arXiv subjects

Farzad Khalvati

Publications and source records attributed to Farzad Khalvati.

At least 19 recordsLinked to original sources

arXiv2026

Automated Chest CT Protocol Selection via Large Language Model Derived Text Embeddings from Imaging Request Text

Purpose: Accurate CT protocol selection is critical for diagnostic quality and patient safety, yet the current process is manual, time-consuming, and prone to inconsistencies. Prior Machine Learning methods using keywords or bag-of-words lack contextual understanding and perform poorly on rare protocols. We propose a decision support system using large language model (LLM) features to recommend protocols from free-text clinical indications, capturing clinical nuance and phrasing variation for more consistent, efficient selection. Methods: In this REB-approved retrospective study, 285,123 chest CT imaging requests from a large academic medical center (2017-2024) were split into training (228,099, 80%) and held-out test (57,024, 20%) sets. Each request included procedure names, clinical indication, HIS comments, and the selected protocol. Clinical text was embedded using a fine-tuned LLM, Meta's LLaMA-3.1-70B; these features input a logistic regression classifier predicting 18 protocol labels (e.g., PE, LDCT). Results: The pipeline achieved a weighted precision of 0.84, weighted F1-score of 0.81, and overall accuracy of 79% across 18 CT protocols. On 300 independent cases with expert consensus, the LLM reached an overall accuracy of 80% versus 83% for radiologists, with no significant difference (p = 0.263). Performance was comparable across most classes, with the LLM exceeding radiologists for some challenging categories, and entropy analyses indicated more balanced protocol use, suggesting reduced variability. Conclusion: An LLM-based recommendation system can leverage general knowledge from a large natural-text corpus to accurately assign chest CT protocols from free-text imaging requests, and may serve as a viable foundation for protocol recommendation tools where inputs require language understanding.

cs.LG↗

arXiv2026

Multimodal Semantic-Aware Contrastive Learning For False Negative Mitigation in 3D Medical Imaging

Multimodal Contrastive Learning (CL) has shown significant performance in aligning representations across various data modalities and improving downstream tasks, especially in healthcare. It works by minimizing the distance between matched (positive) data modalities, while maximizing the distance between mismatched (negative) samples. Traditional CL frameworks typically assume instance-based correspondence within data batches, treating all non-paired samples as negatives. However, this assumption often fails in medical settings, where samples may share high-level semantic attributes, leading to false negatives that degrade representation quality. In this paper, we propose Multimodal Semantic-Aware Contrastive Learning (MseaCL), a CL framework trained on a pediatric cohort of 3D brain magnetic resonance imaging (MRI) scans and radiology reports. The goal of this framework is to mitigate the impact of semantically similar false negative samples by incorporating semantic similarity between radiology reports, as a guiding signal during the learning process. Our results indicate that applying this framework as a pretraining stage can achieve notable improvements in downstream tasks, e.g., at least a 22.6\% increase in the area under the receiver operating characteristic curve (AUC) of pediatric brain tumor molecular classification, demonstrating its potential for more robust and semantically aligned multimodal representations in clinical applications.

cs.LG↗

arXiv2026

Exploring Radiologists' Expectations of Explainable Machine Learning Models in Medical Image Analysis

In spite of the strong performance of machine learning (ML) models in radiology, they have not been widely accepted by radiologists, limiting clinical integration. A key reason is the lack of explainability, which ensures that model predictions are understandable and verifiable by clinicians. Several methods and tools have been proposed to improve explainability, but most reflect developers' perspectives and lack systematic clinical validation. In this work, we gathered insights from radiologists with varying experience and specialties into explainable ML requirements through a structured questionnaire. They also highlighted key clinical tasks where ML could be most beneficial and how it might be deployed. Based on their input, we propose guidelines for designing and developing explainable ML models in radiology. These guidelines can help researchers develop clinically useful models, facilitating integration into radiology practice as a supportive tool.

