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Oct 16

VTOS: Learning to Orchestrate Vision Tools by Co-Searching Solutions and Observers

Vision foundation tools such as open-vocabulary detectors, segmentation models, and post-processing operators are powerful building blocks for computer vision, but their effectiveness depends heavily on how they are orchestrated: which tools are used, in what order, with what parameters, and under what visual conditions. Existing visual-programming agents typically generate a fixed solution pipeline, making them brittle under dense objects, occlusion, small targets, and domain shift. We introduce VTOS (Vision Tools Orchestration Search), a framework for adaptive visual tool orchestration through joint solution-observer search. VTOS co-searches executable solution programs that compose vision tools such as Grounding DINO, SAM, NMS, and slice-and-detect, together with observer programs that diagnose candidate solutions, identify failure modes, and generate actionable feedback. These observations are accumulated in a shared VisionThoughts knowledge base to guide subsequent search. We evaluate VTOS through two case studies: dense object counting on LVIS-Count and zero-shot plant-disease segmentation on PlantSeg-OOD, which stress different orchestration challenges including threshold calibration, NMS, slicing, mask refinement, and domain generalization. Across both tasks, VTOS outperforms static tool pipelines and agentic visual-programming baselines, specifically in complex settings such as dense, occluded scenes and out-of-distribution segmentation where static pipelines leave measurable headroom, rather than in standard tasks where a single well-calibrated tool already approaches its ceiling.

  • 4 authors
·
Sep 1

Adaptive Slicing-Assisted Hyper Inference for Enhanced Small Object Detection in High-Resolution Imagery

Deep learning-based object detectors have achieved remarkable success across numerous computer vision applications, yet they continue to struggle with small object detection in high-resolution aerial and satellite imagery, where dense object distributions, variable shooting angles, diminutive target sizes, and substantial inter-class variability pose formidable challenges. Existing slicing strategies that partition high-resolution images into manageable patches have demonstrated promising results for enlarging the effective receptive field of small targets; however, their reliance on fixed slice dimensions introduces significant redundant computation, inflating inference cost and undermining detection speed. In this paper, we propose Adaptive Slicing-Assisted Hyper Inference (ASAHI), a novel slicing framework that shifts the paradigm from prescribing a fixed slice size to adaptively determining the optimal number of slices according to image resolution, thereby substantially mitigating redundant computation while preserving beneficial overlap between adjacent patches. ASAHI integrates three synergistic components: (1)an adaptive resolution-aware slicing algorithm that dynamically generates 6 or 12 overlapping patches based on a learned threshold, (2)a slicing-assisted fine-tuning (SAF) strategy that constructs augmented training data comprising both full-resolution and sliced image patches, and (3)a Cluster-DIoU-NMS (CDN) post-processing module that combines the geometric merging efficiency of Cluster-NMS with the center-distance-aware suppression of DIoU-NMS to achieve robust duplicate elimination in crowded scenes. Extensive experiments on VisDrone2019 and xView, demonstrate that ASAHI achieves state-of-the-art performance with 56.8% on VisDrone2019-DET-val and 22.7% on xView-test, while reducing inference time by 20-25% compared to the baseline SAHI method.

  • 3 authors
·
Apr 20

Sort & Slice: A Simple and Superior Alternative to Hash-Based Folding for Extended-Connectivity Fingerprints

Extended-connectivity fingerprints (ECFPs) are a ubiquitous tool in current cheminformatics and molecular machine learning, and one of the most prevalent molecular feature extraction techniques used for chemical prediction. Atom features learned by graph neural networks can be aggregated to compound-level representations using a large spectrum of graph pooling methods; in contrast, sets of detected ECFP substructures are by default transformed into bit vectors using only a simple hash-based folding procedure. We introduce a general mathematical framework for the vectorisation of structural fingerprints via a formal operation called substructure pooling that encompasses hash-based folding, algorithmic substructure-selection, and a wide variety of other potential techniques. We go on to describe Sort & Slice, an easy-to-implement and bit-collision-free alternative to hash-based folding for the pooling of ECFP substructures. Sort & Slice first sorts ECFP substructures according to their relative prevalence in a given set of training compounds and then slices away all but the L most frequent substructures which are subsequently used to generate a binary fingerprint of desired length, L. We computationally compare the performance of hash-based folding, Sort & Slice, and two advanced supervised substructure-selection schemes (filtering and mutual-information maximisation) for ECFP-based molecular property prediction. Our results indicate that, despite its technical simplicity, Sort & Slice robustly (and at times substantially) outperforms traditional hash-based folding as well as the other investigated methods across prediction tasks, data splitting techniques, machine-learning models and ECFP hyperparameters. We thus recommend that Sort & Slice canonically replace hash-based folding as the default substructure-pooling technique to vectorise ECFPs for supervised molecular machine learning.

  • 4 authors
·
Mar 10, 2024

AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing in Computational Pathology

Whole-slide image (WSI) preprocessing, typically comprising tissue detection followed by patch extraction, is foundational to AI-driven computational pathology workflows. This remains a major computational bottleneck as existing tools either rely on inaccurate heuristic thresholding for tissue detection, or adopt AI-based approaches trained on limited-diversity data that operate at the patch level, incurring substantial computational complexity. We present AtlasPatch, an efficient and scalable slide preprocessing framework for accurate tissue detection and high-throughput patch extraction with minimal computational overhead. AtlasPatch's tissue detection module is trained on a heterogeneous and semi-manually annotated dataset of ~30,000 WSI thumbnails, using efficient fine-tuning of the Segment-Anything model. The tool extrapolates tissue masks from thumbnails to full-resolution slides to extract patch coordinates at user-specified magnifications, with options to stream patches directly into common image encoders for embedding or store patch images, all efficiently parallelized across CPUs and GPUs. We assess AtlasPatch across segmentation precision, computational complexity, and downstream multiple-instance learning, matching state-of-the-art performance while operating at a fraction of their computational cost. AtlasPatch is open-source and available at https://github.com/AtlasAnalyticsLab/AtlasPatch.

