arXiv subjects

Kayvan Najarian

Publications and source records attributed to Kayvan Najarian.

At least 19 recordsLinked to original sources

arXiv2026

Representation geometry shapes task performance in vision-language modeling for CT enterography

Computed tomography (CT) enterography is a primary imaging modality for assessing inflammatory bowel disease (IBD), yet the representational choices that best support automated analysis of this modality are unknown. We present the first study of vision-language transfer learning on abdominal CT enterography and identify two main findings. First, mean pooling of slice embeddings gives better categorical disease assessment (59.2\% three-class accuracy), whereas attention pooling gives better cross-modal retrieval (0.235 text-to-image MRR). This pattern holds across all LoRA configurations tested and suggests that the two aggregators emphasize different properties of the learned representation. Second, per-slice tissue contrast matters more than broader spatial coverage: multi-window RGB encoding, which maps complementary Hounsfield Unit windows to RGB channels, outperforms all strategies that increase spatial coverage through multiplanar sampling, and in this setting adding coronal and sagittal views reduces classification performance. For report generation, fine-tuning without retrieval context yields within-1 severity accuracy at the prevalence-matched chance level (70.4\% vs.\ 71\% random), suggesting little learned ordering beyond the class distribution. Retrieval-augmented generation (RAG) improves this across all configurations, scoring 7--14 percentage points above the chance baseline and improving ordinal MAE from 0.98 to 0.80--0.89. A three-teacher pseudolabel framework enables all comparisons without expert annotations. Together, these findings provide the first baselines for this underexplored modality and offer practical guidance for building vision-language systems for volumetric medical imaging.

cs.CV↗

arXiv2026

A Causal Machine Learning Framework for Treatment Personalization in Clinical Trials: Application to Ulcerative Colitis

Randomized controlled trials estimate average treatment effects, but treatment response heterogeneity motivates personalized approaches. A critical question is whether statistically detectable heterogeneity translates into improved treatment decisions -- these are distinct questions that can yield contradictory answers. We present a modular causal machine learning framework that evaluates each question separately: permutation importance identifies which features predict heterogeneity, best linear predictor (BLP) testing assesses statistical significance, and doubly robust policy evaluation measures whether acting on the heterogeneity improves patient outcomes. We apply this framework to patient-level data from the UNIFI maintenance trial of ustekinumab in ulcerative colitis, comparing placebo, standard-dose ustekinumab every 12 weeks, and dose-intensified ustekinumab every 8 weeks, using cross-fitted X-learner models with baseline demographics, medication history, week-8 clinical scores, laboratory biomarkers, and video-derived endoscopic features. BLP testing identified strong associations between endoscopic features and treatment effect heterogeneity for ustekinumab versus placebo, yet doubly robust policy evaluation showed no improvement in expected remission from incorporating endoscopic features, and out-of-fold multi-arm evaluation showed worse performance. Diagnostic comparison of prognostic contribution against policy value revealed that endoscopic scores behaved as disease severity markers -- improving outcome prediction in untreated patients but adding noise to treatment selection -- while clinical variables (fecal calprotectin, age, CRP) captured the decision-relevant variation. These results demonstrate that causal machine learning applications to clinical trials should include policy-level evaluation alongside heterogeneity testing.

cs.LG↗

arXiv2025

LISM: Long-range Integrative State space Models via Input-Latent State Interactions

State space models (SSMs) are an emerging paradigm that achieves linear-time scaling, however, they intrinsically suffer from "curse of memory". The memory of SSMs, including Mamba, decays exponentially as long as the recursive update is stable. In this work, we developed Long-range Integrative State space Models (LISM) to mitigate the curse of memory in SSMs. LISM allows the recursive update to occasionally be unstable, which enables longer memory retention, and incorporates a dynamic input-state interaction mechanism to identify inputs that should be memorized for longer periods. We theoretically establish probability bounds for the overall stability of LISM and derive a probabilistic stability condition to guide parameterization and training. We evaluated LISM's performance on multiple tasks, a synthetic Selective Copy task, two real language tasks WikiText-103 and LRA Retrieval, and an additional biological prediction task. LISM achieved the best performance on the Selective Copying task, WikiText-103, and the biological prediction task compared to SSM-based models and achieved comparable performance on the LRA-Retrieval task with the state-of-the-art. Beyond average performance, LISM also shows strong repeatability across runs. In the two real language tasks, LISM reduced the relative performance variance (coefficient of variation) by an average of 33.3%, achieving a standard deviation of $\pm$0.30% on WikiText-103 compared to $\pm$0.46% for Mamba-2. The implementation of LISM is available at https://github.com/CM-Compbio-Group/LISM_dev.

