arXiv subjects

Yiming Qin

Publications and source records attributed to Yiming Qin.

15 recordsLinked to original sources

arXiv2026

DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Models

Designing small molecule ligands that bind with high affinity to specific protein pockets is a fundamental goal in drug discovery, as small molecules constitute a major fraction of approved therapeutics. Recent breakthroughs in structure prediction, such as AlphaFold-3 and Boltz-2, enable accurate biomolecular interaction prediction and show promise as foundation models for downstream tasks, including binding affinity prediction. We propose to leverage these models and introduce DBMol, a new structure predictor-guided framework for de novo small molecule design. DBMol formulates an alternating optimization and projection process. In the optimization stage, DBMol starts from an initial molecule and uses gradient-based optimization to improve pocket-specific interactions and predicted binding affinity using a structure prediction model. In the projection stage, a flow-matching model maps the optimized molecular graph to discrete and chemically valid molecules. Experiments show that DBMol effectively optimizes the Boltz-2 affinity proxy and generates molecules with strong predicted affinity and specificity under Boltz-2 evaluation. To reduce self-confirmation bias, we further evaluate generated molecules using held-out metrics, including AF3-based evaluation. DBMol substantially improves pocket coverage while maintaining molecular diversity over unconditional generation, and is competitive under held-out metrics despite the absence of reference-ligand supervision. These results support the promise of structure prediction models as effective optimization signals for de novo molecular design.

cs.LG↗

arXiv2026

DiPhon: Diffusion on Graphons for Scalable Graph Generation

Diffusion models represent a leading paradigm for graph generation, with notable impact in domains such as molecular design. Yet, scaling these models to large graphs remains an open problem. We approach this question in the dense-graph setting through the lens of graphons, the size-agnostic limit objects of dense graph sequences, to study how structural graph statistics behave across node-size scales. This perspective leads to DiPhon, a diffusion framework for size-scalable graph generation. Specifically, we formulate a continuous diffusion process on the graphon space via a Jacobi stochastic differential equation (SDE), and propose DiPhon, a discretized graph-level process that mimics these dynamics on finite graphs. We further derive the corresponding reverse-time process, which requires access to the marginal score. For the Jacobi process, this score interestingly admits a tractable form, which we estimate from data via graph denoising and plug into the reverse process to generate graph samples. We prove that DiPhon matches exactly the first moment of the marginal distributions induced by the continuous graphon process, and approximates the second moment up to a closed-form discrepancy. Thus, DiPhon inherits key size-agnostic statistical properties of the graphon dynamics, providing a principled route toward scalable graph generation. Empirically, we demonstrate this scalability by training on small graphs and generating progressively larger graphs at inference time, without retraining, while preserving their core topological properties.

stat.ML↗

arXiv2026

Ghosts Beneath Textures: Texture-Relation Cues for Cross-Paradigm AI-Generated Image Detection

AI-generated images have proliferated rapidly, motivating extensive research. Most existing AI-generated image detectors are developed and evaluated under image-free generation paradigms, such as noise-based or text-guided generation. However, image-conditioned generation has become increasingly important in practical applications, as it enables more fine-grained control over generated content. Detecting AI-generated images across these two paradigms creates a critical cross-paradigm detection problem that has long been overlooked. To study this problem, we construct ConImageGen, a benchmark for cross-paradigm AI-generated image detection. Evaluations on ConImageGen show that existing detectors fail to generalize reliably across image-free and image-conditioned generation. To address this failure, this paper identifies a cross-paradigm forensic cue and provides a new perspective for generalized AI-generated image detection. Specifically, by suppressing semantic interference, we visualize, for the first time, semantics-irrelevant texture patterns across generation paradigms. These patterns exhibit structured local-global texture relations, indicating a generalizable form of forensic evidence. Motivated by this finding, we shift the focus from directly exploiting explicit artifacts to modeling texture relations and propose DTS-Det, a detection framework that captures and leverages such relations for generalized AI-generated image detection. Extensive experiments validate the effectiveness of our method. DTS-Det achieves state-of-the-art performance across diverse evaluation settings, reaching 99.6% ACC on ConImageGen with a 10.5% gain over the best baseline. It also achieves 93.2%/94.1% ACC in cross-dataset evaluation on PicoBanana/RAID and maintains detection rates of 95.2%/88.1% under reconstruction attacks and black-box adversarial attacks, respectively.

cs.CV↗

arXiv2026

A specialized reasoning large language model for accelerating rare disease diagnosis: a randomized AI physician assistance trial