Beyond Sparse Captions: Aligning Slide-Level Text and Patch-Level Vision in Pathology

Contrastive vision-language (VL) pretraining in computational pathology has generally relied on curated image-caption datasets sourced from social media, educational videos, and research publications. These corpora are sparse relative to the diversity of tissue morphology and difficult to scale further, as pathologists do not routinely produce descriptive captions in clinical practice. We propose to instead leverage slide-level pathology reports which can be generated during routine diagnostic workflows in a scalable manner. A key challenge in this weakly-supervised setting is that pathology reports describe macroscopic, diagnostic findings while patch-level visual features describe microscopic findings. We introduce Locked Image Multiple Instance PreTraining (LIMIT), which addresses this gap by freezing a pretrained vision encoder and fine-tuning only the text encoder: report embeddings serve as cross-attention queries over bags of patch features, producing report-conditioned slide representations optimized via InfoNCE. Using LIMIT, we establish CONCH-Z, which aligns the text encoder of CONCH v1.5 to 335k clinical reports. Evaluated across 22 tasks spanning patch-level classification, tumor detection, and slide-level subtyping, CONCH-Z establishes state-of-the-art zero-shot performance over VL encoders trained on curated caption datasets, while simultaneously closing the gap with slide-level foundation models trained with substantially more parameters and compute. The code and model is available at https://github.com/mahmoodlab/LIMIT.

  • 9 authors
·
Oct 11

PRISM: A Multi-Modal Generative Foundation Model for Slide-Level Histopathology

Foundation models in computational pathology promise to unlock the development of new clinical decision support systems and models for precision medicine. However, there is a mismatch between most clinical analysis, which is defined at the level of one or more whole slide images, and foundation models to date, which process the thousands of image tiles contained in a whole slide image separately. The requirement to train a network to aggregate information across a large number of tiles in multiple whole slide images limits these models' impact. In this work, we present a slide-level foundation model for H&E-stained histopathology, PRISM, that builds on Virchow tile embeddings and leverages clinical report text for pre-training. Using the tile embeddings, PRISM produces slide-level embeddings with the ability to generate clinical reports, resulting in several modes of use. Using text prompts, PRISM achieves zero-shot cancer detection and sub-typing performance approaching and surpassing that of a supervised aggregator model. Using the slide embeddings with linear classifiers, PRISM surpasses supervised aggregator models. Furthermore, we demonstrate that fine-tuning of the PRISM slide encoder yields label-efficient training for biomarker prediction, a task that typically suffers from low availability of training data; an aggregator initialized with PRISM and trained on as little as 10% of the training data can outperform a supervised baseline that uses all of the data.

  • 22 authors
·
May 16, 2024

Symbrain: A large-scale dataset of MRI images for neonatal brain symmetry analysis

This paper presents an annotated dataset of brain MRI images designed to advance the field of brain symmetry study. Magnetic resonance imaging (MRI) has gained interest in analyzing brain symmetry in neonatal infants, and challenges remain due to the vast size differences between fetal and adult brains. Classification methods for brain structural MRI use scales and visual cues to assess hemisphere symmetry, which can help diagnose neonatal patients by comparing hemispheres and anatomical regions of interest in the brain. Using the Developing Human Connectome Project dataset, this work presents a dataset comprising cerebral images extracted as slices across selected portions of interest for clinical evaluation . All the extracted images are annotated with the brain's midline. All the extracted images are annotated with the brain's midline. From the assumption that a decrease in symmetry is directly related to possible clinical pathologies, the dataset can contribute to a more precise diagnosis because it can be used to train deep learning model application in neonatal cerebral MRI anomaly detection from postnatal infant scans thanks to computer vision. Such models learn to identify and classify anomalies by identifying potential asymmetrical patterns in medical MRI images. Furthermore, this dataset can contribute to the research and development of methods using the relative symmetry of the two brain hemispheres for crucial diagnosis and treatment planning.

  • 5 authors
·
Jan 22, 2024

UltraVR: A Diagnostic Ultra-Resolution Image-VQA Benchmark for Evidence-Grounded Reasoning

Vision-language models (VLMs) excel on visual question answering and multimodal reasoning benchmarks. Yet their capability on ultra-resolution images - where critical evidence is tiny, subtle, spatially distant, or distributed - remains unclear. Existing evaluations largely report final-answer accuracy, offering limited insight into whether models acquire and integrate the necessary visual evidence. We introduce UltraVR, a diagnostic benchmark for evidence-grounded visual reasoning over ultra-resolution images. UltraVR spans four high-value scenarios: CCTV surveillance, remote sensing (RS), whole-slide image (WSI) pathology, and industrial anomaly detection (AD). These domains pose complementary challenges: fine-grained object grounding in crowded CCTV scenes, long-range spatial comparison in RS, multi-scale evidence navigation in WSI, and subtle irregularity detection in repetitive industrial layouts. Beyond standard QA triples, each instance includes a structured ground-truth chain of thought with step-level questions, intermediate answers, and reasoning labels. These labels decompose reasoning into evidence grounding, local perception, quantification, evidence integration, and decision inference, enabling process-level diagnosis over black-box scoring. Using UltraVR, we evaluate frontier VLMs and show that current models remain far from reliable on ultra-resolution reasoning. Importantly, the structured annotations allow us to localize failures across the visual-to-decision pipeline: errors concentrate in evidence grounding and local perception, while downstream inference often recovers when intermediate visual facts are supplied. These findings demonstrate UltraVR as a diagnostic testbed for measuring not only whether VLMs answer correctly, but where their ultra-resolution reasoning process breaks.

  • 9 authors
·
Jun 3

PK-YOLO: Pretrained Knowledge Guided YOLO for Brain Tumor Detection in Multiplanar MRI Slices

Brain tumor detection in multiplane Magnetic Resonance Imaging (MRI) slices is a challenging task due to the various appearances and relationships in the structure of the multiplane images. In this paper, we propose a new You Only Look Once (YOLO)-based detection model that incorporates Pretrained Knowledge (PK), called PK-YOLO, to improve the performance for brain tumor detection in multiplane MRI slices. To our best knowledge, PK-YOLO is the first pretrained knowledge guided YOLO-based object detector. The main components of the new method are a pretrained pure lightweight convolutional neural network-based backbone via sparse masked modeling, a YOLO architecture with the pretrained backbone, and a regression loss function for improving small object detection. The pretrained backbone allows for feature transferability of object queries on individual plane MRI slices into the model encoders, and the learned domain knowledge base can improve in-domain detection. The improved loss function can further boost detection performance on small-size brain tumors in multiplanar two-dimensional MRI slices. Experimental results show that the proposed PK-YOLO achieves competitive performance on the multiplanar MRI brain tumor detection datasets compared to state-of-the-art YOLO-like and DETR-like object detectors. The code is available at https://github.com/mkang315/PK-YOLO.

