arXiv subjects

Mehdi Astaraki

Publications and source records attributed to Mehdi Astaraki.

14 recordsLinked to original sources

arXiv2026

Redefining Instance Matching: A Unified Framework for Part-Aware Matching in Panoptic Segmentation Evaluation

The Panoptic Quality (PQ) metric is the standard for jointly evaluating instance and semantic segmentation. However, its original definition relies on a One-to-One matching between predicted and ground truth segments, which is only straightforward when the IoU threshold exceeds 0.5. Below 0.5, multiple matching strategies emerge in a poorly explored problem space. We systematically elucidate this space by recasting segment matching as a constrained bipartite assignment problem. Independently bounding the prediction- and ground-truth-side degrees yields four matching strategies: One-to-One, Many-to-One, One-to-Many, and Many-to-Many. We show that the first three are well-defined within the PQ framework, while Many-to-Many falls outside it. These strategies become relevant when instances are fragmented, adjacent objects are difficult to delineate, or annotations are noisy. Central to our framework is a vertex-based accounting of TP, FN, and FP, anchored to ground truth and predicted segments rather than to matching edges. We further show that the framework extends naturally to part-aware panoptic segmentation, and we explore part-aware evaluation on biomedical data. Across configurable case studies we report how different combinations of thresholds and matching strategies behave in practice. We release a unified open-source package built on Panoptica. It exposes Voronoi-based region-wise analysis, part-aware evaluation, and Area Under Threshold Curve computations as configurable options.

cs.CV↗

arXiv2026

AEGIS: An Operational Infrastructure for Post-Market Governance of Adaptive Medical AI Under US and EU Regulations

Machine learning systems deployed in medical devices require governance frameworks that ensure safety while enabling continuous improvement. Regulatory bodies including the FDA and European Union have introduced mechanisms such as the Predetermined Change Control Plan (PCCP) and Post-Market Surveillance (PMS) to manage iterative model updates without repeated submissions. This paper presents AI/ML Evaluation and Governance Infrastructure for Safety (AEGIS), a governance framework applicable to any healthcare AI system. AEGIS comprises three modules, i.e., dataset assimilation and retraining, model monitoring, and conditional decision, that operationalize FDA PCCP and EU AI Act Article 43(4) provisions. We implement a four-category deployment decision taxonomy (APPROVE, CONDITIONAL APPROVAL, CLINICAL REVIEW, REJECT) with an independent PMS ALARM signal, enabling detection of the critical state in which no deployable model exists while the released model is simultaneously at risk. To illustrate how AEGIS can be instantiated across heterogeneous clinical contexts, we provide two examples: sepsis prediction from electronic health records and brain tumor segmentation from medical imaging. Both cases use identical governance architecture, differing only in configuration. Across 11 simulated iterations on the sepsis example, AEGIS yielded 8 APPROVE, 1 CONDITIONAL APPROVAL, 1 CLINICAL REVIEW, and 1 REJECT decision, exercising all four categories. ALARM signals were co-issued at iterations 8 and 10, including the critical state where no deployable model exists and the released model is simultaneously failing. AEGIS detected drift before observable performance degradation. These results demonstrate that AEGIS translates regulatory change-control concepts into executable governance procedures, supporting safe continuous learning for adaptive medical AI across diverse clinical applications.

cs.LG↗

arXiv2025

Leveraging Imperfection with MEDLEY A Multi-Model Approach Harnessing Bias in Medical AI

Bias in medical artificial intelligence is conventionally viewed as a defect requiring elimination. However, human reasoning inherently incorporates biases shaped by education, culture, and experience, suggesting their presence may be inevitable and potentially valuable. We propose MEDLEY (Medical Ensemble Diagnostic system with Leveraged diversitY), a conceptual framework that orchestrates multiple AI models while preserving their diverse outputs rather than collapsing them into a consensus. Unlike traditional approaches that suppress disagreement, MEDLEY documents model-specific biases as potential strengths and treats hallucinations as provisional hypotheses for clinician verification. A proof-of-concept demonstrator was developed using over 30 large language models, creating a minimum viable product that preserved both consensus and minority views in synthetic cases, making diagnostic uncertainty and latent biases transparent for clinical oversight. While not yet a validated clinical tool, the demonstration illustrates how structured diversity can enhance medical reasoning under clinician supervision. By reframing AI imperfection as a resource, MEDLEY offers a paradigm shift that opens new regulatory, ethical, and innovation pathways for developing trustworthy medical AI systems.