cs.HC↗

arXiv2026

Artificial Intelligence for Sentiment Analysis of Persian Poetry

Recent advancements of the Artificial Intelligence (AI) have led to the development of large language models (LLMs) that are capable of understanding, analysing, and creating textual data. These language models open a significant opportunity in analyzing the literature and more specifically poetry. In the present work, we employ multiple Bidirectional encoder representations from transformers (BERT) and Generative Pre-trained Transformer (GPT) based language models to analyze the works of two prominent Persian poets: Jalal al-Din Muhammad Rumi (Rumi) and Parvin E'tesami. The main objective of this research is to investigate the capability of the modern language models in grasping complexities of the Persian poetry and explore potential correlations between the poems' sentiment and their meters. Our findings in this study indicates that GPT4o language model can reliably be used in analysis of Persian poetry. Furthermore, the results of our sentiment analysis revealed that in general, Rumi's poems express happier sentiments compared to Parvin E'tesami's poems. Furthermore, comparing the utilization of poetic meters highlighted Rumi's poems superiority in using meters to express a wider variety of sentiments. These findings are significant as they confirm that LLMs can be effectively applied in conducting computer-based semantic studies, where human interpretations are not required, and thereby significantly reducing potential biases in the analysis.

cs.CL↗

arXiv2025

ProtoTopic: Prototypical Network for Few-Shot Medical Topic Modeling

Topic modeling is a useful tool for analyzing large corpora of written documents, particularly academic papers. Despite a wide variety of proposed topic modeling techniques, these techniques do not perform well when applied to medical texts. This can be due to the low number of documents available for some topics in the healthcare domain. In this paper, we propose ProtoTopic, a prototypical network-based topic model used for topic generation for a set of medical paper abstracts. Prototypical networks are efficient, explainable models that make predictions by computing distances between input datapoints and a set of prototype representations, making them particularly effective in low-data or few-shot learning scenarios. With ProtoTopic, we demonstrate improved topic coherence and diversity compared to two topic modeling baselines used in the literature, demonstrating the ability of our model to generate medically relevant topics even with limited data.

cs.LG↗

arXiv2025

A Comparison and Evaluation of Fine-tuned Convolutional Neural Networks to Large Language Models for Image Classification and Segmentation of Brain Tumors on MRI

Large Language Models (LLMs) have shown strong performance in text-based healthcare tasks. However, their utility in image-based applications remains unexplored. We investigate the effectiveness of LLMs for medical imaging tasks, specifically glioma classification and segmentation, and compare their performance to that of traditional convolutional neural networks (CNNs). Using the BraTS 2020 dataset of multi-modal brain MRIs, we evaluated a general-purpose vision-language LLM (LLaMA 3.2 Instruct) both before and after fine-tuning, and benchmarked its performance against custom 3D CNNs. For glioma classification (Low-Grade vs. High-Grade), the CNN achieved 80% accuracy and balanced precision and recall. The general LLM reached 76% accuracy but suffered from a specificity of only 18%, often misclassifying Low-Grade tumors. Fine-tuning improved specificity to 55%, but overall performance declined (e.g., accuracy dropped to 72%). For segmentation, three methods - center point, bounding box, and polygon extraction, were implemented. CNNs accurately localized gliomas, though small tumors were sometimes missed. In contrast, LLMs consistently clustered predictions near the image center, with no distinction of glioma size, location, or placement. Fine-tuning improved output formatting but failed to meaningfully enhance spatial accuracy. The bounding polygon method yielded random, unstructured outputs. Overall, CNNs outperformed LLMs in both tasks. LLMs showed limited spatial understanding and minimal improvement from fine-tuning, indicating that, in their current form, they are not well-suited for image-based tasks. More rigorous fine-tuning or alternative training strategies may be needed for LLMs to achieve better performance, robustness, and utility in the medical space.

cs.CV↗

arXiv2025

ClinicalFMamba: Advancing Clinical Assessment using Mamba-based Multimodal Neuroimaging Fusion