  • 4 authors
·
Oct 29, 2024

MedVista3D: Vision-Language Modeling for Reducing Diagnostic Errors in 3D CT Disease Detection, Understanding and Reporting

Radiologic diagnostic errors-under-reading errors, inattentional blindness, and communication failures-remain prevalent in clinical practice. These issues often stem from missed localized abnormalities, limited global context, and variability in report language. These challenges are amplified in 3D imaging, where clinicians must examine hundreds of slices per scan. Addressing them requires systems with precise localized detection, global volume-level reasoning, and semantically consistent natural language reporting. However, existing 3D vision-language models are unable to meet all three needs jointly, lacking local-global understanding for spatial reasoning and struggling with the variability and noise of uncurated radiology reports. We present MedVista3D, a multi-scale semantic-enriched vision-language pretraining framework for 3D CT analysis. To enable joint disease detection and holistic interpretation, MedVista3D performs local and global image-text alignment for fine-grained representation learning within full-volume context. To address report variability, we apply language model rewrites and introduce a Radiology Semantic Matching Bank for semantics-aware alignment. MedVista3D achieves state-of-the-art performance on zero-shot disease classification, report retrieval, and medical visual question answering, while transferring well to organ segmentation and prognosis prediction. Code and datasets will be released.

  • 6 authors
·
Sep 3, 2025 2

ROADWork: A Dataset and Benchmark for Learning to Recognize, Observe, Analyze and Drive Through Work Zones

Perceiving and autonomously navigating through work zones is a challenging and underexplored problem. Open datasets for this long-tailed scenario are scarce. We propose the ROADWork dataset to learn to recognize, observe, analyze, and drive through work zones. State-of-the-art foundation models fail when applied to work zones. Fine-tuning models on our dataset significantly improves perception and navigation in work zones. With ROADWork dataset, we discover new work zone images with higher precision (+32.5%) at a much higher rate (12.8times) around the world. Open-vocabulary methods fail too, whereas fine-tuned detectors improve performance (+32.2 AP). Vision-Language Models (VLMs) struggle to describe work zones, but fine-tuning substantially improves performance (+36.7 SPICE). Beyond fine-tuning, we show the value of simple techniques. Video label propagation provides additional gains (+2.6 AP) for instance segmentation. While reading work zone signs, composing a detector and text spotter via crop-scaling improves performance +14.2% 1-NED). Composing work zone detections to provide context further reduces hallucinations (+3.9 SPICE) in VLMs. We predict navigational goals and compute drivable paths from work zone videos. Incorporating road work semantics ensures 53.6% goals have angular error (AE) < 0.5 (+9.9 %) and 75.3% pathways have AE < 0.5 (+8.1 %).

  • 10 authors
·
Nov 3, 2025

Toxicity Assessment in Preclinical Histopathology via Class-Aware Mahalanobis Distance for Known and Novel Anomalies

Drug-induced toxicity is a leading cause of preclinical and early-clinical failure, making early detection critical. Histopathology is the gold standard for toxicity assessment but relies on expert pathologists, creating a bottleneck for large-scale screening. We introduce an AI-based anomaly detection framework for whole-slide images (WSIs) of rodent liver that identifies healthy tissue and known pathologies (anomalies) and flags samples without training data as out-of-distribution (OOD). We evaluate OOD detection on two held-out categories: apoptosis (single-cell, near-OOD) and staining/processing artifacts (heterogeneous, far-OOD). We build a novel pixelwise-annotated dataset and fine-tune a pre-trained Vision Transformer (DINOv2) via Low-Rank Adaptation (LoRA) for segmentation, then use the Mahalanobis distance for OOD detection with class-specific thresholds. Optimizing the false positive rate subject to a predefined constraint on the false negative rate yields only 0.16% of pathological tissue classified as healthy and 0.35% of healthy tissue classified as pathological. Our false negative rate does not penalise cross-type errors, reflecting the safety-first objective of never overlooking a lesion; under the stricter correct-class criterion our method assigns 93.93% of ID and 89.38% of OOD findings to their own class. The study demonstrates technical feasibility of pixel-level anomaly detection for mouse liver histopathology, indicating possible applications in improving preclinical workflows and drug development efficiency.

  • 6 authors
·
Jun 29

WeakSTIL: Weak whole-slide image level stromal tumor infiltrating lymphocyte scores are all you need

We present WeakSTIL, an interpretable two-stage weak label deep learning pipeline for scoring the percentage of stromal tumor infiltrating lymphocytes (sTIL%) in H&E-stained whole-slide images (WSIs) of breast cancer tissue. The sTIL% score is a prognostic and predictive biomarker for many solid tumor types. However, due to the high labeling efforts and high intra- and interobserver variability within and between expert annotators, this biomarker is currently not used in routine clinical decision making. WeakSTIL compresses tiles of a WSI using a feature extractor pre-trained with self-supervised learning on unlabeled histopathology data and learns to predict precise sTIL% scores for each tile in the tumor bed by using a multiple instance learning regressor that only requires a weak WSI-level label. By requiring only a weak label, we overcome the large annotation efforts required to train currently existing TIL detection methods. We show that WeakSTIL is at least as good as other TIL detection methods when predicting the WSI-level sTIL% score, reaching a coefficient of determination of 0.45pm0.15 when compared to scores generated by an expert pathologist, and an AUC of 0.89pm0.05 when treating it as the clinically interesting sTIL-high vs sTIL-low classification task. Additionally, we show that the intermediate tile-level predictions of WeakSTIL are highly interpretable, which suggests that WeakSTIL pays attention to latent features related to the number of TILs and the tissue type. In the future, WeakSTIL may be used to provide consistent and interpretable sTIL% predictions to stratify breast cancer patients into targeted therapy arms.

