Sobirov, Ikboljon
HuLP: Human-in-the-Loop for Prognosis
Ridzuan, Muhammad, Kassem, Mai, Saeed, Numan, Sobirov, Ikboljon, Yaqub, Mohammad
This paper introduces HuLP, a Human-in-the-Loop for Prognosis model designed to enhance the reliability and interpretability of prognostic models in clinical contexts, especially when faced with the complexities of missing covariates and outcomes. HuLP offers an innovative approach that enables human expert intervention, empowering clinicians to interact with and correct models' predictions, thus fostering collaboration between humans and AI models to produce more accurate prognosis. Additionally, HuLP addresses the challenges of missing data by utilizing neural networks and providing a tailored methodology that effectively handles missing data. Traditional methods often struggle to capture the nuanced variations within patient populations, leading to compromised prognostic predictions. HuLP imputes missing covariates based on imaging features, aligning more closely with clinician workflows and enhancing reliability. We conduct our experiments on two real-world, publicly available medical datasets to demonstrate the superiority and competitiveness of HuLP.
EDUE: Expert Disagreement-Guided One-Pass Uncertainty Estimation for Medical Image Segmentation
Abutalip, Kudaibergen, Saeed, Numan, Sobirov, Ikboljon, Andrearczyk, Vincent, Depeursinge, Adrien, Yaqub, Mohammad
Deploying deep learning (DL) models in medical applications relies on predictive performance and other critical factors, such as conveying trustworthy predictive uncertainty. Uncertainty estimation (UE) methods provide potential solutions for evaluating prediction reliability and improving the model confidence calibration. Despite increasing interest in UE, challenges persist, such as the need for explicit methods to capture aleatoric uncertainty and align uncertainty estimates with real-life disagreements among domain experts. This paper proposes an Expert Disagreement-Guided Uncertainty Estimation (EDUE) for medical image segmentation. By leveraging variability in ground-truth annotations from multiple raters, we guide the model during training and incorporate random sampling-based strategies to enhance calibration confidence. Our method achieves 55% and 23% improvement in correlation on average with expert disagreements at the image and pixel levels, respectively, better calibration, and competitive segmentation performance compared to the state-of-the-art deep ensembles, requiring only a single forward pass.
Reinforcement Learning for Solving Stochastic Vehicle Routing Problem with Time Windows
Iklassov, Zangir, Sobirov, Ikboljon, Solozabal, Ruben, Takac, Martin
This paper introduces a reinforcement learning approach to optimize the Stochastic Vehicle Routing Problem with Time Windows (SVRP), focusing on reducing travel costs in goods delivery. We develop a novel SVRP formulation that accounts for uncertain travel costs and demands, alongside specific customer time windows. An attention-based neural network trained through reinforcement learning is employed to minimize routing costs. Our approach addresses a gap in SVRP research, which traditionally relies on heuristic methods, by leveraging machine learning. The model outperforms the Ant-Colony Optimization algorithm, achieving a 1.73% reduction in travel costs. It uniquely integrates external information, demonstrating robustness in diverse environments, making it a valuable benchmark for future SVRP studies and industry application.
Super Images -- A New 2D Perspective on 3D Medical Imaging Analysis
Sobirov, Ikboljon, Saeed, Numan, Yaqub, Mohammad
In medical imaging analysis, deep learning has shown promising results. We frequently rely on volumetric data to segment medical images, necessitating the use of 3D architectures, which are commended for their capacity to capture interslice context. However, because of the 3D convolutions, max pooling, up-convolutions, and other operations utilized in these networks, these architectures are often more inefficient in terms of time and computation than their 2D equivalents. Furthermore, there are few 3D pretrained model weights, and pretraining is often difficult. We present a simple yet effective 2D method to handle 3D data while efficiently embedding the 3D knowledge during training. We propose transforming volumetric data into 2D super images and segmenting with 2D networks to solve these challenges. Our method generates a super-resolution image by stitching slices side by side in the 3D image. We expect deep neural networks to capture and learn these properties spatially despite losing depth information. This work aims to present a novel perspective when dealing with volumetric data, and we test the hypothesis using CNN and ViT networks as well as self-supervised pretraining. While attaining equal, if not superior, results to 3D networks utilizing only 2D counterparts, the model complexity is reduced by around threefold. Because volumetric data is relatively scarce, we anticipate that our approach will entice more studies, particularly in medical imaging analysis.
MGMT promoter methylation status prediction using MRI scans? An extensive experimental evaluation of deep learning models
Saeed, Numan, Ridzuan, Muhammad, Alasmawi, Hussain, Sobirov, Ikboljon, Yaqub, Mohammad
The number of studies on deep learning for medical diagnosis is expanding, and these systems are often claimed to outperform clinicians. However, only a few systems have shown medical efficacy. From this perspective, we examine a wide range of deep learning algorithms for the assessment of glioblastoma - a common brain tumor in older adults that is lethal. Surgery, chemotherapy, and radiation are the standard treatments for glioblastoma patients. The methylation status of the MGMT promoter, a specific genetic sequence found in the tumor, affects chemotherapy's effectiveness. MGMT promoter methylation improves chemotherapy response and survival in several cancers. MGMT promoter methylation is determined by a tumor tissue biopsy, which is then genetically tested. This lengthy and invasive procedure increases the risk of infection and other complications. Thus, researchers have used deep learning models to examine the tumor from brain MRI scans to determine the MGMT promoter's methylation state. We employ deep learning models and one of the largest public MRI datasets of 585 participants to predict the methylation status of the MGMT promoter in glioblastoma tumors using MRI scans. We test these models using Grad-CAM, occlusion sensitivity, feature visualizations, and training loss landscapes. Our results show no correlation between these two, indicating that external cohort data should be used to verify these models' performance to assure the accuracy and reliability of deep learning systems in cancer diagnosis.
Object Detection in Aerial Images: What Improves the Accuracy?
Malik, Hashmat Shadab, Sobirov, Ikboljon, Mohamed, Abdelrahman
Object detection is a challenging and popular computer vision problem. The problem is even more challenging in aerial images due to significant variation in scale and viewpoint in a diverse set of object categories. Recently, deep learning-based object detection approaches have been actively explored for the problem of object detection in aerial images. In this work, we investigate the impact of Faster R-CNN for aerial object detection and explore numerous strategies to improve its performance for aerial images. We conduct extensive experiments on the challenging iSAID dataset. The resulting adapted Faster R-CNN obtains a significant Figure 1: The figure shows the results of the improvements mAP gain of 4.96% over its vanilla baseline counterpart introduced on top of the vanilla Faster R-CNN.