Multimodal medical image fusion integrates complementary information from different imaging modalities to enhance diagnostic accuracy and treatment planning. While deep learning methods have advanced performance, existing approaches face critical limitations: Convolutional Neural Networks (CNNs) excel at local feature extraction but struggle to model global context effectively, while Transformers achieve superior long-range modeling at the cost of quadratic computational complexity, limiting clinical deployment. Recent State Space Models (SSMs) offer a promising alternative, enabling efficient long-range dependency modeling in linear time through selective scan mechanisms. Despite these advances, the extension to 3D volumetric data and the clinical validation of fused images remains underexplored. In this work, we propose ClinicalFMamba, a novel end-to-end CNN-Mamba hybrid architecture that synergistically combines local and global feature modeling for 2D and 3D images. We further design a tri-plane scanning strategy for effectively learning volumetric dependencies in 3D images. Comprehensive evaluations on three datasets demonstrate the superior fusion performance across multiple quantitative metrics while achieving real-time fusion. We further validate the clinical utility of our approach on downstream 2D/3D brain tumor classification tasks, achieving superior performance over baseline methods. Our method establishes a new paradigm for efficient multimodal medical image fusion suitable for real-time clinical deployment.

eess.IV↗

arXiv2025

AI-Driven MRI-based Brain Tumour Segmentation Benchmarking

Medical image segmentation has greatly aided medical diagnosis, with U-Net based architectures and nnU-Net providing state-of-the-art performance. There have been numerous general promptable models and medical variations introduced in recent years, but there is currently a lack of evaluation and comparison of these models across a variety of prompt qualities on a common medical dataset. This research uses Segment Anything Model (SAM), Segment Anything Model 2 (SAM 2), MedSAM, SAM-Med-3D, and nnU-Net to obtain zero-shot inference on the BraTS 2023 adult glioma and pediatrics dataset across multiple prompt qualities for both points and bounding boxes. Several of these models exhibit promising Dice scores, particularly SAM and SAM 2 achieving scores of up to 0.894 and 0.893, respectively when given extremely accurate bounding box prompts which exceeds nnU-Net's segmentation performance. However, nnU-Net remains the dominant medical image segmentation network due to the impracticality of providing highly accurate prompts to the models. The model and prompt evaluation, as well as the comparison, are extended through fine-tuning SAM, SAM 2, MedSAM, and SAM-Med-3D on the pediatrics dataset. The improvements in point prompt performance after fine-tuning are substantial and show promise for future investigation, but are unable to achieve better segmentation than bounding boxes or nnU-Net.

cs.CV↗

arXiv2025

Open-radiomics: A Collection of Standardized Datasets and a Technical Protocol for Reproducible Radiomics Machine Learning Pipelines

Background: As an important branch of machine learning pipelines in medical imaging, radiomics faces two major challenges namely reproducibility and accessibility. In this work, we introduce open-radiomics, a set of radiomics datasets along with a comprehensive radiomics pipeline based on our proposed technical protocol to improve the reproducibility of the results. Methods: We curated large-scale radiomics datasets based on three open-source datasets; BraTS 2020 for high-grade glioma (HGG) versus low-grade glioma (LGG) classification and survival analysis, BraTS 2023 for O6-methylguanine-DNA methyltransferase classification, and non-small cell lung cancer survival analysis from the Cancer Imaging Archive. Using BraTS 2020 Magnetic Resonance Imaging (MRI) dataset, we applied our protocol to 369 brain tumor patients (76 LGG, 293 HGG). Leveraging PyRadiomics for LGG vs. HGG classification, we generated 288 datasets from 4 MRI sequences, 3 binWidths, 6 normalization methods, and 4 tumor subregions. Random Forest classifiers were trained and validated (60%,20%,20%) across 100 different data splits (28,800 test results), evaluating Area Under the Receiver Operating Characteristic Curve (AUROC). Results: Unlike binWidth and image normalization, tumor subregion and imaging sequence significantly affected performance of the models. T1 contrast-enhanced sequence and the union of Necrotic and the non-enhancing tumor core subregions resulted in the highest AUROCs (average test AUROC 0.951, 95% confidence interval of (0.949, 0.952)). Although several settings and data splits (28 out of 28800) yielded test AUROC of 1, they were irreproducible. Conclusion: Our experiments demonstrate the sources of variability in radiomics pipelines (e.g., tumor subregion) can have a significant impact on the results, which may lead to superficial perfect performances that are irreproducible.

