arXiv subjects

Jiarui Zhu

Publications and source records attributed to Jiarui Zhu.

6 recordsLinked to original sources

arXiv2026

Large-scale EM Benchmark for Multi-Organelle Instance Segmentation in the Wild

Accurate instance-level segmentation of organelles in electron microscopy (EM) is critical for quantitative analysis of subcellular morphology and inter-organelle interactions. However, current benchmarks, based on small, curated datasets, fail to capture the inherent heterogeneity and large spatial context of in-the-wild EM data, imposing fundamental limitations on current patch-based methods. To address these limitations, we developed a large-scale, multi-source benchmark for multi-organelle instance segmentation, comprising over 100,000 2D EM images across variety cell types and five organelle classes that capture real-world variability. Dataset annotations were generated by our designed connectivity-aware Label Propagation Algorithm (3D LPA) with expert refinement. We further benchmarked several state-of-the-art models, including U-Net, SAM variants, and Mask2Former. Our results show several limitations: current models struggle to generalize across heterogeneous EM data and perform poorly on organelles with global, distributed morphologies (e.g., Endoplasmic Reticulum). These findings underscore the fundamental mismatch between local-context models and the challenge of modeling long-range structural continuity in the presence of real-world variability. The benchmark dataset and labeling tool will be publicly released soon.

cs.CV↗

arXiv2026

AutoBinder Agent: An MCP-Based Agent for End-to-End Protein Binder Design

Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration overhead. We present an agentic end-to-end drug design framework that leverages a Large Language Model (LLM) in conjunction with the Model Context Protocol (MCP) to dynamically coordinate access to biochemical databases, modular toolchains, and task-specific AI models. The system integrates four state-of-the-art components: MaSIF (MaSIF-site and MaSIF-seed-search) for geometric deep learning-based identification of protein-protein interaction (PPI) sites, Rosetta for grafting protein fragments onto protein backbones to form mini proteins, ProteinMPNN for amino acid sequences redesign, and AlphaFold3 for near-experimental accuracy in complex structure prediction. Starting from a target structure, the framework supports de novo binder generation via surface analysis, scaffold grafting and pose construction, sequence optimization, and structure prediction. Additionally, by replacing rigid, script-based workflows with a protocol-driven, LLM-coordinated architecture, the framework improves reproducibility, reduces manual overhead, and ensures extensibility, portability, and auditability across the entire drug design process.

q-bio.BM↗

arXiv2026

RFAssigner: A Generic Label Assignment Strategy for Dense Object Detection

Label assignment is a critical component in training dense object detectors. State-of-the-art methods typically assign each training sample a positive and a negative weight, optimizing the assignment scheme during training. However, these strategies often assign an insufficient number of positive samples to small objects, leading to a scale imbalance during training. To address this limitation, we introduce RFAssigner, a novel assignment strategy designed to enhance the multi-scale learning capabilities of dense detectors. RFAssigner first establishes an initial set of positive samples using a point-based prior. It then leverages a Gaussian Receptive Field (GRF) distance to measure the similarity between the GRFs of unassigned candidate locations and the ground-truth objects. Based on this metric, RFAssigner adaptively selects supplementary positive samples from the unassigned pool, promoting a more balanced learning process across object scales. Comprehensive experiments on three datasets with distinct object scale distributions validate the effectiveness and generalizability of our method. Notably, a single FCOS-ResNet-50 detector equipped with RFAssigner achieves state-of-the-art performance across all object scales, consistently outperforming existing strategies without requiring auxiliary modules or heuristics.

