Development of machine learning schemes for segmentation, characterisation, and evolution prediction of white matter hyperintensities in structural brain MRI

White matter hyperintensities (WMH) are neuroradiological features seen in T2 Fluid-Attenuated Inversion Recovery (T2-FLAIR) brain magnetic resonance imaging (MRI) and have been commonly associated with stroke, ageing, dementia, and Alzheimer’s disease (AD) progression. As a marker of neuro-degenerative disease, WMH may change over time and follow the clinical condition of the patient. In contrast to the early longitudinal studies of WMH, recent studies have suggested that the progression of WMH may be a dynamic, non-linear process where different clusters of WMH may shrink, stay unchanged, or grow. In this thesis, these changes are referred to as the “evolution of WMH”. The main objective of this thesis is to develop machine learning methods for prediction of WMH evolution in structural brain MRI from one-time (baseline) assessment. Predicting the evolution of WMH is challenging because the rate and direction of WMH evolution varies greatly across previous studies. Furthermore, the evolution of WMH is a non-deterministic problem because some clinical factors that possibly influence it are still not known. In this thesis, different learning schemes of deep learning algorithm and data modalities are proposed to produce the best estimation of WMH evolution. Furthermore, a scheme to simulate the non-deterministic nature of WMH evolution, named auxiliary input, was also proposed. In addition to the development of prediction model for WMH evolution, machine learning methods for segmentation of early WMH, characterisation of WMH, and simulation of WMH progression and regression are also developed as parts of this thesis

Improving Segmentation of Objects with Varying Sizes in Biomedical Images using Instance-wise and Center-of-Instance Segmentation Loss Function

In this paper, we propose a novel two-component loss for biomedical image segmentation tasks called the Instance-wise and Center-of-Instance (ICI) loss, a loss function that addresses the instance imbalance problem commonly encountered when using pixel-wise loss functions such as the Dice loss. The Instance-wise component improves the detection of small instances or ``blobs" in image datasets with both large and small instances. The Center-of-Instance component improves the overall detection accuracy. We compared the ICI loss with two existing losses, the Dice loss and the blob loss, in the task of stroke lesion segmentation using the ATLAS R2.0 challenge dataset from MICCAI 2022. Compared to the other losses, the ICI loss provided a better balanced segmentation, and significantly outperformed the Dice loss with an improvement of $1.7-3.7\%$ and the blob loss by $0.6-5.0\%$ in terms of the Dice similarity coefficient on both validation and test set, suggesting that the ICI loss is a potential solution to the instance imbalance problem.Comment: conferenc

Few-shot medical image classification with simple shape and texture text descriptors using vision-language models

In this work, we investigate the usefulness of vision-language models (VLMs) and large language models for binary few-shot classification of medical images. We utilize the GPT-4 model to generate text descriptors that encapsulate the shape and texture characteristics of objects in medical images. Subsequently, these GPT-4 generated descriptors, alongside VLMs pre-trained on natural images, are employed to classify chest X-rays and breast ultrasound images. Our results indicate that few-shot classification of medical images using VLMs and GPT-4 generated descriptors is a viable approach. However, accurate classification requires to exclude certain descriptors from the calculations of the classification scores. Moreover, we assess the ability of VLMs to evaluate shape features in breast mass ultrasound images. We further investigate the degree of variability among the sets of text descriptors produced by GPT-4. Our work provides several important insights about the application of VLMs for medical image analysis.Comment: 13 pages, 5 figure

PEER ASSESSMENT RATING (PAR) INDEX CALCULATION ON 2D DENTAL MODEL IMAGE FOR OVER JET, OPEN BITE, AND TEETH SEGMENTATION ON OCCLUSION SURFACE

