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Vajira Thambawita

Publications and source records attributed to Vajira Thambawita.

47 records · Page 3Linked to original sources

Meta-learning with implicit gradients in a few-shot setting for medical image segmentation

Widely used traditional supervised deep learning methods require a large number of training samples but often fail to generalize on unseen datasets. Therefore, a more general application of any trained model is quite limited for medical imaging for clinical practice. Using separately trained models for each unique lesion category or a unique patient population will require sufficiently large curated datasets, which is not practical to use in a real-world clinical set-up. Few-shot learning approaches can not only minimize the need for an enormous number of reliable ground truth labels that are labour-intensive and expensive but can also be used to model on a dataset coming from a new population. To this end, we propose to exploit an optimization-based implicit model agnostic meta-learning (iMAML) algorithm under few-shot settings for medical image segmentation. Our approach can leverage the learned weights from diverse but small training samples to perform analysis on unseen datasets with high accuracy. We show that, unlike classical few-shot learning approaches, our method improves generalization capability. To our knowledge, this is the first work that exploits iMAML for medical image segmentation and explores the strength of the model on scenarios such as meta-training on unique and mixed instances of lesion datasets. Our quantitative results on publicly available skin and polyp datasets show that the proposed method outperforms the naive supervised baseline model and two recent few-shot segmentation approaches by large margins. In addition, our iMAML approach shows an improvement of 2%-4% in dice score compared to its counterpart MAML for most experiments.

cs.CV↗

DivergentNets: Medical Image Segmentation by Network Ensemble

Detection of colon polyps has become a trending topic in the intersecting fields of machine learning and gastrointestinal endoscopy. The focus has mainly been on per-frame classification. More recently, polyp segmentation has gained attention in the medical community. Segmentation has the advantage of being more accurate than per-frame classification or object detection as it can show the affected area in greater detail. For our contribution to the EndoCV 2021 segmentation challenge, we propose two separate approaches. First, a segmentation model named TriUNet composed of three separate UNet models. Second, we combine TriUNet with an ensemble of well-known segmentation models, namely UNet++, FPN, DeepLabv3, and DeepLabv3+, into a model called DivergentNets to produce more generalizable medical image segmentation masks. In addition, we propose a modified Dice loss that calculates loss only for a single class when performing multiclass segmentation, forcing the model to focus on what is most important. Overall, the proposed methods achieved the best average scores for each respective round in the challenge, with TriUNet being the winning model in Round I and DivergentNets being the winning model in Round II of the segmentation generalization challenge at EndoCV 2021. The implementation of our approach is made publicly available on GitHub.

eess.IV↗

Pyramid-Focus-Augmentation: Medical Image Segmentation with Step-Wise Focus

Segmentation of findings in the gastrointestinal tract is a challenging but also an important task which is an important building stone for sufficient automatic decision support systems. In this work, we present our solution for the Medico 2020 task, which focused on the problem of colon polyp segmentation. We present our simple but efficient idea of using an augmentation method that uses grids in a pyramid-like manner (large to small) for segmentation. Our results show that the proposed methods work as indented and can also lead to comparable results when competing with other methods.

cs.CV↗

An Extensive Study on Cross-Dataset Bias and Evaluation Metrics Interpretation for Machine Learning applied to Gastrointestinal Tract Abnormality Classification

Precise and efficient automated identification of Gastrointestinal (GI) tract diseases can help doctors treat more patients and improve the rate of disease detection and identification. Currently, automatic analysis of diseases in the GI tract is a hot topic in both computer science and medical-related journals. Nevertheless, the evaluation of such an automatic analysis is often incomplete or simply wrong. Algorithms are often only tested on small and biased datasets, and cross-dataset evaluations are rarely performed. A clear understanding of evaluation metrics and machine learning models with cross datasets is crucial to bring research in the field to a new quality level. Towards this goal, we present comprehensive evaluations of five distinct machine learning models using Global Features and Deep Neural Networks that can classify 16 different key types of GI tract conditions, including pathological findings, anatomical landmarks, polyp removal conditions, and normal findings from images captured by common GI tract examination instruments. In our evaluation, we introduce performance hexagons using six performance metrics such as recall, precision, specificity, accuracy, F1-score, and Matthews Correlation Coefficient to demonstrate how to determine the real capabilities of models rather than evaluating them shallowly. Furthermore, we perform cross-dataset evaluations using different datasets for training and testing. With these cross-dataset evaluations, we demonstrate the challenge of actually building a generalizable model that could be used across different hospitals. Our experiments clearly show that more sophisticated performance metrics and evaluation methods need to be applied to get reliable models rather than depending on evaluations of the splits of the same dataset, i.e., the performance metrics should always be interpreted together rather than relying on a single metric.

cs.LG↗

Stacked dense optical flows and dropout layers to predict sperm motility and morphology