cs.CV↗

arXiv2025

Cross-Modal Causal Intervention for Medical Report Generation

Radiology Report Generation (RRG) is essential for computer-aided diagnosis and medication guidance, which can relieve the heavy burden of radiologists by automatically generating the corresponding radiology reports according to the given radiology image. However, generating accurate lesion descriptions remains challenging due to spurious correlations from visual-linguistic biases and inherent limitations of radiological imaging, such as low resolution and noise interference. To address these issues, we propose a two-stage framework named CrossModal Causal Representation Learning (CMCRL), consisting of the Radiological Cross-modal Alignment and Reconstruction Enhanced (RadCARE) pre-training and the Visual-Linguistic Causal Intervention (VLCI) fine-tuning. In the pre-training stage, RadCARE introduces a degradation-aware masked image restoration strategy tailored for radiological images, which reconstructs high-resolution patches from low-resolution inputs to mitigate noise and detail loss. Combined with a multiway architecture and four adaptive training strategies (e.g., text postfix generation with degraded images and text prefixes), RadCARE establishes robust cross-modal correlations even with incomplete data. In the VLCI phase, we deploy causal front-door intervention through two modules: the Visual Deconfounding Module (VDM) disentangles local-global features without fine-grained annotations, while the Linguistic Deconfounding Module (LDM) eliminates context bias without external terminology databases. Experiments on IU-Xray and MIMIC-CXR show that our CMCRL pipeline significantly outperforms state-of-the-art methods, with ablation studies confirming the necessity of both stages. Code and models are available at https://github.com/WissingChen/CMCRL.

cs.CV↗

arXiv2025

LD4MRec: Simplifying and Powering Diffusion Model for Multimedia Recommendation

Multimedia recommendation aims to predict users' future behaviors based on observed behaviors and item content information. However, the inherent noise contained in observed behaviors easily leads to suboptimal recommendation performance. Recently, the diffusion model's ability to generate information from noise presents a promising solution to this issue, prompting us to explore its application in multimedia recommendation. Nonetheless, several challenges must be addressed: 1) The diffusion model requires simplification to meet the efficiency requirements of real-time recommender systems, 2) The generated behaviors must align with user preference. To address these challenges, we propose a Light Diffusion model for Multimedia Recommendation (LD4MRec). LD4MRec largely reduces computational complexity by employing a forward-free inference strategy, which directly predicts future behaviors from observed noisy behaviors. Meanwhile, to ensure the alignment between generated behaviors and user preference, we propose a novel Conditional neural Network (C-Net). C-Net achieves guided generation by leveraging two key signals, collaborative signals and personalized modality preference signals, thereby improving the semantic consistency between generated behaviors and user preference. Experiments conducted on three real-world datasets demonstrate the effectiveness of LD4MRec.

cs.IR↗

arXiv2023

Feature-oriented Deep Learning Framework for Pulmonary Cone-beam CT (CBCT) Enhancement with Multi-task Customized Perceptual Loss

Cone-beam computed tomography (CBCT) is routinely collected during image-guided radiation therapy (IGRT) to provide updated patient anatomy information for cancer treatments. However, CBCT images often suffer from streaking artifacts and noise caused by under-rate sampling projections and low-dose exposure, resulting in low clarity and information loss. While recent deep learning-based CBCT enhancement methods have shown promising results in suppressing artifacts, they have limited performance on preserving anatomical details since conventional pixel-to-pixel loss functions are incapable of describing detailed anatomy. To address this issue, we propose a novel feature-oriented deep learning framework that translates low-quality CBCT images into high-quality CT-like imaging via a multi-task customized feature-to-feature perceptual loss function. The framework comprises two main components: a multi-task learning feature-selection network(MTFS-Net) for customizing the perceptual loss function; and a CBCT-to-CT translation network guided by feature-to-feature perceptual loss, which uses advanced generative models such as U-Net, GAN and CycleGAN. Our experiments showed that the proposed framework can generate synthesized CT (sCT) images for the lung that achieved a high similarity to CT images, with an average SSIM index of 0.9869 and an average PSNR index of 39.9621. The sCT images also achieved visually pleasing performance with effective artifacts suppression, noise reduction, and distinctive anatomical details preservation. Our experiment results indicate that the proposed framework outperforms the state-of-the-art models for pulmonary CBCT enhancement. This framework holds great promise for generating high-quality anatomical imaging from CBCT that is suitable for various clinical applications.

cs.CV↗