cs.LG↗

arXiv2025

LoRA-based methods on Unet for transfer learning in Subarachnoid Hematoma Segmentation

Aneurysmal subarachnoid hemorrhage (SAH) is a life-threatening neurological emergency with mortality rates exceeding 30%. Transfer learning from related hematoma types represents a potentially valuable but underexplored approach. Although Unet architectures remain the gold standard for medical image segmentation due to their effectiveness on limited datasets, Low-Rank Adaptation (LoRA) methods for parameter-efficient transfer learning have been rarely applied to convolutional neural networks in medical imaging contexts. We implemented a Unet architecture pre-trained on computed tomography scans from 124 traumatic brain injury patients across multiple institutions, then fine-tuned on 30 aneurysmal SAH patients from the University of Michigan Health System using 3-fold cross-validation. We developed a novel CP-LoRA method based on tensor CP-decomposition and introduced DoRA variants (DoRA-C, convDoRA, CP-DoRA) that decompose weight matrices into magnitude and directional components. We compared these approaches against existing LoRA methods (LoRA-C, convLoRA) and standard fine-tuning strategies across different modules on a multi-view Unet model. LoRA-based methods consistently outperformed standard Unet fine-tuning. Performance varied by hemorrhage volume, with all methods showing improved accuracy for larger volumes. CP-LoRA achieved comparable performance to existing methods while using significantly fewer parameters. Over-parameterization with higher ranks consistently yielded better performance than strictly low-rank adaptations. This study demonstrates that transfer learning between hematoma types is feasible and that LoRA-based methods significantly outperform conventional Unet fine-tuning for aneurysmal SAH segmentation.

eess.IV↗

arXiv2025

Supervised Coupled Matrix-Tensor Factorization (SCMTF) for Computational Phenotyping of Patient Reported Outcomes in Ulcerative Colitis

Phenotyping is the process of distinguishing groups of patients to identify different types of disease progression. A recent trend employs low-rank matrix and tensor factorization methods for their capability of dealing with multi-modal, heterogeneous, and missing data. Symptom quantification is crucial for understanding patient experiences in inflammatory bowel disease, especially in conditions such as ulcerative colitis (UC). However, patient-reported symptoms are typically noisy, subjective, and significantly more sparse than other data types. For this reason, they are usually not included in phenotyping and other machine learning methods. This paper explores the application of computational phenotyping to leverage Patient-Reported Outcomes (PROs) using a novel supervised coupled matrix-tensor factorization (SCMTF) method, which integrates temporal PROs and temporal labs with static features to predict medication persistence in ulcerative colitis. This is the first tensor-based method that is both supervised and coupled, it is the first application to the UC domain, and the first application to PROs. We use a deep learning framework that makes the model flexible and easy to train. The proposed method allows us to handle the large amount of missing data in the PROs. The best model predicts changes in medication 8 and 20 months in the future with AUCs of 0.853 and 0.803 on the test set respectively. We derive interpretable phenotypes consisting of static features and temporal features (including their temporal patterns). We show that low-rank matrix and tensor based phenotyping can be successfully applied to the UC domain and to highly missing PRO data. We identify phenotypes useful to predict medication persistence - these phenotypes include several symptom variables, showing that PROs contain relevant infromation that is usually discarded.

