How Scopus is Shaping the Research Publications of Feature Fusion-Based Image Retrieval

Research trends have shown an increase in the preferences for feature fusion-based image retrieval. The primary objective of this study is to show the current state of research regarding image retrieval and feature fusion. The research papers indexed in the Scopus database are considered here for quantitative analysis. A bibliometric analysis of the research publications indexed in Scopus is presented in this study. During this study, 461 documents from 276 different sources are obtained. The important keywords, sources, authors, countries, and funding agencies are presented, which will help future researchers in research directions

Nuclei & Glands Instance Segmentation in Histology Images: A Narrative Review

Instance segmentation of nuclei and glands in the histology images is an important step in computational pathology workflow for cancer diagnosis, treatment planning and survival analysis. With the advent of modern hardware, the recent availability of large-scale quality public datasets and the community organized grand challenges have seen a surge in automated methods focusing on domain specific challenges, which is pivotal for technology advancements and clinical translation. In this survey, 126 papers illustrating the AI based methods for nuclei and glands instance segmentation published in the last five years (2017-2022) are deeply analyzed, the limitations of current approaches and the open challenges are discussed. Moreover, the potential future research direction is presented and the contribution of state-of-the-art methods is summarized. Further, a generalized summary of publicly available datasets and a detailed insights on the grand challenges illustrating the top performing methods specific to each challenge is also provided. Besides, we intended to give the reader current state of existing research and pointers to the future directions in developing methods that can be used in clinical practice enabling improved diagnosis, grading, prognosis, and treatment planning of cancer. To the best of our knowledge, no previous work has reviewed the instance segmentation in histology images focusing towards this direction.Comment: 60 pages, 14 figure

Hierarchical Classification of Scientific Taxonomies with Autonomous Underwater Vehicles

Autonomous Underwater Vehicles (AUVs) have catalysed a significant shift in the way marine habitats are studied. It is now possible to deploy an AUV from a ship, and capture tens of thousands of georeferenced images in a matter of hours. There is a growing body of research investigating ways to automatically apply semantic labels to this data, with two goals. The task of manually labelling a large number of images is time consuming and error prone. Further, there is the potential to change AUV surveys from being geographically defined (based on a pre-planned route), to permitting the AUV to adapt the mission plan in response to semantic observations. This thesis focusses on frameworks that permit a unified machine learning approach with applicability to a wide range of geographic areas, and diverse areas of interest for marine scientists. This can be addressed through the use of hierarchical classification; in which machine learning algorithms are trained to predict not just a binary or multi-class outcome, but a hierarchy of related output labels which are not mutually exclusive, such as a scientific taxonomy. In order to investigate classification on larger hierarchies with greater geographic diversity, the BENTHOZ-2015 data set was assembled as part of a collaboration between five Australian research groups. Existing labelled data was re-mapped to the CATAMI hierarchy, in total more than 400,000 point labels, conforming to a hierarchy of around 150 classes. The common hierarchical classification approach of building a network of binary classifiers was applied to the BENTHOZ-2015 data set, and a novel application of Bayesian Network theory and probability calibration was used as a theoretical foundation for the approach, resulting in improved classifier performance. This was extended to a more complex hidden node Bayesian Network structure, which permits inclusion of additional sensor modalities, and tuning for better performance in particular geographic regions

Pre-Operative Prediction of Mediastinal Node Metastasis Using Radiomics Model Based on 18F-FDG PET/CT of the Primary Tumor in Non-Small Cell Lung Cancer Patients

Purpose: We investigated whether a fluorine-18-fluorodeoxy glucose positron emission tomography/computed tomography (18F-FDG PET/CT)-based radiomics model (RM) could predict the pathological mediastinal lymph node staging (pN staging) in patients with non-small cell lung cancer (NSCLC) undergoing surgery.Methods: A total of 716 patients with a clinicopathological diagnosis of NSCLC were included in this retrospective study. The prediction model was developed in a training cohort that consisted of 501 patients. Radiomics features were extracted from the 18F-FDG PET/CT of the primary tumor. Support vector machine and extremely randomized trees were used to build the RM. Internal validation was assessed. An independent testing cohort contained the remaining 215 patients. The performances of the RM and clinical node staging (cN staging) in predicting pN staging (pN0 vs. pN1 and N2) were compared for each cohort. The area under the curve (AUC) of the receiver operating characteristic curve was applied to assess the model's performance.Results: The AUC of the RM [0.81 (95% CI, 0.771–0.848); sensitivity: 0.794; specificity: 0.704] for the predictive performance of pN1 and N2 was significantly better than that of cN in the training cohort [0.685 (95% CI, 0.644–0.728); sensitivity: 0.804; specificity: 0.568], (P-value = 8.29e-07, as assessed by the Delong test). In the testing cohort, the AUC of the RM [0.766 (95% CI, 0.702–0.830); sensitivity: 0.688; specificity: 0.704] was also significantly higher than that of cN [0.685 (95% CI, 0.619–0.747); sensitivity: 0.799; specificity: 0.568], (P = 0.0371, Delong test).Conclusions: The RM based on 18F-FDG PET/CT has a potential for the pN staging in patients with NSCLC, suggesting that therapeutic planning could be tailored according to the predictions