cs.AI↗

arXiv2025

ChEmbed: Enhancing Chemical Literature Search Through Domain-Specific Text Embeddings

Retrieval-Augmented Generation (RAG) systems in chemistry heavily depend on accurate and relevant retrieval of chemical literature. However, general-purpose text embedding models frequently fail to adequately represent complex chemical terminologies, resulting in suboptimal retrieval quality. Specialized embedding models tailored to chemical literature retrieval have not yet been developed, leaving a substantial performance gap. To address this challenge, we introduce ChEmbed, a domain-adapted family of text embedding models fine-tuned on a dataset comprising chemistry-specific text from the PubChem, Semantic Scholar, and ChemRxiv corpora. To create effective training data, we employ large language models to synthetically generate queries, resulting in approximately 1.7 million high-quality query-passage pairs. Additionally, we augment the tokenizer by adding 900 chemically specialized tokens to previously unused slots, which significantly reduces the fragmentation of chemical entities, such as IUPAC names. ChEmbed also maintains a 8192-token context length, enabling the efficient retrieval of longer passages compared to many other open-source embedding models, which typically have a context length of 512 or 2048 tokens. Evaluated on our newly introduced ChemRxiv Retrieval benchmark, ChEmbed outperforms state-of-the-art general embedding models, raising nDCG@10 from 0.82 to 0.91 (+9 pp). ChEmbed represents a practical, lightweight, and reproducible embedding solution that effectively improves retrieval for chemical literature search.

cs.IR↗

arXiv2025

Analysis of the 2024 BraTS Meningioma Radiotherapy Planning Automated Segmentation Challenge

The 2024 Brain Tumor Segmentation Meningioma Radiotherapy (BraTS-MEN-RT) challenge aimed to advance automated segmentation algorithms using the largest known multi-institutional dataset of 750 radiotherapy planning brain MRIs with expert-annotated target labels for patients with intact or postoperative meningioma that underwent either conventional external beam radiotherapy or stereotactic radiosurgery. Each case included a defaced 3D post-contrast T1-weighted radiotherapy planning MRI in its native acquisition space, accompanied by a single-label "target volume" representing the gross tumor volume (GTV) and any at-risk post-operative site. Target volume annotations adhered to established radiotherapy planning protocols, ensuring consistency across cases and institutions, and were approved by expert neuroradiologists and radiation oncologists. Six participating teams developed, containerized, and evaluated automated segmentation models using this comprehensive dataset. Team rankings were assessed using a modified lesion-wise Dice Similarity Coefficient (DSC) and 95% Hausdorff Distance (95HD). The best reported average lesion-wise DSC and 95HD was 0.815 and 26.92 mm, respectively. BraTS-MEN-RT is expected to significantly advance automated radiotherapy planning by enabling precise tumor segmentation and facilitating tailored treatment, ultimately improving patient outcomes. We describe the design and results from the BraTS-MEN-RT challenge.

cs.CV↗

arXiv2025

BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis

BrainLesion Suite is a versatile toolkit for building modular brain lesion image analysis pipelines in Python. Following Pythonic principles, BrainLesion Suite is designed to provide a 'brainless' development experience, minimizing cognitive effort and streamlining the creation of complex workflows for clinical and scientific practice. At its core is an adaptable preprocessing module that performs co-registration, atlas registration, and optional skull-stripping and defacing on arbitrary multi-modal input images. BrainLesion Suite leverages algorithms from the BraTS challenge to synthesize missing modalities, inpaint lesions, and generate pathology-specific tumor segmentations. BrainLesion Suite also enables quantifying segmentation model performance, with tools such as panoptica to compute lesion-wise metrics. Although BrainLesion Suite was originally developed for image analysis pipelines of brain lesions such as glioma, metastasis, and multiple sclerosis, it can be adapted for other biomedical image analysis applications. The individual BrainLesion Suite packages and tutorials are accessible on GitHub.

cs.CV↗

arXiv2025

BraTS orchestrator : Democratizing and Disseminating state-of-the-art brain tumor image analysis