q-bio.QM↗

arXiv2024

Edge-Enhanced Dilated Residual Attention Network for Multimodal Medical Image Fusion

Multimodal medical image fusion is a crucial task that combines complementary information from different imaging modalities into a unified representation, thereby enhancing diagnostic accuracy and treatment planning. While deep learning methods, particularly Convolutional Neural Networks (CNNs) and Transformers, have significantly advanced fusion performance, some of the existing CNN-based methods fall short in capturing fine-grained multiscale and edge features, leading to suboptimal feature integration. Transformer-based models, on the other hand, are computationally intensive in both the training and fusion stages, making them impractical for real-time clinical use. Moreover, the clinical application of fused images remains unexplored. In this paper, we propose a novel CNN-based architecture that addresses these limitations by introducing a Dilated Residual Attention Network Module for effective multiscale feature extraction, coupled with a gradient operator to enhance edge detail learning. To ensure fast and efficient fusion, we present a parameter-free fusion strategy based on the weighted nuclear norm of softmax, which requires no additional computations during training or inference. Extensive experiments, including a downstream brain tumor classification task, demonstrate that our approach outperforms various baseline methods in terms of visual quality, texture preservation, and fusion speed, making it a possible practical solution for real-world clinical applications. The code will be released at https://github.com/simonZhou86/en_dran.

eess.IV↗

arXiv2024

Tumor Location-weighted MRI-Report Contrastive Learning: A Framework for Improving the Explainability of Pediatric Brain Tumor Diagnosis

Despite the promising performance of convolutional neural networks (CNNs) in brain tumor diagnosis from magnetic resonance imaging (MRI), their integration into the clinical workflow has been limited. That is mainly due to the fact that the features contributing to a model's prediction are unclear to radiologists and hence, clinically irrelevant, i.e., lack of explainability. As the invaluable sources of radiologists' knowledge and expertise, radiology reports can be integrated with MRI in a contrastive learning (CL) framework, enabling learning from image-report associations, to improve CNN explainability. In this work, we train a multimodal CL architecture on 3D brain MRI scans and radiology reports to learn informative MRI representations. Furthermore, we integrate tumor location, salient to several brain tumor analysis tasks, into this framework to improve its generalizability. We then apply the learnt image representations to improve explainability and performance of genetic marker classification of pediatric Low-grade Glioma, the most prevalent brain tumor in children, as a downstream task. Our results indicate a Dice score of 31.1% between the model's attention maps and manual tumor segmentation (as an explainability measure) with test classification performance of 87.7%, significantly outperforming the baselines. These enhancements can build trust in our model among radiologists, facilitating its integration into clinical practices for more efficient tumor diagnosis.

eess.IV↗

arXiv2024

Generative Adversarial Networks for Weakly Supervised Generation and Evaluation of Brain Tumor Segmentations on MR Images

Segmentation of regions of interest (ROIs) for identifying abnormalities is a leading problem in medical imaging. Using machine learning for this problem generally requires manually annotated ground-truth segmentations, demanding extensive time and resources from radiologists. This work presents a weakly supervised approach that utilizes binary image-level labels, which are much simpler to acquire, to effectively segment anomalies in 2D magnetic resonance images without ground truth annotations. We train a generative adversarial network (GAN) that converts cancerous images to healthy variants, which are used along with localization seeds as priors to generate improved weakly supervised segmentations. The non-cancerous variants can also be used to evaluate the segmentations in a weakly supervised fashion, which allows for the most effective segmentations to be identified and then applied to downstream clinical classification tasks. On the Multimodal Brain Tumor Segmentation (BraTS) 2020 dataset, our proposed method generates and identifies segmentations that achieve test Dice coefficients of 83.91%. Using these segmentations for pathology classification results with a test AUC of 93.32% which is comparable to the test AUC of 95.80% achieved when using true segmentations.

eess.IV↗

arXiv2024

Opportunities for Persian Digital Humanities Research with Artificial Intelligence Language Models; Case Study: Forough Farrokhzad