Evaluation of different segmentation-based approaches for skin disorders from dermoscopic images

Treballs Finals de Grau d'Enginyeria Biomèdica. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona. Curs: 2022-2023. Tutor/Director: Sala Llonch, Roser, Mata Miquel, Christian, Munuera, JosepSkin disorders are the most common type of cancer in the world and the incident has been lately increasing over the past decades. Even with the most complex and advanced technologies, current image acquisition systems do not permit a reliable identification of the skin lesion by visual examination due to the challenging structure of the malignancy. This promotes the need for the implementation of automatic skin lesion segmentation methods in order to assist in physicians’ diagnostic when determining the lesion's region and to serve as a preliminary step for the classification of the skin lesion. Accurate and precise segmentation is crucial for a rigorous screening and monitoring of the disease's progression. For the purpose of the commented concern, the present project aims to accomplish a state-of-the-art review about the most predominant conventional segmentation models for skin lesion segmentation, alongside with a market analysis examination. With the rise of automatic segmentation tools, a wide number of algorithms are currently being used, but many are the drawbacks when employing them for dermatological disorders due to the high-level presence of artefacts in the image acquired. In light of the above, three segmentation techniques have been selected for the completion of the work: level set method, an algorithm combining GrabCut and k-means methods and an intensity automatic algorithm developed by Hospital Sant Joan de Déu de Barcelona research group. In addition, a validation of their performance is conducted for a further implementation of them in clinical training. The proposals, together with the got outcomes, have been accomplished by means of a publicly available skin lesion image database

Object Recognition

Vision-based object recognition tasks are very familiar in our everyday activities, such as driving our car in the correct lane. We do these tasks effortlessly in real-time. In the last decades, with the advancement of computer technology, researchers and application developers are trying to mimic the human's capability of visually recognising. Such capability will allow machine to free human from boring or dangerous jobs

Connectionist-Symbolic Machine Intelligence using Cellular Automata based Reservoir-Hyperdimensional Computing

We introduce a novel framework of reservoir computing, that is capable of both connectionist machine intelligence and symbolic computation. Cellular automaton is used as the reservoir of dynamical systems. Input is randomly projected onto the initial conditions of automaton cells and nonlinear computation is performed on the input via application of a rule in the automaton for a period of time. The evolution of the automaton creates a space-time volume of the automaton state space, and it is used as the reservoir. The proposed framework is capable of long short-term memory and it requires orders of magnitude less computation compared to Echo State Networks. We prove that cellular automaton reservoir holds a distributed representation of attribute statistics, which provides a more effective computation than local representation. It is possible to estimate the kernel for linear cellular automata via metric learning, that enables a much more efficient distance computation in support vector machine framework. Also, binary reservoir feature vectors can be combined using Boolean operations as in hyperdimensional computing, paving a direct way for concept building and symbolic processing.Comment: Corrected Typos. Responded some comments on section 8. Added appendix for details. Recurrent architecture emphasize

