sampling exhibit correlations. This limitation could potentially undermine the distortion-free property. Our studies reveal that key collisions are inevitable due to the limited availability of watermark keys, and existing distortion-free watermarks exhibit a significant distribution bias toward the original LM distribution in the presence of key collisions. Moreover, achieving a perfect distortion-free watermark is impossible as no statistical signal can be embedded under key collisions. To reduce the distribution bias caused by key collisions, we introduce a new family of distortion-free watermarks--beta-watermark. Experimental results support that the beta-watermark can effectively reduce the distribution bias under key collisions.

cs.CR↗