  • 6 authors
·
Sep 13, 2021

Pathology-CoT: Learning Visual Chain-of-Thought Agent from Expert Whole Slide Image Diagnosis Behavior

Diagnosing a whole-slide image is an interactive, multi-stage process involving changes in magnification and movement between fields. Although recent pathology foundation models are strong, practical agentic systems that decide what field to examine next, adjust magnification, and deliver explainable diagnoses are still lacking. The blocker is data: scalable, clinically aligned supervision of expert viewing behavior that is tacit and experience-based, not written in textbooks or online, and therefore absent from large language model training. We introduce the AI Session Recorder, which works with standard WSI viewers to unobtrusively record routine navigation and convert the viewer logs into standardized behavioral commands (inspect or peek at discrete magnifications) and bounding boxes. A lightweight human-in-the-loop review turns AI-drafted rationales into the Pathology-CoT dataset, a form of paired "where to look" and "why it matters" supervision produced at roughly six times lower labeling time. Using this behavioral data, we build Pathologist-o3, a two-stage agent that first proposes regions of interest and then performs behavior-guided reasoning. On gastrointestinal lymph-node metastasis detection, it achieved 84.5% precision, 100.0% recall, and 75.4% accuracy, exceeding the state-of-the-art OpenAI o3 model and generalizing across backbones. To our knowledge, this constitutes one of the first behavior-grounded agentic systems in pathology. Turning everyday viewer logs into scalable, expert-validated supervision, our framework makes agentic pathology practical and establishes a path to human-aligned, upgradeable clinical AI.

zhihuanglab Zhi Huang Lab
·
Oct 6, 2025 2

SLICEMATE: Accurate and Scalable Static Program Slicing via LLM-Powered Agents

Static program slicing, which extracts the executable portions of a program that affect the values at a specific location, supports many software analysis tasks such as debugging and security auditing. However, traditional slicing tools rely on computationally expensive reachability analysis over dependency graphs, which struggle to scale to large programs and often fail to handle code with incomplete syntax. Recently emerged learning-based methods, while more robust to such cases, still fall short of achieving comparable performance to traditional methods on well-formed code. In this work, we propose SliceMate, a novel static program slicing solution powered by Large Language Model (LLM) agents. It bypasses the need for explicit dependency graph construction and achieving superior slicing accuracy. Concretely, SliceMate integrates three specialized agents: (1) a synthesis agent that produces candidate slices by incrementally expanding the scan scope across functions and files guided by LLM-inferred dependencies; (2) a verification agent that performs conciseness and completeness checks of the candidate slices, detecting missing or irrelevant statements; and (3) a refinement agent that repairs the slices with minimal edits in accordance with the verification results. These agents are orchestrated by a control module that ensures timely convergence and outputs high-quality slices without manual intervention. For rigorous evaluation, we construct a new and high-quality benchmark, SliceBench, comprising 2,200 manually annotated Java and Python programs, with program lengths ranging from 5 to 8,577 lines, significantly larger than those in existing slicing benchmarks. Experimental results show that SliceMate greatly outperforms both traditional and learning-based slicing tools.

  • 8 authors
·
Jul 24, 2025

REDACT: A Systematically Controlled Multilingual Benchmark for Personal Information Detection

Benchmark infrastructure for personally identifiable information (PII) detection remains limited: existing corpora cover few entity types, use ad hoc generation conditions, and do not show which surface conditions cause detector failures. We present REDACT, a systematically controlled multilingual PII benchmark with 13,427 records, 324,078 entity annotations, 51 entity types, 4,127 surface-form patterns, and 25 languages across 9 scripts. A strength-2 covering-array sampler controls nine generation axes: domain, format, difficulty, length, density, code-switching, language, adjacency, and co-occurrence. Three entity-level metadata fields (disclosure status, disclosure form, and a GDPR-aligned sensitivity tier) enable stratified evaluation beyond aggregate or per-type F1. From the full benchmark, we evaluate five detectors (Presidio, GLiNER, the OpenAI Privacy Filter, GPT-4.1, and Claude Sonnet 4.6) on a locked, language-stratified sample of 1,000 records. Aggregate F1 masks an architecture-dependent failure structure: the rule-based detector performs poorly on the highest-stakes data, including HIGH-sensitivity categories (recall 0.07) and non-verbatim disclosure forms, while the LLM detectors remain more robust, with the HIGH tier as their strongest sensitivity slice. A three-model reference-free LLM-as-judge assessment corroborates that sensitivity-tier assignment is the task's hardest axis. We release the benchmark, schema, prompts, and stratified evaluation harness.

  • 8 authors
·
Jun 18

Presenting a Paper is an Art: Self-Improvement Aesthetic Agents for Academic Presentations

The promotion of academic papers has become an important means of enhancing research visibility. However, existing automated methods struggle limited storytelling, insufficient aesthetic quality, and constrained self-adjustment, making it difficult to achieve efficient and engaging dissemination. At the heart of those challenges is a simple principle: there is no way to improve it when you cannot evaluate it right. To address this, we introduce EvoPresent, a self-improvement agent framework that unifies coherent narratives, aesthetic-aware designs, and realistic presentation delivery via virtual characters. Central to EvoPresent is PresAesth, a multi-task reinforcement learning (RL) aesthetic model that provides reliable aesthetic scoring, defect adjustment, and comparative feedback, enabling iterative self-improvement even under limited aesthetic training data. To systematically evaluate the methods, we introduce EvoPresent Benchmark, a comprehensive benchmark comprising: Presentation Generation Quality, built on 650 top-tier AI conference papers with multimodal resources (slides, videos and scripts) to assess both content and design; and Aesthetic Awareness, consisting of 2,000 slide pairs with varying aesthetic levels, supporting joint training and evaluation on scoring, defect adjustment, and comparison. Our findings highlight that (i) High-quality feedback is essential for agent self-improvement, while initial capability alone does not guarantee effective self-correction. (ii) Automated generation pipelines exhibit a trade-off between visual design and content construction. (iii) Multi-task RL training shows stronger generalization in aesthetic awareness tasks.

ucsbai UCSB AI Group
·
Oct 7, 2025 2

S2LIC: Learned Image Compression with the SwinV2 Block, Adaptive Channel-wise and Global-inter Attention Context

Recently, deep learning technology has been successfully applied in the field of image compression, leading to superior rate-distortion performance. It is crucial to design an effective and efficient entropy model to estimate the probability distribution of the latent representation. However, the majority of entropy models primarily focus on one-dimensional correlation processing between channel and spatial information. In this paper, we propose an Adaptive Channel-wise and Global-inter attention Context (ACGC) entropy model, which can efficiently achieve dual feature aggregation in both inter-slice and intraslice contexts. Specifically, we divide the latent representation into different slices and then apply the ACGC model in a parallel checkerboard context to achieve faster decoding speed and higher rate-distortion performance. In order to capture redundant global features across different slices, we utilize deformable attention in adaptive global-inter attention to dynamically refine the attention weights based on the actual spatial relationships and context. Furthermore, in the main transformation structure, we propose a high-performance S2LIC model. We introduce the residual SwinV2 Transformer model to capture global feature information and utilize a dense block network as the feature enhancement module to improve the nonlinear representation of the image within the transformation structure. Experimental results demonstrate that our method achieves faster encoding and decoding speeds and outperforms VTM-17.1 and some recent learned image compression methods in both PSNR and MS-SSIM metrics.