Rare diseases affect millions of individuals worldwide, yet timely diagnosis remains a major public health challenge due to scarcity of specialized clinical expertise. While large language models (LLMs) show promise to support rare disease diagnosis, current models are constrained by insufficient clinical deployability, limited clinically grounded evidence, and scarcity of training data. Here we present RaDaR (Rare Disease navigatoR), an open-source, compact reasoning LLM (32B parameters) for rare disease diagnosis. RaDaR was trained with 49,170 publicly available free-text cases and 104,666 synthetic cases with reasoning-enhanced training. RaDaR showed the strongest performance among evaluated open-source models, including the 671B DeepSeek-R1, across public benchmarks and four external validation centers. In a retrospective cohort, RaDaR prioritized the final diagnosis before documented clinical suspicion in 61.06 percent of cases, corresponding to a potential lead time of 1.87 months and 50.18 percent of the within-center interval. In a randomized physician-assistance trial, RaDaR assistance improved physicians' rare-disease diagnostic accuracy by 21.44 percentage points compared with internet search alone. Synthetic-data ablations suggested that phenotype-anchored narratives provide useful training signal for long-tail rare diseases, with a monotonic scaling trend within the tested data range. Together, RaDaR and its development and validation framework provide a deployable rare-disease reasoning model and a reproducible development framework for diagnostic AI under data scarcity.

cs.AI↗

arXiv2026

Fixed-Point Masked Generative Modeling

Masked Generative Models (MGMs) enable parallel decoding and achieve strong performance across modalities, but require full-sequence bidirectional transformers at every step, making training costly and degrading quality under low sampling budgets. Existing work improves efficiency via better samplers or cheaper fixed-depth denoisers, but they still allocate a fixed amount of denoiser computation to each refinement step. We introduce Fixed-Point Masked Generative Models (FP-MGMs), which replace part of the denoiser with a fixed-point solver over shared attention layers to enable adaptive depth with fewer parameters. To make it more effective for masked generation, we first introduce a cross-step consistency loss, which aligns hidden representations at neighboring denoising steps and, second, three-state reuse (3SR) which warm-starts the solver using the previous solution by treating differently unchanged, still-masked, and newly revealed tokens respectively. Together, these components define our complete training-to-inference framework for fixed-point masked generation, \emph{CoFRe}. We also show that pre-trained MGMs can be converted into FP-MGMs with short fine-tuning, avoiding full retraining. Across modalities, CoFRe improves the quality and cost trade-off. On OpenWebText, CoFRe reduces parameters by 38.8\%, training time by 11.5\%, and VRAM by 16.9\%, while improving generative perplexity from 830.8 to 101.8 at a budget of $96$ transformer-block forward passes, compared to MDLM. In ImageNette, CoFRe reduces training time by 48.6\% and VRAM by 50.7\%, while improving FID in all sample budgets tested. Overall, CoFRe offers a practical framework for cheaper training and stronger low-budget masked generation.

cs.LG↗

arXiv2026

PromptForge-350k: A Large-Scale Dataset and Contrastive Framework for Prompt-Based AI Image Forgery Localization

The rapid democratization of prompt-based AI image editing has recently exacerbated the risks associated with malicious content fabrication and misinformation. However, forgery localization methods targeting these emerging editing techniques remain significantly under-explored. To bridge this gap, we first introduce a fully automated mask annotating framework that leverages keypoint alignment and semantic space similarity to generate precise ground-truth masks for edited regions. Based on this framework, we construct PromptForge-350k, a large-scale forgery localization dataset covering four state-of-the-art prompt-based AI image editing models, thereby mitigating the data scarcity in this domain. Furthermore, we propose ICL-Net, an effective forgery localization network featuring a triple-stream backbone and intra-image contrastive learning. This design enables the model to capture highly robust and generalizable forensic features. Extensive experiments demonstrate that our method achieves an IoU of 62.5% on PromptForge-350k, outperforming SOTA methods by 5.1%. Additionally, it exhibits strong robustness against common degradations with an IoU drop of less than 1%, and shows promising generalization capabilities on unseen editing models, achieving an average IoU of 41.5%.

cs.CV↗

arXiv2026

Balancing Symmetry and Efficiency in Graph Flow Matching

Equivariance is central to graph generative models, as it ensures the model respects the permutation symmetry of graphs. However, strict equivariance can increase computational cost due to added architectural constraints, and can slow down convergence because the model must be consistent across a large space of possible node permutations. We study this trade-off for graph generative models. Specifically, we start from an equivariant discrete flow-matching model, and relax its equivariance during training via a controllable symmetry modulation scheme based on sinusoidal positional encodings and node permutations. Experiments first show that symmetry-breaking can accelerate early training by providing an easier learning signal, but at the expense of encouraging shortcut solutions that can cause overfitting, where the model repeatedly generates graphs that are duplicates of the training set. On the contrary, properly modulating the symmetry signal can delay overfitting while accelerating convergence, allowing the model to reach stronger performance with $19\%$ of the baseline training epochs.

