arXiv subjects

Anran Liu

Publications and source records attributed to Anran Liu.

12 recordsLinked to original sources

arXiv2026

Agents-K1: Towards Agent-native Knowledge Orchestration

Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration. Existing works often reduce papers to abstracts, surface mentions, and flat \texttt{cites} edges, omitting key entities, claims, evidence, mechanisms, and method lineages essential for scientific reasoning. To this end, we introduce \textbf{Agents-K1}, an end-to-end knowledge orchestration pipeline that converts raw documents into agent-native scientific knowledge graphs. Agents-K1 integrates three components under a unifying theoretical foundation: a multimodal parser whose five-module schema captures entities, multimodal evidence, citations, and typed inter-entity relations across the full paper rather than abstracts alone; a 4B information-extraction backbone trained with GRPO under a rule-based reward; and a graphanything CLI, a tri-source agent interface that unifies web search, multimodal graph retrieval, and cross-document traversal. On top of this, we process 2.46 million scientific papers across six subjects to produce \textbf{Scholar-KG}, of which we release a one-million-paper subset, and the full Scholar-KG is accessible via the SCP link below. The same pipeline can be extended to general-domain corpora and to schema-conformant data synthesis. Extensive experiments demonstrate that Agents-K1 achieves superior performance in scientific information extraction, knowledge graph construction, and multi-hop scientific reasoning.

cs.AI↗

arXiv2025

CoFi-Dec: Hallucination-Resistant Decoding via Coarse-to-Fine Generative Feedback in Large Vision-Language Models

Large Vision-Language Models (LVLMs) have achieved impressive progress in multi-modal understanding and generation. However, they still tend to produce hallucinated content that is inconsistent with the visual input, which limits their reliability in real-world applications. We propose \textbf{CoFi-Dec}, a training-free decoding framework that mitigates hallucinations by integrating generative self-feedback with coarse-to-fine visual conditioning. Inspired by the human visual process from global scene perception to detailed inspection, CoFi-Dec first generates two intermediate textual responses conditioned on coarse- and fine-grained views of the original image. These responses are then transformed into synthetic images using a text-to-image model, forming multi-level visual hypotheses that enrich grounding cues. To unify the predictions from these multiple visual conditions, we introduce a Wasserstein-based fusion mechanism that aligns their predictive distributions into a geometrically consistent decoding trajectory. This principled fusion reconciles high-level semantic consistency with fine-grained visual grounding, leading to more robust and faithful outputs. Extensive experiments on six hallucination-focused benchmarks show that CoFi-Dec substantially reduces both entity-level and semantic-level hallucinations, outperforming existing decoding strategies. The framework is model-agnostic, requires no additional training, and can be seamlessly applied to a wide range of LVLMs. The implementation is available at https://github.com/AI-Researcher-Team/CoFi-Dec.

cs.CV↗

arXiv2025

TV-RAG: A Temporal-aware and Semantic Entropy-Weighted Framework for Long Video Retrieval and Understanding

Large Video Language Models (LVLMs) have rapidly emerged as the focus of multimedia AI research. Nonetheless, when confronted with lengthy videos, these models struggle: their temporal windows are narrow, and they fail to notice fine-grained semantic shifts that unfold over extended durations. Moreover, mainstream text-based retrieval pipelines, which rely chiefly on surface-level lexical overlap, ignore the rich temporal interdependence among visual, audio, and subtitle channels. To mitigate these limitations, we propose TV-RAG, a training-free architecture that couples temporal alignment with entropy-guided semantics to improve long-video reasoning. The framework contributes two main mechanisms: \emph{(i)} a time-decay retrieval module that injects explicit temporal offsets into the similarity computation, thereby ranking text queries according to their true multimedia context; and \emph{(ii)} an entropy-weighted key-frame sampler that selects evenly spaced, information-dense frames, reducing redundancy while preserving representativeness. By weaving these temporal and semantic signals together, TV-RAG realises a dual-level reasoning routine that can be grafted onto any LVLM without re-training or fine-tuning. The resulting system offers a lightweight, budget-friendly upgrade path and consistently surpasses most leading baselines across established long-video benchmarks such as Video-MME, MLVU, and LongVideoBench, confirming the effectiveness of our model. The code can be found at https://github.com/AI-Researcher-Team/TV-RAG.

cs.CV↗

arXiv2025

PurifyGen: A Risk-Discrimination and Semantic-Purification Model for Safe Text-to-Image Generation