cs.LG↗

arXiv2023

Tensor Denoising via Amplification and Stable Rank Methods

Tensors in the form of multilinear arrays are ubiquitous in data science applications. Captured real-world data, including video, hyperspectral images, and discretized physical systems, naturally occur as tensors and often come with attendant noise. Under the additive noise model and with the assumption that the underlying clean tensor has low rank, many denoising methods have been created that utilize tensor decomposition to effect denoising through low rank tensor approximation. However, all such decomposition methods require estimating the tensor rank, or related measures such as the tensor spectral and nuclear norms, all of which are NP-hard problems. In this work we leverage our previously developed framework of $\textit{tensor amplification}$, which provides good approximations of the spectral and nuclear tensor norms, to denoising synthetic tensors of various sizes, ranks, and noise levels, along with real-world tensors derived from physiological signals. We also introduce two new notions of tensor rank -- $\textit{stable slice rank}$ and $\textit{stable }$$X$$\textit{-rank}$ -- and new denoising methods based on their estimation. The experimental results show that in the low rank context, tensor-based amplification provides comparable denoising performance in high signal-to-noise ratio (SNR) settings and superior performance in noisy (i.e., low SNR) settings, while the stable $X$-rank method achieves superior denoising performance on the physiological signal data.

cs.LG↗

arXiv2022

Prediction of Oral Food Challenge Outcomes via Ensemble Learning

Oral Food Challenges (OFCs) are essential to accurately diagnosing food allergy due to the limitations of existing clinical testing. However, some patients are hesitant to undergo OFCs, while those willing suffer from limited access to allergists in rural/community healthcare settings. Despite its success in predicting patient outcomes in other clinical settings, few applications of machine learning to food allergy have been developed. Thus, in this study, we seek to leverage machine learning methodologies for OFC outcome prediction. Retrospective data was gathered from 1,112 patients who collectively underwent a total of 1,284 OFCs, and consisted of clinical factors including serum-specific Immunoglobulin E (IgE), total IgE, skin prick tests (SPTs), comorbidities, sex, and age. Using these features, multiple machine learning models were constructed to predict OFC outcomes for three common allergens: peanut, egg, and milk. The best performing model for each allergen was an ensemble of random forest (egg) or Learning Using Concave and Convex Kernels (LUCCK) (peanut, milk) models, which achieved an Area under the Curve (AUC) of 0.91, 0.96, and 0.94, in predicting OFC outcomes for peanut, egg, and milk, respectively. Moreover, all such models had sensitivity and specificity values 89%. Model interpretation via SHapley Additive exPlanations (SHAP) indicates that specific IgE, along with wheal and flare values from SPTs, are highly predictive of OFC outcomes. The results of this analysis suggest that ensemble learning has the potential to predict OFC outcomes and reveal relevant clinical factors for further study.

cs.LG↗

arXiv2021

A Novel Tropical Geometry-based Interpretable Machine Learning Method: Application in Prognosis of Advanced Heart Failure

A model's interpretability is essential to many practical applications such as clinical decision support systems. In this paper, a novel interpretable machine learning method is presented, which can model the relationship between input variables and responses in humanly understandable rules. The method is built by applying tropical geometry to fuzzy inference systems, wherein variable encoding functions and salient rules can be discovered by supervised learning. Experiments using synthetic datasets were conducted to investigate the performance and capacity of the proposed algorithm in classification and rule discovery. Furthermore, the proposed method was applied to a clinical application that identified heart failure patients that would benefit from advanced therapies such as heart transplant or durable mechanical circulatory support. Experimental results show that the proposed network achieved great performance on the classification tasks. In addition to learning humanly understandable rules from the dataset, existing fuzzy domain knowledge can be easily transferred into the network and used to facilitate model training. From our results, the proposed model and the ability of learning existing domain knowledge can significantly improve the model generalizability. The characteristics of the proposed network make it promising in applications requiring model reliability and justification.