Vessel identification in diabetic retinopathy

Diabetic retinopathy is the single largest cause of sight loss and blindness in 18 to 65 year olds. Screening programs for the estimated one to six per- cent of the diabetic population have been demonstrated to be cost and sight saving, howeverthere are insufficient screening resources. Automatic screen-ing systems may help solve this resource short fall. This thesis reports on research into an aspect of automatic grading of diabetic retinopathy; namely the identification of the retinal blood vessels in fundus photographs. It de-velops two vessels segmentation strategies and assess their accuracies. A literature review of retinal vascular segmentation found few results, and indicated a need for further development. The two methods for vessel segmentation were investigated in this thesis are based on mathematical morphology and neural networks. Both methodologies are verified on independently labeled data from two institutions and results are presented that characterisethe trade off betweenthe ability to identify vesseland non-vessels data. These results are based on thirty five images with their retinal vessels labeled. Of these images over half had significant pathology and or image acquisition artifacts. The morphological segmentation used ten images from one dataset for development. The remaining images of this dataset and the entire set of 20 images from the seconddataset were then used to prospectively verify generaliastion. For the neural approach, the imageswere pooled and 26 randomly chosenimageswere usedin training whilst 9 were reserved for prospective validation. Assuming equal importance, or cost, for vessel and non-vessel classifications, the following results were obtained; using mathematical morphology 84% correct classification of vascular and non-vascular pixels was obtained in the first dataset. This increased to 89% correct for the second dataset. Using the pooled data the neural approach achieved 88% correct identification accuracy. The spread of accuracies observed varied. It was highest in the small initial dataset with 16 and 10 percent standard deviation in vascular and non-vascular cases respectively. The lowest variability was observed in the neural classification, with a standard deviation of 5% for both accuracies. The less tangible outcomes of the research raises the issueof the selection and subsequent distribution of the patterns for neural network training. Unfortunately this indication would require further labeling of precisely those cases that were felt to be the most difficult. I.e. the small vessels and border conditions between pathology and the retina. The more concrete, evidence based conclusions,characterise both the neural and the morphological methods over a range of operating points. Many of these operating points are comparable to the few results presented in the literature. The advantage of the author's approach lies in the neural method's consistent as well as accurate vascular classification

Artificial intelligence for breast cancer precision pathology

Breast cancer is the most common cancer type in women globally but is associated with a continuous decline in mortality rates. The improved prognosis can be partially attributed to effective treatments developed for subgroups of patients. However, nowadays, it remains challenging to optimise treatment plans for each individual. To improve disease outcome and to decrease the burden associated with unnecessary treatment and adverse drug effects, the current thesis aimed to develop artificial intelligence based tools to improve individualised medicine for breast cancer patients. In study I, we developed a deep learning based model (DeepGrade) to stratify patients that were associated with intermediate risks. The model was optimised with haematoxylin and eosin (HE) stained whole slide images (WSIs) with grade 1 and 3 tumours and applied to stratify grade 2 tumours into grade 1-like (DG2-low) and grade 3-like (DG2-high) subgroups. The efficacy of the DeepGrade model was validated using recurrence free survival where the dichotomised groups exhibited an adjusted hazard ratio (HR) of 2.94 (95% confidence interval [CI] 1.24-6.97, P = 0.015). The observation was further confirmed in the external test cohort with an adjusted HR of 1.91 (95% CI: 1.11-3.29, P = 0.019). In study II, we investigated whether deep learning models were capable of predicting gene expression levels using the morphological patterns from tumours. We optimised convolutional neural networks (CNNs) to predict mRNA expression for 17,695 genes using HE stained WSIs from the training set. An initial evaluation on the validation set showed that a significant correlation between the RNA-seq measurements and model predictions was observed for 52.75% of the genes. The models were further tested in the internal and external test sets. Besides, we compared the model's efficacy in predicting RNA-seq based proliferation scores. Lastly, the ability of capturing spatial gene expression variations for the optimised CNNs was evaluated and confirmed using spatial transcriptomics profiling. In study III, we investigated the relationship between intra-tumour gene expression heterogeneity and patient survival outcomes. Deep learning models optimised from study II were applied to generate spatial gene expression predictions for the PAM50 gene panel. A set of 11 texture based features and one slide average gene expression feature per gene were extracted as input to train a Cox proportional hazards regression model with elastic net regularisation to predict patient risk of recurrence. Through nested cross-validation, the model dichotomised the training cohort into low and high risk groups with an adjusted HR of 2.1 (95% CI: 1.30-3.30, P = 0.002). The model was further validated on two external cohorts. In study IV, we investigated the agreement between the Stratipath Breast, which is the modified, commercialised DeepGrade model developed in study I, and the Prosigna® test. Both tests sought to stratify patients with distinct prognosis. The outputs from Stratipath Breast comprise a risk score and a two-level risk stratification whereas the outputs from Prosigna® include the risk of recurrence score and a three-tier risk stratification. By comparing the number of patients assigned to ‘low’ or ‘high’ risk groups, we found an overall moderate agreement (76.09%) between the two tests. Besides, the risk scores by two tests also revealed a good correlation (Spearman's rho = 0.59, P = 1.16E-08). In addition, a good correlation was observed between the risk score from each test and the Ki67 index. The comparison was also carried out in the subgroup of patients with grade 2 tumours where similar but slightly dropped correlations were found

La perception d'attributs visuels de premier et deuxième ordres

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