This study explores the integration of advanced Natural Language Processing (NLP) and Artificial Intelligence (AI) techniques to analyze and interpret Persian literature, focusing on the poetry of Forough Farrokhzad. Utilizing computational methods, we aim to unveil thematic, stylistic, and linguistic patterns in Persian poetry. Specifically, the study employs AI models including transformer-based language models for clustering of the poems in an unsupervised framework. This research underscores the potential of AI in enhancing our understanding of Persian literary heritage, with Forough Farrokhzad's work providing a comprehensive case study. This approach not only contributes to the field of Persian Digital Humanities but also sets a precedent for future research in Persian literary studies using computational techniques.

cs.CL↗

arXiv2024

Non-invasive Liver Fibrosis Screening on CT Images using Radiomics

Objectives: To develop and evaluate a radiomics machine learning model for detecting liver fibrosis on CT of the liver. Methods: For this retrospective, single-centre study, radiomic features were extracted from Regions of Interest (ROIs) on CT images of patients who underwent simultaneous liver biopsy and CT examinations. Combinations of contrast, normalization, machine learning model, and feature selection method were determined based on their mean test Area Under the Receiver Operating Characteristic curve (AUC) on randomly placed ROIs. The combination and selected features with the highest AUC were used to develop a final liver fibrosis screening model. Results: The study included 101 male and 68 female patients (mean age = 51.2 years $\pm$ 14.7 [SD]). When averaging the AUC across all combinations, non-contrast enhanced (NC) CT (AUC, 0.6100; 95% CI: 0.5897, 0.6303) outperformed contrast-enhanced CT (AUC, 0.5680; 95% CI: 0.5471, 0.5890). The combination of hyperparameters and features that yielded the highest AUC was a logistic regression model with inputs features of maximum, energy, kurtosis, skewness, and small area high gray level emphasis extracted from non-contrast enhanced NC CT normalized using Gamma correction with $γ$ = 1.5 (AUC, 0.7833; 95% CI: 0.7821, 0.7845), (sensitivity, 0.9091; 95% CI: 0.9091, 0.9091). Conclusions: Radiomics-based machine learning models allow for the detection of liver fibrosis with reasonable accuracy and high sensitivity on NC CT. Thus, these models can be used to non-invasively screen for liver fibrosis, contributing to earlier detection of the disease at a potentially curable stage.

cs.CV↗

arXiv2024

Improving Pediatric Low-Grade Neuroepithelial Tumors Molecular Subtype Identification Using a Novel AUROC Loss Function for Convolutional Neural Networks

Pediatric Low-Grade Neuroepithelial Tumors (PLGNT) are the most common pediatric cancer type, accounting for 40% of brain tumors in children, and identifying PLGNT molecular subtype is crucial for treatment planning. However, the gold standard to determine the PLGNT subtype is biopsy, which can be impractical or dangerous for patients. This research improves the performance of Convolutional Neural Networks (CNNs) in classifying PLGNT subtypes through MRI scans by introducing a loss function that specifically improves the model's Area Under the Receiver Operating Characteristic (ROC) Curve (AUROC), offering a non-invasive diagnostic alternative. In this study, a retrospective dataset of 339 children with PLGNT (143 BRAF fusion, 71 with BRAF V600E mutation, and 125 non-BRAF) was curated. We employed a CNN model with Monte Carlo random data splitting. The baseline model was trained using binary cross entropy (BCE), and achieved an AUROC of 86.11% for differentiating BRAF fusion and BRAF V600E mutations, which was improved to 87.71% using our proposed AUROC loss function (p-value 0.045). With multiclass classification, the AUROC improved from 74.42% to 76. 59% (p-value 0.0016).

eess.IV↗

arXiv2024

Deep Superpixel Generation and Clustering for Weakly Supervised Segmentation of Brain Tumors in MR Images