cs.LG↗

arXiv2025

Chain-of-Visual-Thought: Teaching VLMs to See and Think Better with Continuous Visual Tokens

Vision-Language Models (VLMs) excel at reasoning in linguistic space but struggle with perceptual understanding that requires dense visual perception, e.g., spatial reasoning and geometric awareness. This limitation stems from the fact that current VLMs have limited mechanisms to capture dense visual information across spatial dimensions. We introduce Chain-of-Visual-Thought (COVT), a framework that enables VLMs to reason not only in words but also through continuous visual tokens-compact latent representations that encode rich perceptual cues. Within a small budget of roughly 20 tokens, COVT distills knowledge from lightweight vision experts, capturing complementary properties such as 2D appearance, 3D geometry, spatial layout, and edge structure. During training, the VLM with COVT autoregressively predicts these visual tokens to reconstruct dense supervision signals (e.g., depth, segmentation, edges, and DINO features). At inference, the model reasons directly in the continuous visual token space, preserving efficiency while optionally decoding dense predictions for interpretability. Evaluated across more than ten diverse perception benchmarks, including CV-Bench, MMVP, RealWorldQA, MMStar, WorldMedQA, and HRBench, integrating COVT into strong VLMs such as Qwen2.5-VL and LLaVA consistently improves performance by 3% to 16% and demonstrates that compact continuous visual thinking enables more precise, grounded, and interpretable multimodal intelligence.

cs.CV↗

arXiv2025

Generating Directed Graphs with Dual Attention and Asymmetric Encoding

Directed graphs naturally model systems with asymmetric, ordered relationships, essential to applications in biology, transportation, social networks, and visual understanding. Generating such graphs enables tasks such as simulation, data augmentation and novel instance discovery; however, directed graph generation remains underexplored. We identify two key factors limiting progress in this direction: first, modeling edge directionality introduces a substantially larger dependency space, making the underlying distribution harder to learn; second, the absence of standardized benchmarks hinders rigorous evaluation. Addressing the former requires more expressive models that are sensitive to directional topologies. We propose Directo, the first generative model for directed graphs built upon the discrete flow matching framework. Our approach combines: (i) principled positional encodings tailored to asymmetric pairwise relations, (ii) a dual-attention mechanism capturing both incoming and outgoing dependencies, and (iii) a robust, discrete generative framework. To support evaluation, we introduce a benchmark suite covering synthetic and real-world datasets. It shows that our method performs strongly across diverse settings and even competes with specialized models for particular classes, such as directed acyclic graphs. Our results highlight the effectiveness and generality of our approach, establishing a solid foundation for future research in directed graph generation.

cs.LG↗

arXiv2025

MEMOIR: Lifelong Model Editing with Minimal Overwrite and Informed Retention for LLMs

Language models deployed in real-world systems often require post-hoc updates to incorporate new or corrected knowledge. However, editing such models efficiently and reliably-without retraining or forgetting previous information-remains a major challenge. Existing methods for lifelong model editing either compromise generalization, interfere with past edits, or fail to scale to long editing sequences. We propose MEMOIR, a novel scalable framework that injects knowledge through a residual memory, i.e., a dedicated parameter module, while preserving the core capabilities of the pre-trained model. By sparsifying input activations through sample-dependent masks, MEMOIR confines each edit to a distinct subset of the memory parameters, minimizing interference among edits. At inference, it identifies relevant edits by comparing the sparse activation patterns of new queries to those stored during editing. This enables generalization to rephrased queries by activating only the relevant knowledge while suppressing unnecessary memory activation for unrelated prompts. Experiments on question answering, hallucination correction, and out-of-distribution generalization benchmarks for LLaMA-3 and Mistral backbones demonstrate that MEMOIR achieves state-of-the-art performance across reliability, generalization, and locality metrics, scaling to thousands of sequential edits with minimal forgetting.

cs.CL↗

arXiv2025

Apply Hierarchical-Chain-of-Generation to Complex Attributes Text-to-3D Generation

