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1.
Hum Brain Mapp ; 45(11): e26803, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-39119860

ABSTRACT

Accurate segmentation of chronic stroke lesions from mono-spectral magnetic resonance imaging scans (e.g., T1-weighted images) is a difficult task due to the arbitrary shape, complex texture, variable size and intensities, and varied locations of the lesions. Due to this inherent spatial heterogeneity, existing machine learning methods have shown moderate performance for chronic lesion delineation. In this study, we introduced: (1) a method that integrates transformers' deformable feature attention mechanism with convolutional deep learning architecture to improve the accuracy and generalizability of stroke lesion segmentation, and (2) an ecological data augmentation technique based on inserting real lesions into intact brain regions. Our combination of these two approaches resulted in a significant increase in segmentation performance, with a Dice index of 0.82 (±0.39), outperforming the existing methods trained and tested on the same Anatomical Tracings of Lesions After Stroke (ATLAS) 2022 dataset. Our method performed relatively well even for cases with small stroke lesions. We validated the robustness of our method through an ablation study and by testing it on new unseen brain scans from the Ischemic Stroke Lesion Segmentation (ISLES) 2015 dataset. Overall, our proposed approach of transformers with ecological data augmentation offers a robust way to delineate chronic stroke lesions with clinically relevant accuracy. Our method can be extended to other challenging tasks that require automated detection and segmentation of diverse brain abnormalities from clinical scans.


Subject(s)
Deep Learning , Magnetic Resonance Imaging , Stroke , Humans , Magnetic Resonance Imaging/methods , Magnetic Resonance Imaging/standards , Stroke/diagnostic imaging , Stroke/pathology , Neuroimaging/methods , Neuroimaging/standards , Ischemic Stroke/diagnostic imaging , Image Processing, Computer-Assisted/methods , Aged , Brain/diagnostic imaging , Brain/pathology
2.
J Digit Imaging ; 36(4): 1653-1662, 2023 08.
Article in English | MEDLINE | ID: mdl-37059892

ABSTRACT

Tissue phenotyping is a fundamental step in computational pathology for the analysis of tumor micro-environment in whole slide images (WSIs). Automatic tissue phenotyping in whole slide images (WSIs) of colorectal cancer (CRC) assists pathologists in better cancer grading and prognostication. In this paper, we propose a novel algorithm for the identification of distinct tissue components in colon cancer histology images by blending a comprehensive learning system with deep features extraction in the current work. Firstly, we extracted the features from the pre-trained VGG19 network which are then transformed into mapped features space for nodes enhancement generation. Utilizing both mapped features and enhancement nodes, the proposed algorithm classifies seven distinct tissue components including stroma, tumor, complex stroma, necrotic, normal benign, lymphocytes, and smooth muscle. To validate our proposed model, the experiments are performed on two publicly available colorectal cancer histology datasets. We showcase that our approach achieves a remarkable performance boost surpassing existing state-of-the-art methods by (1.3% AvTP, 2% F1) and (7% AvTP, 6% F1) on CRCD-1, and CRCD-2, respectively.


Subject(s)
Algorithms , Colorectal Neoplasms , Humans , Learning , Pathologists , Colorectal Neoplasms/diagnostic imaging , Tumor Microenvironment
3.
Sensors (Basel) ; 22(4)2022 Feb 21.
Article in English | MEDLINE | ID: mdl-35214568

ABSTRACT

Human beings tend to incrementally learn from the rapidly changing environment without comprising or forgetting the already learned representations. Although deep learning also has the potential to mimic such human behaviors to some extent, it suffers from catastrophic forgetting due to which its performance on already learned tasks drastically decreases while learning about newer knowledge. Many researchers have proposed promising solutions to eliminate such catastrophic forgetting during the knowledge distillation process. However, to our best knowledge, there is no literature available to date that exploits the complex relationships between these solutions and utilizes them for the effective learning that spans over multiple datasets and even multiple domains. In this paper, we propose a continual learning objective that encompasses mutual distillation loss to understand such complex relationships and allows deep learning models to effectively retain the prior knowledge while adapting to the new classes, new datasets, and even new applications. The proposed objective was rigorously tested on nine publicly available, multi-vendor, and multimodal datasets that span over three applications, and it achieved the top-1 accuracy of 0.9863% and an F1-score of 0.9930.