Abstract Malocclusion is a clinical symptom, in which the teeth of maxilla and mandible are not located at the proper location. If malocclusion left untreated, it can lead to complications in the digestive system, headache, and periodontal disease disorders. Malocclusion problems involving abnormalities of teeth, bones, and muscles around the jaw are obligation of orthodontic specialists to treat them. The treatments can be varying based on the type of malocclusion, including tooth extraction and tooth braces. To know certain degree of malocclusion experienced by the patient, an assessment method called Peer Assessment Rating (PAR) Index is usually used by the specialist. To help the works of orthodontic specialists in Indonesia, a new automated calculation system based on 2D image of tooth model for PAR Index is being developed. In this paper, the calculation system for over-jet, open-bite, and teeth segmentation is developed. The result of the developed system is then compared with manual assessment done by orthodontic specialist, in order to verify the accuracy of the system

PERFORMANCE COMPARISON OF USART COMMUNICATION BETWEEN REAL TIME OPERATING SYSTEM (RTOS) AND NATIVE INTERRUPT

Comunication between microcontrollers is one of the crucial point in embedded sytems. On the other hand, embedded system must be able to run many parallel task simultaneously. To handle this, we need a reliabe system that can do a multitasking without decreasing every task’s performance. The most widely used methods for multitasking in embedded systems are using Interrupt Service Routine (ISR) or using Real Time Operating System (RTOS). This research compared perfomance of USART communication on system with RTOS to a system that use interrupt. Experiments run on two identical development board XMega A3BU-Xplained which used intenal sensor (light and temperature) and used servo as external component. Perfomance comparison done by counting ping time (elapsing time to transmit data and get a reply as a mark that data has been received) and compare it. This experiments divided into two scenarios: (1) system loaded with many tasks, (2) system loaded with few tasks. Result of the experiments show that communication will be faster if system only loaded with few tasks. System with RTOS has won from interrupt in case (1), but lose to interrupt in case (2)

PARTICLE SWARM OPTIMIZATION (PSO) FOR TRAINING OPTIMIZATION ON CONVOLUTIONAL NEURAL NETWORK (CNN)

Neural network attracts plenty of researchers lately. Substantial number of renowned universities have developed neural network for various both academically and industrially applications. Neural network shows considerable performance on various purposes. Nevertheless, for complex applications, neural network’s accuracy significantly deteriorates. To tackle the aforementioned drawback, lot of researches had been undertaken on the improvement of the standard neural network. One of the most promising modifications on standard neural network for complex applications is deep learning method. In this paper, we proposed the utilization of Particle Swarm Optimization (PSO) in Convolutional Neural Networks (CNNs), which is one of the basic methods in deep learning. The use of PSO on the training process aims to optimize the results of the solution vectors on CNN in order to improve the recognition accuracy. The data used in this research is handwritten digit from MNIST. The experiments exhibited that the accuracy can be attained in 4 epoch is 95.08%. This result was better than the conventional CNN and DBN.  The execution time was also almost similar to the conventional CNN. Therefore, the proposed method was a promising method.

SIMULATION OF LANDMARK APPROACH FOR WALL FOLLOWING ALGORITHM ON FIRE-FIGHTING ROBOT USING V-REP

Autonomous mobile robot has been implemented to assist humans in their daily activity. Autonomous robots have also contributed significantly in human safety. Autonomous mobile robot have been implemented to assist humans in their daily activity. Autonomous robots Have also contributed significantly in human safety. An example of the autonomous robot in the human safety sector is the fire fighting robot, which is the main topic of this paper. As an autonomous robot, the fire fighting robot needs a robust navigation ability to execute a given task in the shortest time interval. Wall-following algorithm is one of several navigating algorithm that simplifies this autonomous navigation problem. As a contribution, we propose two methods that could be combined to make the existing wall-following algorithm more robust. The combined wall-flowing algorithm will be compared to the original wall-following algorithm. By doing so, we could determine which method has more impact on the robot’s navigation robustness. Our goal is to see which method is more effective when combined with the wall-following algorithm