Recent text-to-3D models can render high-quality assets, yet they still stumble on objects with complex attributes. The key obstacles are: (1) existing text-to-3D approaches typically lift text-to-image models to extract semantics via text encoders, while the text encoder exhibits limited comprehension ability for long descriptions, leading to deviated cross-attention focus, subsequently wrong attribute binding in generated results. (2) Occluded object parts demand a disciplined generation order and explicit part disentanglement. Though some works introduce manual efforts to alleviate the above issues, their quality is unstable and highly reliant on manual information. To tackle above problems, we propose a automated method Hierarchical-Chain-of-Generation (HCoG). It leverages a large language model to decompose the long description into blocks representing different object parts, and orders them from inside out according to occlusions, forming a hierarchical chain. Within each block we first coarsely create components, then precisely bind attributes via target-region localization and corresponding 3D Gaussian kernel optimization. Between blocks, we introduce Gaussian Extension and Label Elimination to seamlessly generate new parts by extending new Gaussian kernels, re-assigning semantic labels, and eliminating unnecessary kernels, ensuring that only relevant parts are added without disrupting previously optimized parts. Experiments confirm that HCoG yields structurally coherent, attribute-faithful 3D objects with complex attributes. The code is available at https://github.com/Wakals/GASCOL .

cs.CV↗

arXiv2024

DeFoG: Discrete Flow Matching for Graph Generation

Graph generative models are essential across diverse scientific domains by capturing complex distributions over relational data. Among them, graph diffusion models achieve superior performance but face inefficient sampling and limited flexibility due to the tight coupling between training and sampling stages. We introduce DeFoG, a novel graph generative framework that disentangles sampling from training, enabling a broader design space for more effective and efficient model optimization. DeFoG employs a discrete flow-matching formulation that respects the inherent symmetries of graphs. We theoretically ground this disentangled formulation by explicitly relating the training loss to the sampling algorithm and showing that DeFoG faithfully replicates the ground truth graph distribution. Building on these foundations, we thoroughly investigate DeFoG's design space and propose novel sampling methods that significantly enhance performance and reduce the required number of refinement steps. Extensive experiments demonstrate state-of-the-art performance across synthetic, molecular, and digital pathology datasets, covering both unconditional and conditional generation settings. It also outperforms most diffusion-based models with just 5-10% of their sampling steps.

cs.LG↗

arXiv2024

Sparse Training of Discrete Diffusion Models for Graph Generation

Generative graph models struggle to scale due to the need to predict the existence or type of edges between all node pairs. To address the resulting quadratic complexity, existing scalable models often impose restrictive assumptions such as a cluster structure within graphs, thus limiting their applicability. To address this, we introduce SparseDiff, a novel diffusion model based on the observation that almost all large graphs are sparse. By selecting a subset of edges, SparseDiff effectively leverages sparse graph representations both during the noising process and within the denoising network, which ensures that space complexity scales linearly with the number of chosen edges. During inference, SparseDiff progressively fills the adjacency matrix with the selected subsets of edges, mirroring the training process. Our model demonstrates state-of-the-art performance across multiple metrics on both small and large datasets, confirming its effectiveness and robustness across varying graph sizes. It also ensures faster convergence, particularly on larger graphs, achieving a fourfold speedup on the large Ego dataset compared to dense models, thereby paving the way for broader applications.

cs.LG↗

arXiv2024

Diff-BGM: A Diffusion Model for Video Background Music Generation

When editing a video, a piece of attractive background music is indispensable. However, video background music generation tasks face several challenges, for example, the lack of suitable training datasets, and the difficulties in flexibly controlling the music generation process and sequentially aligning the video and music. In this work, we first propose a high-quality music-video dataset BGM909 with detailed annotation and shot detection to provide multi-modal information about the video and music. We then present evaluation metrics to assess music quality, including music diversity and alignment between music and video with retrieval precision metrics. Finally, we propose the Diff-BGM framework to automatically generate the background music for a given video, which uses different signals to control different aspects of the music during the generation process, i.e., uses dynamic video features to control music rhythm and semantic features to control the melody and atmosphere. We propose to align the video and music sequentially by introducing a segment-aware cross-attention layer. Experiments verify the effectiveness of our proposed method. The code and models are available at https://github.com/sizhelee/Diff-BGM.

cs.CV↗

arXiv2023

Class-Balancing Diffusion Models

Diffusion-based models have shown the merits of generating high-quality visual data while preserving better diversity in recent studies. However, such observation is only justified with curated data distribution, where the data samples are nicely pre-processed to be uniformly distributed in terms of their labels. In practice, a long-tailed data distribution appears more common and how diffusion models perform on such class-imbalanced data remains unknown. In this work, we first investigate this problem and observe significant degradation in both diversity and fidelity when the diffusion model is trained on datasets with class-imbalanced distributions. Especially in tail classes, the generations largely lose diversity and we observe severe mode-collapse issues. To tackle this problem, we set from the hypothesis that the data distribution is not class-balanced, and propose Class-Balancing Diffusion Models (CBDM) that are trained with a distribution adjustment regularizer as a solution. Experiments show that images generated by CBDM exhibit higher diversity and quality in both quantitative and qualitative ways. Our method benchmarked the generation results on CIFAR100/CIFAR100LT dataset and shows outstanding performance on the downstream recognition task.

cs.CV↗