  • 4 authors
·
Mar 21, 2024

Joint Self-Supervised Image-Volume Representation Learning with Intra-Inter Contrastive Clustering

Collecting large-scale medical datasets with fully annotated samples for training of deep networks is prohibitively expensive, especially for 3D volume data. Recent breakthroughs in self-supervised learning (SSL) offer the ability to overcome the lack of labeled training samples by learning feature representations from unlabeled data. However, most current SSL techniques in the medical field have been designed for either 2D images or 3D volumes. In practice, this restricts the capability to fully leverage unlabeled data from numerous sources, which may include both 2D and 3D data. Additionally, the use of these pre-trained networks is constrained to downstream tasks with compatible data dimensions. In this paper, we propose a novel framework for unsupervised joint learning on 2D and 3D data modalities. Given a set of 2D images or 2D slices extracted from 3D volumes, we construct an SSL task based on a 2D contrastive clustering problem for distinct classes. The 3D volumes are exploited by computing vectored embedding at each slice and then assembling a holistic feature through deformable self-attention mechanisms in Transformer, allowing incorporating long-range dependencies between slices inside 3D volumes. These holistic features are further utilized to define a novel 3D clustering agreement-based SSL task and masking embedding prediction inspired by pre-trained language models. Experiments on downstream tasks, such as 3D brain segmentation, lung nodule detection, 3D heart structures segmentation, and abnormal chest X-ray detection, demonstrate the effectiveness of our joint 2D and 3D SSL approach. We improve plain 2D Deep-ClusterV2 and SwAV by a significant margin and also surpass various modern 2D and 3D SSL approaches.

  • 10 authors
·
Dec 4, 2022

LADDER: Language Driven Slice Discovery and Error Rectification

Error slice discovery is crucial to diagnose and mitigate model errors. Current clustering or discrete attribute-based slice discovery methods face key limitations: 1) clustering results in incoherent slices, while assigning discrete attributes to slices leads to incomplete coverage of error patterns due to missing or insufficient attributes; 2) these methods lack complex reasoning, preventing them from fully explaining model biases; 3) they fail to integrate domain knowledge, limiting their usage in specialized fields \eg radiology. We propose\ladder (Language-Driven Discovery and Error Rectification), to address the limitations by: (1) leveraging the flexibility of natural language to address incompleteness, (2) employing LLM's latent domain knowledge and advanced reasoning to analyze sentences and derive testable hypotheses directly, identifying biased attributes, and form coherent error slices without clustering. Existing mitigation methods typically address only the worst-performing group, often amplifying errors in other subgroups. In contrast,\ladder generates pseudo attributes from the discovered hypotheses to mitigate errors across all biases without explicit attribute annotations or prior knowledge of bias. Rigorous evaluations on 6 datasets spanning natural and medical images -- comparing 200+ classifiers with diverse architectures, pretraining strategies, and LLMs -- show that\ladder consistently outperforms existing baselines in discovering and mitigating biases.

BostonU Boston University
·
Jul 31, 2024

MSM-Seg: A Modality-and-Slice Memory Framework with Category-Agnostic Prompting for Multi-Modal Brain Tumor Segmentation

Multi-modal brain tumor segmentation is critical for clinical diagnosis, and it requires accurate identification of distinct internal anatomical subregions. While the recent prompt-based segmentation paradigms enable interactive experiences for clinicians, existing methods ignore cross-modal correlations and rely on labor-intensive category-specific prompts, limiting their applicability in real-world scenarios. To address these issues, we propose a MSM-Seg framework for multi-modal brain tumor segmentation. The MSM-Seg introduces a novel dual-memory segmentation paradigm that synergistically integrates multi-modal and inter-slice information with the efficient category-agnostic prompt for brain tumor understanding. To this end, we first devise a modality-and-slice memory attention (MSMA) to exploit the cross-modal and inter-slice relationships among the input scans. Then, we propose a multi-scale category-agnostic prompt encoder (MCP-Encoder) to provide tumor region guidance for decoding. Moreover, we devise a modality-adaptive fusion decoder (MF-Decoder) that leverages the complementary decoding information across different modalities to improve segmentation accuracy. Extensive experiments on different MRI datasets demonstrate that our MSM-Seg framework outperforms state-of-the-art methods in multi-modal metastases and glioma tumor segmentation. The code is available at https://github.com/xq141839/MSM-Seg.

  • 6 authors
·
Oct 12, 2025

Surface morphology and thickness variation estimation of zeolites via electron ptychography

Zeolites, as representative porous materials, possess intricate three-dimensional frameworks that endow them with high surface areas and remarkable catalytic properties. There are a few factors that give a huge influence on the catalytic properties, including the size and connectivity of these three-dimensional channels and atomic level defects. In additional to that, the surface morphology and thickness variation of zeolites particles are essential to their catalytic performances as well. However, it is a significant challenge to characterize these macroscopic properties of zeolites using conventional techniques due to their sensitivity to electron beams. In this study, we introduce surface-adaptive electron ptychography, an advanced approach based on multi-slice electron ptychography, which enables high-precision reconstruction of both local atomic configurations and global structural features in zeolite nanoparticles. By adaptively optimizing probe defocus and slice thickness during the reconstruction process, SAEP successfully resolves surface morphology, thickness variations and atomic structure simultaneously. This integrated framework facilitates a direct and intuitive correlation between zeolite channel structures and particle thickness. Our findings open new pathways for large-scale, comprehensive structure property analysis of beam-sensitive porous materials, deepening the understanding of their catalytic behavior.