The Brain Tumor Segmentation (BraTS) cluster of challenges has significantly advanced brain tumor image analysis by providing large, curated datasets and addressing clinically relevant tasks. However, despite its success and popularity, algorithms and models developed through BraTS have seen limited adoption in both scientific and clinical communities. To accelerate their dissemination, we introduce BraTS orchestrator, an open-source Python package that provides seamless access to state-of-the-art segmentation and synthesis algorithms for diverse brain tumors from the BraTS challenge ecosystem. Available on GitHub (https://github.com/BrainLesion/BraTS), the package features intuitive tutorials designed for users with minimal programming experience, enabling both researchers and clinicians to easily deploy winning BraTS algorithms for inference. By abstracting the complexities of modern deep learning, BraTS orchestrator democratizes access to the specialized knowledge developed within the BraTS community, making these advances readily available to broader neuro-radiology and neuro-oncology audiences.

eess.IV↗

arXiv2025

MAIA: A Collaborative Medical AI Platform for Integrated Healthcare Innovation

The integration of Artificial Intelligence (AI) into clinical workflows requires robust collaborative platforms that are able to bridge the gap between technical innovation and practical healthcare applications. This paper introduces MAIA (Medical Artificial Intelligence Assistant), an open-source platform designed to facilitate interdisciplinary collaboration among clinicians, researchers, and AI developers. Built on Kubernetes, MAIA offers a modular, scalable environment with integrated tools for data management, model development, annotation, deployment, and clinical feedback. Key features include project isolation, CI/CD automation, integration with high-computing infrastructures and in clinical workflows. MAIA supports real-world use cases in medical imaging AI, with deployments in both academic and clinical environments. By promoting collaborations and interoperability, MAIA aims to accelerate the translation of AI research into impactful clinical solutions while promoting reproducibility, transparency, and user-centered design. We showcase the use of MAIA with different projects, both at KTH Royal Institute of Technology and Karolinska University Hospital.

cs.AI↗

arXiv2024

Lesion Segmentation in Whole-Body Multi-Tracer PET-CT Images; a Contribution to AutoPET 2024 Challenge

The automatic segmentation of pathological regions within whole-body PET-CT volumes has the potential to streamline various clinical applications such as diagno-sis, prognosis, and treatment planning. This study aims to address this challenge by contributing to the AutoPET MICCAI 2024 challenge through a proposed workflow that incorporates image preprocessing, tracer classification, and lesion segmentation steps. The implementation of this pipeline led to a significant enhancement in the segmentation accuracy of the models. This improvement is evidenced by an average overall Dice score of 0.548 across 1611 training subjects, 0.631 and 0.559 for classi-fied FDG and PSMA subjects of the training set, and 0.792 on the preliminary testing phase dataset.

eess.IV↗

arXiv2023

SegRap2023: A Benchmark of Organs-at-Risk and Gross Tumor Volume Segmentation for Radiotherapy Planning of Nasopharyngeal Carcinoma

Radiation therapy is a primary and effective NasoPharyngeal Carcinoma (NPC) treatment strategy. The precise delineation of Gross Tumor Volumes (GTVs) and Organs-At-Risk (OARs) is crucial in radiation treatment, directly impacting patient prognosis. Previously, the delineation of GTVs and OARs was performed by experienced radiation oncologists. Recently, deep learning has achieved promising results in many medical image segmentation tasks. However, for NPC OARs and GTVs segmentation, few public datasets are available for model development and evaluation. To alleviate this problem, the SegRap2023 challenge was organized in conjunction with MICCAI2023 and presented a large-scale benchmark for OAR and GTV segmentation with 400 Computed Tomography (CT) scans from 200 NPC patients, each with a pair of pre-aligned non-contrast and contrast-enhanced CT scans. The challenge's goal was to segment 45 OARs and 2 GTVs from the paired CT scans. In this paper, we detail the challenge and analyze the solutions of all participants. The average Dice similarity coefficient scores for all submissions ranged from 76.68\% to 86.70\%, and 70.42\% to 73.44\% for OARs and GTVs, respectively. We conclude that the segmentation of large-size OARs is well-addressed, and more efforts are needed for GTVs and small-size or thin-structure OARs. The benchmark will remain publicly available here: https://segrap2023.grand-challenge.org

eess.IV↗

arXiv2023

Fully Automatic Segmentation of Gross Target Volume and Organs-at-Risk for Radiotherapy Planning of Nasopharyngeal Carcinoma