Training machine learning models to segment tumors and other anomalies in medical images is an important step for developing diagnostic tools but generally requires manually annotated ground truth segmentations, which necessitates significant time and resources. This work proposes the use of a superpixel generation model and a superpixel clustering model to enable weakly supervised brain tumor segmentations. The proposed method utilizes binary image-level classification labels, which are readily accessible, to significantly improve the initial region of interest segmentations generated by standard weakly supervised methods without requiring ground truth annotations. We used 2D slices of magnetic resonance brain scans from the Multimodal Brain Tumor Segmentation Challenge 2020 dataset and labels indicating the presence of tumors to train the pipeline. On the test cohort, our method achieved a mean Dice coefficient of 0.691 and a mean 95% Hausdorff distance of 18.1, outperforming existing superpixel-based weakly supervised segmentation methods.

cs.CV↗

arXiv2023

Improving Deep Learning Models for Pediatric Low-Grade Glioma Tumors Molecular Subtype Identification Using 3D Probability Distributions of Tumor Location

Background and Purpose: Pediatric low-grade glioma (pLGG) is the most common type of brain tumor in children, and identification of molecular markers for pLGG is crucial for successful treatment planning. Convolutional Neural Network (CNN) models for pLGG subtype identification rely on tumor segmentation. We hypothesize tumor segmentations are suboptimal and thus, we propose to augment the CNN models using tumor location probability in MRI data. Materials and Methods: Our REB-approved retrospective study included MRI Fluid-Attenuated Inversion Recovery (FLAIR) sequences of 143 BRAF fused and 71 BRAF V600E mutated tumors. Tumor segmentations (regions of interest (ROIs)) were provided by a pediatric neuroradiology fellow and verified by a senior pediatric neuroradiologist. In each experiment, we randomly split the data into development and test with an 80/20 ratio. We combined the 3D binary ROI masks for each class in the development dataset to derive the probability density functions (PDF) of tumor location, and developed three pipelines: location-based, CNN-based, and hybrid. Results: We repeated the experiment with different model initializations and data splits 100 times and calculated the Area Under Receiver Operating Characteristic Curve (AUC). The location-based classifier achieved an AUC of 77.90, 95% confidence interval (CI) (76.76, 79.03). CNN-based classifiers achieved AUC of 86.11, CI (84.96, 87.25), while the tumor-location-guided CNNs outperformed the formers with an average AUC of 88.64 CI (87.57, 89.72), which was statistically significant (Student's t-test p-value 0.0018). Conclusion: We achieved statistically significant improvements by incorporating tumor location into the CNN models. Our results suggest that manually segmented ROIs may not be optimal.

cs.CV↗

arXiv2023

Generating 3D Brain Tumor Regions in MRI using Vector-Quantization Generative Adversarial Networks

Medical image analysis has significantly benefited from advancements in deep learning, particularly in the application of Generative Adversarial Networks (GANs) for generating realistic and diverse images that can augment training datasets. However, the effectiveness of such approaches is often limited by the amount of available data in clinical settings. Additionally, the common GAN-based approach is to generate entire image volumes, rather than solely the region of interest (ROI). Research on deep learning-based brain tumor classification using MRI has shown that it is easier to classify the tumor ROIs compared to the entire image volumes. In this work, we present a novel framework that uses vector-quantization GAN and a transformer incorporating masked token modeling to generate high-resolution and diverse 3D brain tumor ROIs that can be directly used as augmented data for the classification of brain tumor ROI. We apply our method to two imbalanced datasets where we augment the minority class: (1) the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2019 dataset to generate new low-grade glioma (LGG) ROIs to balance with high-grade glioma (HGG) class; (2) the internal pediatric LGG (pLGG) dataset tumor ROIs with BRAF V600E Mutation genetic marker to balance with BRAF Fusion genetic marker class. We show that the proposed method outperforms various baseline models in both qualitative and quantitative measurements. The generated data was used to balance the data in the brain tumor types classification task. Using the augmented data, our approach surpasses baseline models by 6.4% in AUC on the BraTS 2019 dataset and 4.3% in AUC on our internal pLGG dataset. The results indicate the generated tumor ROIs can effectively address the imbalanced data problem. Our proposed method has the potential to facilitate an accurate diagnosis of rare brain tumors using MRI scans.

cs.CV↗