  • 6 authors
·
Apr 23, 2025

SILSA: Sliding-Window Slice Latents for Topology-Preserving High-Resolution 3D Generation

High-resolution 3D generation increasingly relies on voxel latents and multi-stage pipelines that first predict active structure and then synthesize local geometry. While effective, this design fragments continuous surfaces into many local tokens, inflates generation cost, and often weakens topological consistency for thin or highly connected shapes. We introduce SILSA, a topology-aware 3D generation framework that represents shapes with compact sliding-window slice latents. Instead of generating expensive voxel tokens, SILSA uses a fixed set of overlapping slices along the three canonical axes, where each token summarizes a local depth window to preserve cross-sectional continuity and support single-stage rectified-flow generation. A Slice VAE encodes oriented surface samples into multi-axis slice latents and reconstructs them with a sparse volumetric decoder, while a Volumetric Anchor Lattice coordinates directional slice streams through a shared 3D workspace. To preserve structural correctness, we introduce slice-level topology supervision that matches persistence diagrams and aligns Betti transitions across neighboring slices. Experiments show that SILSA improves structural fidelity while substantially reducing generation cost. SILSA improves PSNR by 8.7%, coverage by 5.96 absolute points, and Betti error by 9.2% over the strongest baseline, while using 70.0% fewer tokens than the next-most compact baseline and over 98% fewer tokens than sparse or hierarchical tokenizers, effectively reducing training memory by 40.4% and inference time by 58.5%. Qualitative results further show improved preservation of thin structures, repeated components, and long-range connectivity.

I$^3$Net: Inter-Intra-slice Interpolation Network for Medical Slice Synthesis

Medical imaging is limited by acquisition time and scanning equipment. CT and MR volumes, reconstructed with thicker slices, are anisotropic with high in-plane resolution and low through-plane resolution. We reveal an intriguing phenomenon that due to the mentioned nature of data, performing slice-wise interpolation from the axial view can yield greater benefits than performing super-resolution from other views. Based on this observation, we propose an Inter-Intra-slice Interpolation Network (I^3Net), which fully explores information from high in-plane resolution and compensates for low through-plane resolution. The through-plane branch supplements the limited information contained in low through-plane resolution from high in-plane resolution and enables continual and diverse feature learning. In-plane branch transforms features to the frequency domain and enforces an equal learning opportunity for all frequency bands in a global context learning paradigm. We further propose a cross-view block to take advantage of the information from all three views online. Extensive experiments on two public datasets demonstrate the effectiveness of I^3Net, and noticeably outperforms state-of-the-art super-resolution, video frame interpolation and slice interpolation methods by a large margin. We achieve 43.90dB in PSNR, with at least 1.14dB improvement under the upscale factor of times2 on MSD dataset with faster inference. Code is available at https://github.com/DeepMed-Lab-ECNU/Medical-Image-Reconstruction.

  • 5 authors
·
May 4, 2024

H-DenseUNet: Hybrid Densely Connected UNet for Liver and Tumor Segmentation from CT Volumes

Liver cancer is one of the leading causes of cancer death. To assist doctors in hepatocellular carcinoma diagnosis and treatment planning, an accurate and automatic liver and tumor segmentation method is highly demanded in the clinical practice. Recently, fully convolutional neural networks (FCNs), including 2D and 3D FCNs, serve as the back-bone in many volumetric image segmentation. However, 2D convolutions can not fully leverage the spatial information along the third dimension while 3D convolutions suffer from high computational cost and GPU memory consumption. To address these issues, we propose a novel hybrid densely connected UNet (H-DenseUNet), which consists of a 2D DenseUNet for efficiently extracting intra-slice features and a 3D counterpart for hierarchically aggregating volumetric contexts under the spirit of the auto-context algorithm for liver and tumor segmentation. We formulate the learning process of H-DenseUNet in an end-to-end manner, where the intra-slice representations and inter-slice features can be jointly optimized through a hybrid feature fusion (HFF) layer. We extensively evaluated our method on the dataset of MICCAI 2017 Liver Tumor Segmentation (LiTS) Challenge and 3DIRCADb Dataset. Our method outperformed other state-of-the-arts on the segmentation results of tumors and achieved very competitive performance for liver segmentation even with a single model.

  • 6 authors
·
Sep 21, 2017

LLM as Dataset Analyst: Subpopulation Structure Discovery with Large Language Model

The distribution of subpopulations is an important property hidden within a dataset. Uncovering and analyzing the subpopulation distribution within datasets provides a comprehensive understanding of the datasets, standing as a powerful tool beneficial to various downstream tasks, including Dataset Subpopulation Organization, Subpopulation Shift, and Slice Discovery. Despite its importance, there has been no work that systematically explores the subpopulation distribution of datasets to our knowledge. To address the limitation and solve all the mentioned tasks in a unified way, we introduce a novel concept of subpopulation structures to represent, analyze, and utilize subpopulation distributions within datasets. To characterize the structures in an interpretable manner, we propose the Subpopulation Structure Discovery with Large Language Models (SSD-LLM) framework, which employs world knowledge and instruction-following capabilities of Large Language Models (LLMs) to linguistically analyze informative image captions and summarize the structures. Furthermore, we propose complete workflows to address downstream tasks, named Task-specific Tuning, showcasing the application of the discovered structure to a spectrum of subpopulation-related tasks, including dataset subpopulation organization, subpopulation shift, and slice discovery. Furthermore, we propose complete workflows to address downstream tasks, named Task-specific Tuning, showcasing the application of the discovered structure to a spectrum of subpopulation-related tasks, including dataset subpopulation organization, subpopulation shift, and slice discovery.

  • 6 authors
·
May 3, 2024

MedRegion-CT: Region-Focused Multimodal LLM for Comprehensive 3D CT Report Generation

The recent release of RadGenome-Chest CT has significantly advanced CT-based report generation. However, existing methods primarily focus on global features, making it challenging to capture region-specific details, which may cause certain abnormalities to go unnoticed. To address this, we propose MedRegion-CT, a region-focused Multi-Modal Large Language Model (MLLM) framework, featuring three key innovations. First, we introduce Region Representative (R^2) Token Pooling, which utilizes a 2D-wise pretrained vision model to efficiently extract 3D CT features. This approach generates global tokens representing overall slice features and region tokens highlighting target areas, enabling the MLLM to process comprehensive information effectively. Second, a universal segmentation model generates pseudo-masks, which are then processed by a mask encoder to extract region-centric features. This allows the MLLM to focus on clinically relevant regions, using six predefined region masks. Third, we leverage segmentation results to extract patient-specific attributions, including organ size, diameter, and locations. These are converted into text prompts, enriching the MLLM's understanding of patient-specific contexts. To ensure rigorous evaluation, we conducted benchmark experiments on report generation using the RadGenome-Chest CT. MedRegion-CT achieved state-of-the-art performance, outperforming existing methods in natural language generation quality and clinical relevance while maintaining interpretability. The code for our framework is publicly available.