Target segmentation in CT images of Head&Neck (H&N) region is challenging due to low contrast between adjacent soft tissue. The SegRap 2023 challenge has been focused on benchmarking the segmentation algorithms of Nasopharyngeal Carcinoma (NPC) which would be employed as auto-contouring tools for radiation treatment planning purposes. We propose a fully-automatic framework and develop two models for a) segmentation of 45 Organs at Risk (OARs) and b) two Gross Tumor Volumes (GTVs). To this end, we preprocess the image volumes by harmonizing the intensity distributions and then automatically cropping the volumes around the target regions. The preprocessed volumes were employed to train a standard 3D U-Net model for each task, separately. Our method took second place for each of the tasks in the validation phase of the challenge. The proposed framework is available at https://github.com/Astarakee/segrap2023

eess.IV↗

arXiv2023

AutoPaint: A Self-Inpainting Method for Unsupervised Anomaly Detection

Robust and accurate detection and segmentation of heterogenous tumors appearing in different anatomical organs with supervised methods require large-scale labeled datasets covering all possible types of diseases. Due to the unavailability of such rich datasets and the high cost of annotations, unsupervised anomaly detection (UAD) methods have been developed aiming to detect the pathologies as deviation from the normality by utilizing the unlabeled healthy image data. However, developed UAD models are often trained with an incomplete distribution of healthy anatomies and have difficulties in preserving anatomical constraints. This work intends to, first, propose a robust inpainting model to learn the details of healthy anatomies and reconstruct high-resolution images by preserving anatomical constraints. Second, we propose an autoinpainting pipeline to automatically detect tumors, replace their appearance with the learned healthy anatomies, and based on that segment the tumoral volumes in a purely unsupervised fashion. Three imaging datasets, including PET, CT, and PET-CT scans of lung tumors and head and neck tumors, are studied as benchmarks for evaluation. Experimental results demonstrate the significant superiority of the proposed method over a wide range of state-of-the-art UAD methods. Moreover, the unsupervised method we propose produces comparable results to a robust supervised segmentation method when applied to multimodal images.

cs.CV↗

arXiv2022

PriorNet: lesion segmentation in PET-CT including prior tumor appearance information

Tumor segmentation in PET-CT images is challenging due to the dual nature of the acquired information: low metabolic information in CT and low spatial resolution in PET. U-Net architecture is the most common and widely recognized approach when developing a fully automatic image segmentation method in the medical field. We proposed a two-step approach, aiming to refine and improve the segmentation performances of tumoral lesions in PET-CT. The first step generates a prior tumor appearance map from the PET-CT volumes, regarded as prior tumor information. The second step, consisting of a standard U-Net, receives the prior tumor appearance map and PET-CT images to generate the lesion mask. We evaluated the method on the 1014 cases available for the AutoPET 2022 challenge, and the results showed an average Dice score of 0.701 on the positive cases.

eess.IV↗

arXiv2021

Development and evaluation of a 3D annotation software for interactive COVID-19 lesion segmentation in chest CT

Segmentation of COVID-19 lesions from chest CT scans is of great importance for better diagnosing the disease and investigating its extent. However, manual segmentation can be very time consuming and subjective, given the lesions' large variation in shape, size and position. On the other hand, we still lack large manually segmented datasets that could be used for training machine learning-based models for fully automatic segmentation. In this work, we propose a new interactive and user-friendly tool for COVID-19 lesion segmentation, which works by alternating automatic steps (based on level-set segmentation and statistical shape modeling) with manual correction steps. The present software was tested by two different expertise groups: one group of three radiologists and one of three users with an engineering background. Promising segmentation results were obtained by both groups, which achieved satisfactory agreement both between- and within-group. Moreover, our interactive tool was shown to significantly speed up the lesion segmentation process, when compared to fully manual segmentation. Finally, we investigated inter-observer variability and how it is strongly influenced by several subjective factors, showing the importance for AI researchers and clinical doctors to be aware of the uncertainty in lesion segmentation results.

eess.IV↗