cs.LG↗

arXiv2021

Motion-based Camera Localization System in Colonoscopy Videos

Optical colonoscopy is an essential diagnostic and prognostic tool for many gastrointestinal diseases, including cancer screening and staging, intestinal bleeding, diarrhea, abdominal symptom evaluation, and inflammatory bowel disease assessment. Automated assessment of colonoscopy is of interest considering the subjectivity present in qualitative human interpretations of colonoscopy findings. Localization of the camera is essential to interpreting the meaning and context of findings for diseases evaluated by colonoscopy. In this study, we propose a camera localization system to estimate the relative location of the camera and classify the colon into anatomical segments. The camera localization system begins with non-informative frame detection and removal. Then a self-training end-to-end convolutional neural network is built to estimate the camera motion, where several strategies are proposed to improve its robustness and generalization on endoscopic videos. Using the estimated camera motion a camera trajectory can be derived and a relative location index calculated. Based on the estimated location index, anatomical colon segment classification is performed by constructing a colon template. The proposed motion estimation algorithm was evaluated on an external dataset containing the ground truth for camera pose. The experimental results show that the performance of the proposed method is superior to other published methods. The relative location index estimation and anatomical region classification were further validated using colonoscopy videos collected from routine clinical practice. This validation yielded an average accuracy in classification of 0.754, which is substantially higher than the performances obtained using location indices built from other methods.

cs.CV↗

arXiv2020

Radial basis function kernel optimization for Support Vector Machine classifiers

Support Vector Machines (SVMs) are still one of the most popular and precise classifiers. The Radial Basis Function (RBF) kernel has been used in SVMs to separate among classes with considerable success. However, there is an intrinsic dependence on the initial value of the kernel hyperparameter. In this work, we propose OKSVM, an algorithm that automatically learns the RBF kernel hyperparameter and adjusts the SVM weights simultaneously. The proposed optimization technique is based on a gradient descent method. We analyze the performance of our approach with respect to the classical SVM for classification on synthetic and real data. Experimental results show that OKSVM performs better irrespective of the initial values of the RBF hyperparameter.

cs.LG↗

arXiv2020

Algebraic Methods for Tensor Data

We develop algebraic methods for computations with tensor data. We give 3 applications: extracting features that are invariant under the orthogonal symmetries in each of the modes, approximation of the tensor spectral norm, and amplification of low rank tensor structure. We introduce colored Brauer diagrams, which are used for algebraic computations and in analyzing their computational complexity. We present numerical experiments whose results show that the performance of the alternating least square algorithm for the low rank approximation of tensors can be improved using tensor amplification.

math.RT↗

arXiv2019

Dense Pooling layers in Fully Convolutional Network for Skin Lesion Segmentation

One of the essential tasks in medical image analysis is segmentation and accurate detection of borders. Lesion segmentation in skin images is an essential step in the computerized detection of skin cancer. However, many of the state-of-the-art segmentation methods have deficiencies in their border detection phase. In this paper, a new class of fully convolutional network is proposed, with new dense pooling layers for segmentation of lesion regions in skin images. This network leads to highly accurate segmentation of lesions on skin lesion datasets which outperforms state-of-the-art algorithms in the skin lesion segmentation.

cs.CV↗

arXiv2019

Gland Segmentation in Histopathology Images Using Deep Networks and Handcrafted Features

Histopathology images contain essential information for medical diagnosis and prognosis of cancerous disease. Segmentation of glands in histopathology images is a primary step for analysis and diagnosis of an unhealthy patient. Due to the widespread application and the great success of deep neural networks in intelligent medical diagnosis and histopathology, we propose a modified version of LinkNet for gland segmentation and recognition of malignant cases. We show that using specific handcrafted features such as invariant local binary pattern drastically improves the system performance. The experimental results demonstrate the competency of the proposed system against state-of-the-art methods. We achieved the best results in testing on section B images of the Warwick-QU dataset and obtained comparable results on section A images.

eess.IV↗

arXiv2019

Fetal Ultrasound Image Segmentation for Measuring Biometric Parameters Using Multi-Task Deep Learning

Ultrasound imaging is a standard examination during pregnancy that can be used for measuring specific biometric parameters towards prenatal diagnosis and estimating gestational age. Fetal head circumference (HC) is one of the significant factors to determine the fetus growth and health. In this paper, a multi-task deep convolutional neural network is proposed for automatic segmentation and estimation of HC ellipse by minimizing a compound cost function composed of segmentation dice score and MSE of ellipse parameters. Experimental results on fetus ultrasound dataset in different trimesters of pregnancy show that the segmentation results and the extracted HC match well with the radiologist annotations. The obtained dice scores of the fetal head segmentation and the accuracy of HC evaluations are comparable to the state-of-the-art.