  • 10 authors
·
Jun 29, 2025

PROFASR-BENCH: A Benchmark for Context-Conditioned ASR in High-Stakes Professional Speech

Automatic Speech Recognition (ASR) in professional settings faces challenges that existing benchmarks underplay: dense domain terminology, formal register variation, and near-zero tolerance for critical entity errors. We present ProfASR-Bench, a professional-talk evaluation suite for high-stakes applications across finance, medicine, legal, and technology. Each example pairs a natural-language prompt (domain cue and/or speaker profile) with an entity-rich target utterance, enabling controlled measurement of context-conditioned recognition. The corpus supports conventional ASR metrics alongside entity-aware scores and slice-wise reporting by accent and gender. Using representative families Whisper (encoder-decoder ASR) and Qwen-Omni (audio language models) under matched no-context, profile, domain+profile, oracle, and adversarial conditions, we find a consistent pattern: lightweight textual context produces little to no change in average word error rate (WER), even with oracle prompts, and adversarial prompts do not reliably degrade performance. We term this the context-utilization gap (CUG): current systems are nominally promptable yet underuse readily available side information. ProfASR-Bench provides a standardized context ladder, entity- and slice-aware reporting with confidence intervals, and a reproducible testbed for comparing fusion strategies across model families. Dataset: https://huggingface.co/datasets/prdeepakbabu/ProfASR-Bench Code: https://github.com/prdeepakbabu/ProfASR-Bench

  • 1 authors
·
Dec 29, 2025

Generative Enhancement for 3D Medical Images

The limited availability of 3D medical image datasets, due to privacy concerns and high collection or annotation costs, poses significant challenges in the field of medical imaging. While a promising alternative is the use of synthesized medical data, there are few solutions for realistic 3D medical image synthesis due to difficulties in backbone design and fewer 3D training samples compared to 2D counterparts. In this paper, we propose GEM-3D, a novel generative approach to the synthesis of 3D medical images and the enhancement of existing datasets using conditional diffusion models. Our method begins with a 2D slice, noted as the informed slice to serve the patient prior, and propagates the generation process using a 3D segmentation mask. By decomposing the 3D medical images into masks and patient prior information, GEM-3D offers a flexible yet effective solution for generating versatile 3D images from existing datasets. GEM-3D can enable dataset enhancement by combining informed slice selection and generation at random positions, along with editable mask volumes to introduce large variations in diffusion sampling. Moreover, as the informed slice contains patient-wise information, GEM-3D can also facilitate counterfactual image synthesis and dataset-level de-enhancement with desired control. Experiments on brain MRI and abdomen CT images demonstrate that GEM-3D is capable of synthesizing high-quality 3D medical images with volumetric consistency, offering a straightforward solution for dataset enhancement during inference. The code is available at https://github.com/HKU-MedAI/GEM-3D.

  • 6 authors
·
Mar 19, 2024

Robotic Ultrasound Makes CBCT Alive

Intraoperative Cone Beam Computed Tomography (CBCT) provides a reliable 3D anatomical context essential for interventional planning. However, its static nature fails to provide continuous monitoring of soft-tissue deformations induced by respiration, probe pressure, and surgical manipulation, leading to navigation discrepancies. We propose a deformation-aware CBCT updating framework that leverages robotic ultrasound as a dynamic proxy to infer tissue motion and update static CBCT slices in real time. Starting from calibration-initialized alignment with linear correlation of linear combination (LC2)-based rigid refinement, our method establishes accurate multimodal correspondence. To capture intraoperative dynamics, we introduce the ultrasound correlation UNet (USCorUNet), a lightweight network trained with optical flow-guided supervision to learn deformation-aware correlation representations, enabling accurate, real-time dense deformation field estimation from ultrasound streams. The inferred deformation is spatially regularized and transferred to the CBCT reference to produce deformation-consistent visualizations without repeated radiation exposure. We validate the proposed approach through deformation estimation and ultrasound-guided CBCT updating experiments. Results demonstrate real-time end-to-end CBCT slice updating and physically plausible deformation estimation, enabling dynamic refinement of static CBCT guidance during robotic ultrasound-assisted interventions. The source code is publicly available at https://github.com/anonymous-codebase/us-cbct-demo.

  • 5 authors
·
Mar 9

OpenClaw PRISM: A Zero-Fork, Defense-in-Depth Runtime Security Layer for Tool-Augmented LLM Agents

Tool-augmented LLM agents introduce security risks that extend beyond user-input filtering, including indirect prompt injection through fetched content, unsafe tool execution, credential leakage, and tampering with local control files. We present OpenClaw PRISM, a zero-fork runtime security layer for OpenClaw-based agent gateways. PRISM combines an in-process plugin with optional sidecar services and distributes enforcement across ten lifecycle hooks spanning message ingress, prompt construction, tool execution, tool-result persistence, outbound messaging, sub-agent spawning, and gateway startup. Rather than introducing a novel detection model, PRISM integrates a hybrid heuristic-plus-LLM scanning pipeline, conversation- and session-scoped risk accumulation with TTL-based decay, policy-enforced controls over tools, paths, private networks, domain tiers, and outbound secret patterns, and a tamper-evident audit and operations plane with integrity verification and hot-reloadable policy management. We outline an evaluation methodology and benchmark pipeline for measuring security effectiveness, false positives, layer contribution, runtime overhead, and operational recoverability in an agent-runtime setting, and we report current preliminary benchmark results on curated same-slice experiments and operational microbenchmarks. The system targets deployable runtime defense for real agent gateways rather than benchmark-only detection.