In this paper, we analyse two deep learning methods to predict sperm motility and sperm morphology from sperm videos. We use two different inputs: stacked pure frames of videos and dense optical flows of video frames. To solve this regression task of predicting motility and morphology, stacked dense optical flows and extracted original frames from sperm videos were used with the modified state of the art convolution neural networks. For modifications of the selected models, we have introduced an additional multi-layer perceptron to overcome the problem of over-fitting. The method which had an additional multi-layer perceptron with dropout layers, shows the best results when the inputs consist of both dense optical flows and an original frame of videos.

eess.IV↗

Extracting temporal features into a spatial domain using autoencoders for sperm video analysis

In this paper, we present a two-step deep learning method that is used to predict sperm motility and morphology-based on video recordings of human spermatozoa. First, we use an autoencoder to extract temporal features from a given semen video and plot these into image-space, which we call feature-images. Second, these feature-images are used to perform transfer learning to predict the motility and morphology values of human sperm. The presented method shows it's capability to extract temporal information into spatial domain feature-images which can be used with traditional convolutional neural networks. Furthermore, the accuracy of the predicted motility of a given semen sample shows that a deep learning-based model can capture the temporal information of microscopic recordings of human semen.

cs.CV↗

Machine Learning-Based Analysis of Sperm Videos and Participant Data for Male Fertility Prediction

Methods for automatic analysis of clinical data are usually targeted towards a specific modality and do not make use of all relevant data available. In the field of male human reproduction, clinical and biological data are not used to its fullest potential. Manual evaluation of a semen sample using a microscope is time-consuming and requires extensive training. Furthermore, the validity of manual semen analysis has been questioned due to limited reproducibility, and often high inter-personnel variation. The existing computer-aided sperm analyzer systems are not recommended for routine clinical use due to methodological challenges caused by the consistency of the semen sample. Thus, there is a need for an improved methodology. We use modern and classical machine learning techniques together with a dataset consisting of 85 videos of human semen samples and related participant data to automatically predict sperm motility. Used techniques include simple linear regression and more sophisticated methods using convolutional neural networks. Our results indicate that sperm motility prediction based on deep learning using sperm motility videos is rapid to perform and consistent. The algorithms performed worse when participant data was added. In conclusion, machine learning-based automatic analysis may become a valuable tool in male infertility investigation and research.

cs.LG↗

An optimized Parallel Failure-less Aho-Corasick algorithm for DNA sequence matching

The Aho-Corasick algorithm is multiple patterns searching algorithm running sequentially in various applications like network intrusion detection and bioinformatics for finding several input strings within a given large input string. The parallel version of the Aho-Corasick algorithm is called as Parallel Failure-less Aho-Corasick algorithm because it doesn't need failure links like in the original Aho-Corasick algorithm. In this research, we implemented an application specific parallel failureless Aho-Corasick algorithm to the general purpose graphics processing unit by applying several cache optimization techniques for matching DNA sequences. Our parallel Aho-Corasick algorithm shows better performance than the available parallel Aho-Corasick algorithm library due to its simplicity and optimized cache memory usage of graphics processing units for matching DNA sequences.

cs.DC↗

The Medico-Task 2018: Disease Detection in the Gastrointestinal Tract using Global Features and Deep Learning

In this paper, we present our approach for the 2018 Medico Task classifying diseases in the gastrointestinal tract. We have proposed a system based on global features and deep neural networks. The best approach combines two neural networks, and the reproducible experimental results signify the efficiency of the proposed model with an accuracy rate of 95.80%, a precision of 95.87%, and an F1-score of 95.80%.

cs.LG↗

To Use or Not to Use: CPUs' Cache Optimization Techniques on GPGPUs

General Purpose Graphic Processing Unit(GPGPU) is used widely for achieving high performance or high throughput in parallel programming. This capability of GPGPUs is very famous in the new era and mostly used for scientific computing which requires more processing power than normal personal computers. Therefore, most of the programmers, researchers and industry use this new concept for their work. However, achieving high-performance or high-throughput using GPGPUs are not an easy task compared with conventional programming concepts in the CPU side. In this research, the CPU's cache memory optimization techniques have been adopted to the GPGPU's cache memory to identify rare performance improvement techniques compared to GPGPU's best practices. The cache optimization techniques of blocking, loop fusion, array merging and array transpose were tested on GPGPUs for finding suitability of these techniques. Finally, we identified that some of the CPU cache optimization techniques go well with the cache memory system of the GPGPU and shows performance improvements while some others show the opposite effect on the GPGPUs compared with the CPUs.

cs.DC↗

To Use or Not to Use: Graphics Processing Units for Pattern Matching Algorithms

String matching is an important part in today's computer applications and Aho-Corasick algorithm is one of the main string matching algorithms used to accomplish this. This paper discusses that when can the GPUs be used for string matching applications using the Aho-Corasick algorithm as a benchmark. We have to identify the best unit to run our string matching algorithm according to the performance of our devices and the applications. Sometimes CPU gives better performance than GPU and sometimes GPU gives better performance than CPU. Therefore, identifying this critical point is significant task for researchers who are using GPUs to improve the performance of their string matching applications based on string matching algorithms.

cs.DC↗