Recent advances in diffusion models have notably enhanced text-to-image (T2I) generation quality, but they also raise the risk of generating unsafe content. Traditional safety methods like text blacklisting or harmful content classification have significant drawbacks: they can be easily circumvented or require extensive datasets and extra training. To overcome these challenges, we introduce PurifyGen, a novel, training-free approach for safe T2I generation that retains the model's original weights. PurifyGen introduces a dual-stage strategy for prompt purification. First, we evaluate the safety of each token in a prompt by computing its complementary semantic distance, which measures the semantic proximity between the prompt tokens and concept embeddings from predefined toxic and clean lists. This enables fine-grained prompt classification without explicit keyword matching or retraining. Tokens closer to toxic concepts are flagged as risky. Second, for risky prompts, we apply a dual-space transformation: we project toxic-aligned embeddings into the null space of the toxic concept matrix, effectively removing harmful semantic components, and simultaneously align them into the range space of clean concepts. This dual alignment purifies risky prompts by both subtracting unsafe semantics and reinforcing safe ones, while retaining the original intent and coherence. We further define a token-wise strategy to selectively replace only risky token embeddings, ensuring minimal disruption to safe content. PurifyGen offers a plug-and-play solution with theoretical grounding and strong generalization to unseen prompts and models. Extensive testing shows that PurifyGen surpasses current methods in reducing unsafe content across five datasets and competes well with training-dependent approaches. The code can refer to https://github.com/AI-Researcher-Team/PurifyGen.

cs.CV↗

arXiv2025

Disentangled Multi-modal Learning of Histology and Transcriptomics for Cancer Characterization

Histopathology remains the gold standard for cancer diagnosis and prognosis. With the advent of transcriptome profiling, multi-modal learning combining transcriptomics with histology offers more comprehensive information. However, existing multi-modal approaches are challenged by intrinsic multi-modal heterogeneity, insufficient multi-scale integration, and reliance on paired data, restricting clinical applicability. To address these challenges, we propose a disentangled multi-modal framework with four contributions: 1) To mitigate multi-modal heterogeneity, we decompose WSIs and transcriptomes into tumor and microenvironment subspaces using a disentangled multi-modal fusion module, and introduce a confidence-guided gradient coordination strategy to balance subspace optimization. 2) To enhance multi-scale integration, we propose an inter-magnification gene-expression consistency strategy that aligns transcriptomic signals across WSI magnifications. 3) To reduce dependency on paired data, we propose a subspace knowledge distillation strategy enabling transcriptome-agnostic inference through a WSI-only student model. 4) To improve inference efficiency, we propose an informative token aggregation module that suppresses WSI redundancy while preserving subspace semantics. Extensive experiments on cancer diagnosis, prognosis, and survival prediction demonstrate our superiority over state-of-the-art methods across multiple settings. Code is available at https://github.com/helenypzhang/Disentangled-Multimodal-Learning.

eess.IV↗

arXiv2025

Score-based Diffusion Model for Unpaired Virtual Histology Staining

Hematoxylin and eosin (H&E) staining visualizes histology but lacks specificity for diagnostic markers. Immunohistochemistry (IHC) staining provides protein-targeted staining but is restricted by tissue availability and antibody specificity. Virtual staining, i.e., computationally translating the H&E image to its IHC counterpart while preserving the tissue structure, is promising for efficient IHC generation. Existing virtual staining methods still face key challenges: 1) effective decomposition of staining style and tissue structure, 2) controllable staining process adaptable to diverse tissue and proteins, and 3) rigorous structural consistency modelling to handle the non-pixel-aligned nature of paired H&E and IHC images. This study proposes a mutual-information (MI)-guided score-based diffusion model for unpaired virtual staining. Specifically, we design 1) a global MI-guided energy function that disentangles the tissue structure and staining characteristics across modalities, 2) a novel timestep-customized reverse diffusion process for precise control of the staining intensity and structural reconstruction, and 3) a local MI-driven contrastive learning strategy to ensure the cellular level structural consistency between H&E-IHC images. Extensive experiments demonstrate the our superiority over state-of-the-art approaches, highlighting its biomedical potential. Codes will be open-sourced upon acceptance.

eess.IV↗

arXiv2024

MDDC: An R and Python Package for Adverse Event Identification in Pharmacovigilance Data

The safety of medical products continues to be a significant health concern worldwide. Spontaneous reporting systems (SRS) and pharmacovigilance databases are essential tools for postmarketing surveillance of medical products. Various SRS are employed globally, such as the Food and Drug Administration Adverse Event Reporting System (FAERS), EudraVigilance, and VigiBase. In the pharmacovigilance literature, numerous methods have been proposed to assess product - adverse event pairs for potential signals. In this paper, we introduce an R and Python package that implements a novel pattern discovery method for postmarketing adverse event identification, named Modified Detecting Deviating Cells (MDDC). The package also includes a data generation function that considers adverse events as groups, as well as additional utility functions. We illustrate the usage of the package through the analysis of real datasets derived from the FAERS database.