  • 1 authors
·
Mar 11

GBT-SAM: Adapting a Foundational Deep Learning Model for Generalizable Brain Tumor Segmentation via Efficient Integration of Multi-Parametric MRI Data

Gliomas are aggressive brain tumors that require accurate imaging-based diagnosis, with segmentation playing a critical role in evaluating morphology and treatment decisions. Manual delineation of gliomas is time-consuming and prone to variability, motivating the use of deep learning to improve consistency and alleviate clinical workload. However, existing methods often fail to fully exploit the information available in multi-parametric MRI (mp-MRI), particularly inter-slice contextual features, and typically require considerable computational resources while lacking robustness across tumor type variations. We present GBT-SAM, a parameter-efficient deep learning framework that adapts the Segment Anything Model (SAM), a large-scale vision model, to volumetric mp-MRI data. GBT-SAM reduces input complexity by selecting fewer than 2.6\% of slices per scan while incorporating all four MRI modalities, preserving essential tumor-related information with minimal cost. Furthermore, our model is trained by a two-step fine-tuning strategy that incorporates a depth-aware module to capture inter-slice correlations and lightweight adaptation layers, resulting in just 6.5M trainable parameters, which is the lowest among SAM-based approaches. GBT-SAM achieves a Dice Score of 93.54 on the BraTS Adult Glioma dataset and demonstrates robust performance on Meningioma, Pediatric Glioma, and Sub-Saharan Glioma datasets. These results highlight GBT-SAM's potential as a computationally efficient and domain-robust framework for brain tumor segmentation using mp-MRI. Our code and models are available at https://github.com/vpulab/med-sam-brain .

  • 5 authors
·
Mar 6, 2025

Rethinking Brain Tumor Segmentation from the Frequency Domain Perspective

Precise segmentation of brain tumors, particularly contrast-enhancing regions visible in post-contrast MRI (areas highlighted by contrast agent injection), is crucial for accurate clinical diagnosis and treatment planning but remains challenging. However, current methods exhibit notable performance degradation in segmenting these enhancing brain tumor areas, largely due to insufficient consideration of MRI-specific tumor features such as complex textures and directional variations. To address this, we propose the Harmonized Frequency Fusion Network (HFF-Net), which rethinks brain tumor segmentation from a frequency-domain perspective. To comprehensively characterize tumor regions, we develop a Frequency Domain Decomposition (FDD) module that separates MRI images into low-frequency components, capturing smooth tumor contours and high-frequency components, highlighting detailed textures and directional edges. To further enhance sensitivity to tumor boundaries, we introduce an Adaptive Laplacian Convolution (ALC) module that adaptively emphasizes critical high-frequency details using dynamically updated convolution kernels. To effectively fuse tumor features across multiple scales, we design a Frequency Domain Cross-Attention (FDCA) integrating semantic, positional, and slice-specific information. We further validate and interpret frequency-domain improvements through visualization, theoretical reasoning, and experimental analyses. Extensive experiments on four public datasets demonstrate that HFF-Net achieves an average relative improvement of 4.48\% (ranging from 2.39\% to 7.72\%) in the mean Dice scores across the three major subregions, and an average relative improvement of 7.33% (ranging from 5.96% to 8.64%) in the segmentation of contrast-enhancing tumor regions, while maintaining favorable computational efficiency and clinical applicability. Code: https://github.com/VinyehShaw/HFF.

  • 8 authors
·
Jun 11, 2025

Better Tokens for Better 3D: Advancing Vision-Language Modeling in 3D Medical Imaging

Recent progress in vision-language modeling for 3D medical imaging has been fueled by large-scale computed tomography (CT) corpora with paired free-text reports, stronger architectures, and powerful pretrained models. This has enabled applications such as automated report generation and text-conditioned 3D image synthesis. Yet, current approaches struggle with high-resolution, long-sequence volumes: contrastive pretraining often yields vision encoders that are misaligned with clinical language, and slice-wise tokenization blurs fine anatomy, reducing diagnostic performance on downstream tasks. We introduce BTB3D (Better Tokens for Better 3D), a causal convolutional encoder-decoder that unifies 2D and 3D training and inference while producing compact, frequency-aware volumetric tokens. A three-stage training curriculum enables (i) local reconstruction, (ii) overlapping-window tiling, and (iii) long-context decoder refinement, during which the model learns from short slice excerpts yet generalizes to scans exceeding 300 slices without additional memory overhead. BTB3D sets a new state-of-the-art on two key tasks: it improves BLEU scores and increases clinical F1 by 40% over CT2Rep, CT-CHAT, and Merlin for report generation; and it reduces FID by 75% and halves FVD compared to GenerateCT and MedSyn for text-to-CT synthesis, producing anatomically consistent 512*512*241 volumes. These results confirm that precise three-dimensional tokenization, rather than larger language backbones alone, is essential for scalable vision-language modeling in 3D medical imaging. The codebase is available at: https://github.com/ibrahimethemhamamci/BTB3D

  • 10 authors
·
Oct 23, 2025

IMVS: Interactive Medical Volume Segmentation with Test-Time Adaptation - A New Method for Annotating Radiology Datasets

Annotating large radiology datasets is bottlenecked by the manual effort of delineating structures slice-by-slice in 3D volumes. Interactive methods reduce this effort but stay interaction-inefficient: slice-wise methods (including many foundation models) ignore inter-slice continuity, while 3D and video-based methods propagate a prompt with a fixed propagator that never adapts to the target volume, so it drifts on low-contrast or pathological structures and must be re-prompted. We present IMVS, a human-in-the-loop annotation framework that composes three components into a closed loop rather than a new segmentation primitive: a lightweight 2D Slice Mask Adapter (SMA) fine-tuned online from user scribbles, a frozen Volume Mask Tracker (VMT) that propagates corrected masks across adjacent slices, and a soft teacher--student alignment that limits forgetting. The SMA is backbone-agnostic (UNet++, DeepLabV3, TransUNet). Across 8 public CT/MRI datasets, IMVS matches strong interactive baselines in quality while sharply cutting annotation effort: 14.4times faster than a proficient copy-based manual workflow (22.3times over naive manual), 4.6times over slice-wise and 1.9times over 3D interactive methods. MedSAM2 and ScribblePrompt stay competitive or stronger on well-delineated organs; IMVS's advantage is largest on challenging targets and on interaction efficiency. Source code and Demo Video: https://github.com/AbhilakshSinghReen/imvs.

  • 3 authors
·
Sep 14