BEAGLEBOARD EMBEDDED SYSTEM FOR ADAPTIVE TRAFFIC LIGHT CONTROL SYSTEM WITH CAMERA SENSOR

Traffic is one of the most important aspects in human daily life because traffic affects smoothness of capital flows, logistics, and other community activities. Without appropriate traffic light control system, possibility of traffic congestion will be very high and hinder people’s life in urban areas. Adaptive traffic light control system can be used to solve traffic congestions in an intersection because it can adaptively change the durations of green light each lane in an intersection depend on traffic density. The proposed adaptive traffic light control system prototype uses Beagleboard-xM, CCTV camera, and AVR microcontrollers. We use computer vision technique to obtain information on traffic density combining Viola-Jones method with Kalman Filter method. To calculate traffic light time of each traffic light in intersection, we use Distributed Constraint Satisfaction Problem (DCSP). From implementations and experiments results, we conclude that BeagleBoard-xM can be used as main engine of adaptive traffic light control system with 91.735% average counting rate. Lalu intas adalah salah satu aspek yang paling penting dalam kehidupan sehari-hari manusia karena lalu lintas memengaruhi kelancaran arus modal, logistik, dan kegiatan masyarakat lainnya. Tanpa sistem kontrol lampu lalu lintas yang memadai, kemungkinan kemacetan lalu lintas akan sangat tinggi dan menghambat kehidupan masyarakat di perkotaan. Sistem kontrol lampu lalu lintas adaptif dapat digunakan untuk memecahkan kemacetan lalu lintas di persimpangan karena dapat mengubah durasi lampu hijau di setiap persimpangan jalan tergantung pada kepadatan lalu lintas. Prototipe sistem kontrol lampu lalu lintas menggunakan BeagleBoard-XM, kamera CCTV, dan mikrokontroler AVR. Peneliti menggunakan teknik computer vision untuk mendapatkan informasi tentang kepadatan lalu lintas dengan menggabungkan metode Viola-Jones dan metode Filter Kalman. Untuk menghitung waktu setiap lampu lalu lintas di persimpangan, peneliti menggunakan Distributed Constraint Satisfaction Problem (DCSP). Dari hasil implementasi dan percobaan dapat disimpulkan bahwa BeagleBoard-XM dapat digunakan sebagai mesin utama sistem kontrol lampu lalu lintas adaptif dengan tingkat akurasi penghitungan rata-rata sebesar 91.735%

Automatic Spatial Estimation of White Matter Hyperintensities Evolution in Brain MRI using Disease Evolution Predictor Deep Neural Networks

Funds from the Indonesia Endowment Fund for Education (LPDP), Ministry of Finance, Republic of Indonesia (MFR); Row Fogo Charitable Trust (Grant No. BRO-D.FID3668413)(MCVH); Wellcome Trust (patient recruitment, scanning, primary study Ref No. WT088134/Z/09/A); Fondation Leducq (Perivascular Spaces Transatlantic Network of Excellence); EU Horizon 2020 (SVDs@Target); and the MRC UK Dementia Research Institute at the University of Edinburgh (Wardlaw programme) are gratefully acknowledged. The Titan Xp used for this research was donated by the NVIDIA Corporation.Peer reviewedPublisher PD

COMPARISON OF IMAGE ENHANCEMENT METHODS FOR CHROMOSOME KARYOTYPE IMAGE ENHANCEMENT

The chromosome is a set of DNA structure that carry information about our life. The information can be obtained through Karyotyping. The process requires a clear image so the chromosome can be evaluate well. Preprocessing have to be done on chromosome images that is image enhancement. The process starts with image background removing. The image will be cleaned background color. The next step is image enhancement. This paper compares several methods for image enhancement. We evaluate some method in image enhancement like Histogram Equalization (HE), Contrast-limiting Adaptive Histogram Equalization (CLAHE), Histogram Equalization with 3D Block Matching (HE+BM3D), and basic image enhancement, unsharp masking. We examine and discuss the best method for enhancing chromosome image. Therefore, to evaluate the methods, the original image was manipulated by the addition of some noise and blur. Peak Signal-to-noise Ratio (PSNR) and Structural Similarity Index (SSIM) are used to examine method performance. The output of enhancement method will be compared with result of Professional software for karyotyping analysis named Ikaros MetasystemT M . Based on experimental results, HE+BM3D method gets a stable result on both scenario noised and blur image.