eess.IV↗

arXiv2019

An Unsupervised Feature Learning Approach to Reduce False Alarm Rate in ICUs

The high rate of false alarms in intensive care units (ICUs) is one of the top challenges of using medical technology in hospitals. These false alarms are often caused by patients' movements, detachment of monitoring sensors, or different sources of noise and interference that impact the collected signals from different monitoring devices. In this paper, we propose a novel set of high-level features based on unsupervised feature learning technique in order to effectively capture the characteristics of different arrhythmia in electrocardiogram (ECG) signal and differentiate them from irregularity in signals due to different sources of signal disturbances. This unsupervised feature learning technique, first extracts a set of low-level features from all existing heart cycles of a patient, and then clusters these segments for each individual patient to provide a set of prominent high-level features. The objective of the clustering phase is to enable the classification method to differentiate between the high-level features extracted from normal and abnormal cycles (i.e., either due to arrhythmia or different sources of distortions in signal) in order to put more attention to the features extracted from abnormal portion of the signal that contribute to the alarm. The performance of this method is evaluated using the 2015 PhysioNet/Computing in Cardiology Challenge dataset for reducing false arrhythmia alarms in the ICUs. As confirmed by the experimental results, the proposed method offers a considerable performance in terms of accuracy, sensitivity and specificity of alarm detection only using a few high-level features that are extracted from one single lead ECG signal.

cs.LG↗

arXiv2019

Liver Segmentation in Abdominal CT Images by Adaptive 3D Region Growing

Automatic liver segmentation plays an important role in computer-aided diagnosis and treatment. Manual segmentation of organs is a difficult and tedious task and so prone to human errors. In this paper, we propose an adaptive 3D region growing with subject-specific conditions. For this aim we use the intensity distribution of most probable voxels in prior map along with location prior. We also incorporate the boundary of target organs to restrict the region growing. In order to obtain strong edges and high contrast, we propose an effective contrast enhancement algorithm to facilitate more accurate segmentation. In this paper, 92.56% Dice score is achieved. We compare our method with the method of hard thresholding on Deeds prior map and also with the majority voting on Deeds registration with 13 organs.

cs.CV↗

arXiv2018

ReDMark: Framework for Residual Diffusion Watermarking on Deep Networks

Due to the rapid growth of machine learning tools and specifically deep networks in various computer vision and image processing areas, application of Convolutional Neural Networks for watermarking have recently emerged. In this paper, we propose a deep end-to-end diffusion watermarking framework (ReDMark) which can be adapted for any desired transform space. The framework is composed of two Fully Convolutional Neural Networks with the residual structure for embedding and extraction. The whole deep network is trained end-to-end to conduct a blind secure watermarking. The framework is customizable for the level of robustness vs. imperceptibility. It is also adjustable for the trade-off between capacity and robustness. The proposed framework simulates various attacks as a differentiable network layer to facilitate end-to-end training. For JPEG attack, a differentiable approximation is utilized, which drastically improves the watermarking robustness to this attack. Another important characteristic of the proposed framework, which leads to improved security and robustness, is its capability to diffuse watermark information among a relatively wide area of the image. Comparative results versus recent state-of-the-art researches highlight the superiority of the proposed framework in terms of imperceptibility and robustness.

cs.MM↗

arXiv2018

Adaptive Blind Image Watermarking Using Fuzzy Inference System Based on Human Visual Perception

Development of digital content has increased the necessity of copyright protection by means of watermarking. Imperceptibility and robustness are two important features of watermarking algorithms. The goal of watermarking methods is to satisfy the tradeoff between these two contradicting characteristics. Recently watermarking methods in transform domains have displayed favorable results. In this paper, we present an adaptive blind watermarking method which has high transparency in areas that are important to human visual system. We propose a fuzzy system for adaptive control of the embedding strength factor. Features such as saliency, intensity, and edge-concentration, are used as fuzzy attributes. Redundant embedding in discrete cosine transform (DCT) of wavelet domain has increased the robustness of our method. Experimental results show the efficiency of the proposed method and better results are obtained as compared to comparable methods with same size of watermark logo.

cs.MM↗