stat.CO↗

arXiv2024

Part123: Part-aware 3D Reconstruction from a Single-view Image

Recently, the emergence of diffusion models has opened up new opportunities for single-view reconstruction. However, all the existing methods represent the target object as a closed mesh devoid of any structural information, thus neglecting the part-based structure, which is crucial for many downstream applications, of the reconstructed shape. Moreover, the generated meshes usually suffer from large noises, unsmooth surfaces, and blurry textures, making it challenging to obtain satisfactory part segments using 3D segmentation techniques. In this paper, we present Part123, a novel framework for part-aware 3D reconstruction from a single-view image. We first use diffusion models to generate multiview-consistent images from a given image, and then leverage Segment Anything Model (SAM), which demonstrates powerful generalization ability on arbitrary objects, to generate multiview segmentation masks. To effectively incorporate 2D part-based information into 3D reconstruction and handle inconsistency, we introduce contrastive learning into a neural rendering framework to learn a part-aware feature space based on the multiview segmentation masks. A clustering-based algorithm is also developed to automatically derive 3D part segmentation results from the reconstructed models. Experiments show that our method can generate 3D models with high-quality segmented parts on various objects. Compared to existing unstructured reconstruction methods, the part-aware 3D models from our method benefit some important applications, including feature-preserving reconstruction, primitive fitting, and 3D shape editing.

cs.GR↗

arXiv2023

Existence of global solutions to the nonlocal mKdV equation on the line

In this paper, we address the existence of global solutions to the Cauchy problem for the integrable nonlocal modified Korteweg-de vries (nonlocal mKdV) equation with the initial data $u_0 \in H^{3}(\mathbb{R}) \cap H^{1,1}(\mathbb{R}) $ with the $L^1(\mathbb{R})$ small-norm assumption. A Lipschitz $L^2$-bijection map between potential and reflection coefficient is established by using inverse scattering method based on a Riemann-Hilbert problem associated with the Cauchy problem. The map from initial potential to reflection coefficient is obtained in direct scattering transform. The inverse scattering transform goes back to the map from scattering coefficient to potential by applying the reconstruction formula and Cauchy integral operator. The bijective relation naturally yields the existence of a global solutions in a Sobolev space $H^3(\mathbb{R})\cap H^{1,1}(\mathbb{R})$ to the Cauchy problem.

math.AP↗

arXiv2022

Prognostic Significance of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images in Colorectal Cancers

Purpose Tumor-infiltrating lymphocytes (TILs) have significant prognostic values in cancers. However, very few automated, deep-learning-based TIL scoring algorithms have been developed for colorectal cancers (CRC). Methods We developed an automated, multiscale LinkNet workflow for quantifying cellular-level TILs for CRC tumors using H&E-stained images. The predictive performance of the automatic TIL scores (TIL) for disease progression and overall survival was evaluate using two international datasets, including 554 CRC patients from The Cancer Genome Atlas (TCGA) and 1130 CRC patients from Molecular and Cellular Oncology (MCO). Results The LinkNet model provided an outstanding precision (0.9508), recall (0.9185), and overall F1 score (0.9347). Clear dose-response relationships were observed between TILs and risk of disease progression or death decreased in both TCGA and MCO cohorts. Both univariate and multivariate Cox regression analyses for the TCGA data demonstrated that patients with high TILs had significant (approx. 75%) reduction of risk for disease progression. In both MCO and TCGA studies, the TIL-high group was significantly associated with improved overall survival in univariate analysis (30% and 54% reduction in risk, respectively). However, potential confounding was observed in the MCO dataset. The favorable effects of high TILs were consistently observed in different subgroups according to know risk factors. Conclusion A deep-learning workflow for automatic TIL quantification based on LinkNet was successfully developed.

q-bio.QM↗

arXiv2021

Discovering Distinctive "Semantics" in Super-Resolution Networks

Image super-resolution (SR) is a representative low-level vision problem. Although deep SR networks have achieved extraordinary success, we are still unaware of their working mechanisms. Specifically, whether SR networks can learn semantic information, or just perform complex mapping function? What hinders SR networks from generalizing to real-world data? These questions not only raise our curiosity, but also influence SR network development. In this paper, we make the primary attempt to answer the above fundamental questions. After comprehensively analyzing the feature representations (via dimensionality reduction and visualization), we successfully discover the distinctive "semantics" in SR networks, i.e., deep degradation representations (DDR), which relate to image degradation instead of image content. We show that a well-trained deep SR network is naturally a good descriptor of degradation information. Our experiments also reveal two key factors (adversarial learning and global residual) that influence the extraction of such semantics. We further apply DDR in several interesting applications (such as distortion identification, blind SR and generalization evaluation) and achieve promising results, demonstrating the correctness and effectiveness of our findings.

cs.CV↗

arXiv2021

Blind Image Super-Resolution: A Survey and Beyond

Blind image super-resolution (SR), aiming to super-resolve low-resolution images with unknown degradation, has attracted increasing attention due to its significance in promoting real-world applications. Many novel and effective solutions have been proposed recently, especially with the powerful deep learning techniques. Despite years of efforts, it still remains as a challenging research problem. This paper serves as a systematic review on recent progress in blind image SR, and proposes a taxonomy to categorize existing methods into three different classes according to their ways of degradation modelling and the data used for solving the SR model. This taxonomy helps summarize and distinguish among existing methods. We hope to provide insights into current research states, as well as to reveal novel research directions worth exploring. In addition, we make a summary on commonly used datasets and previous competitions related to blind image SR. Last but not least, a comparison among different methods is provided with detailed analysis on their merits and demerits using both synthetic and real testing images.

cs.CV↗