Subject(s)
Neural Networks, Computer , Humans
4.
J Digit Imaging ; 35(3): 678-691, 2022 06.
Article in English | MEDLINE | ID: mdl-35182292

ABSTRACT

This study aims at investigating the classification power of different b-values of the diffusion-weighted magnetic resonance images (DWI) as indicator of prostate cancer. This paper investigates several techniques for analyzing data from DWI acquired at a range of b-values for the purpose of detecting prostate cancer. In the first phase of experiments, we analyze the available data by producing two main parametric maps using two common models, namely: the intra-voxel incoherent motion (IVIM) model and the mono-exponential ADC model. Accordingly, we evaluated the benign/malignant tissue classification potential of several parametric maps produced using different combinations of b-values and fitting models. In the second phase, we utilized the maps that performed best in the first phase of experiments to design a machine learning-based computer-assisted diagnosis system for the detection of early stage prostate cancer. The system performance was cross-validated using data from 20 patients. On a fivefold cross-validation scheme, a maximum accuracy and an area under the receiver operating characteristic (AUC) of 90% and 0.978, respectively, was achieved by a system that uses ADC maps fitted using the mono-exponential model at 11 different b-values. The results suggest that the proposed machine learning-based diagnosis system is potentially powerful in differentiating between malignant and benign prostate tissues when combined with carefully generated ADC maps.


Subject(s)
Diffusion Magnetic Resonance Imaging , Prostatic Neoplasms , Diffusion Magnetic Resonance Imaging/methods , Humans , Magnetic Resonance Imaging , Male , Motion , Prostatic Neoplasms/diagnostic imaging , ROC Curve
5.
Sensors (Basel) ; 20(22)2020 Nov 12.
Article in English | MEDLINE | ID: mdl-33198071

ABSTRACT

Screening baggage against potential threats has become one of the prime aviation security concerns all over the world, where manual detection of prohibited items is a time-consuming and hectic process. Many researchers have developed autonomous systems to recognize baggage threats using security X-ray scans. However, all of these frameworks are vulnerable against screening cluttered and concealed contraband items. Furthermore, to the best of our knowledge, no framework possesses the capacity to recognize baggage threats across multiple scanner specifications without an explicit retraining process. To overcome this, we present a novel meta-transfer learning-driven tensor-shot detector that decomposes the candidate scan into dual-energy tensors and employs a meta-one-shot classification backbone to recognize and localize the cluttered baggage threats. In addition, the proposed detection framework can be well-generalized to multiple scanner specifications due to its capacity to generate object proposals from the unified tensor maps rather than diversified raw scans. We have rigorously evaluated the proposed tensor-shot detector on the publicly available SIXray and GDXray datasets (containing a cumulative of 1,067,381 grayscale and colored baggage X-ray scans). On the SIXray dataset, the proposed framework achieved a mean average precision (mAP) of 0.6457, and on the GDXray dataset, it achieved the precision and F1 score of 0.9441 and 0.9598, respectively. Furthermore, it outperforms state-of-the-art frameworks by 8.03% in terms of mAP, 1.49% in terms of precision, and 0.573% in terms of F1 on the SIXray and GDXray dataset, respectively.

6.
J Digit Imaging ; 32(5): 793-807, 2019 10.
Article in English | MEDLINE | ID: mdl-30506124

ABSTRACT

We address the problem of prostate lesion detection, localization, and segmentation in T2W magnetic resonance (MR) images. We train a deep convolutional encoder-decoder architecture to simultaneously segment the prostate, its anatomical structure, and the malignant lesions. To incorporate the 3D contextual spatial information provided by the MRI series, we propose a novel 3D sliding window approach, which preserves the 2D domain complexity while exploiting 3D information. Experiments on data from 19 patients provided for the public by the Initiative for Collaborative Computer Vision Benchmarking (I2CVB) show that our approach outperforms traditional pattern recognition and machine learning approaches by a significant margin. Particularly, for the task of cancer detection and localization, the system achieves an average AUC of 0.995, an accuracy of 0.894, and a recall of 0.928. The proposed mono-modal deep learning-based system performs comparably to other multi-modal MR-based systems. It could improve the performance of a radiologist in prostate cancer diagnosis and treatment planning.


Subject(s)
Deep Learning , Image Interpretation, Computer-Assisted/methods , Magnetic Resonance Imaging/methods , Prostatic Neoplasms/diagnostic imaging , Adult , Aged , Aged, 80 and over , Humans , Male , Middle Aged , Prostate/diagnostic imaging
7.
IEEE J Biomed Health Inform ; 28(2): 952-963, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37999960

ABSTRACT

Early-stage cancer diagnosis potentially improves the chances of survival for many cancer patients worldwide. Manual examination of Whole Slide Images (WSIs) is a time-consuming task for analyzing tumor-microenvironment. To overcome this limitation, the conjunction of deep learning with computational pathology has been proposed to assist pathologists in efficiently prognosing the cancerous spread. Nevertheless, the existing deep learning methods are ill-equipped to handle fine-grained histopathology datasets. This is because these models are constrained via conventional softmax loss function, which cannot expose them to learn distinct representational embeddings of the similarly textured WSIs containing an imbalanced data distribution. To address this problem, we propose a novel center-focused affinity loss (CFAL) function that exhibits 1) constructing uniformly distributed class prototypes in the feature space, 2) penalizing difficult samples, 3) minimizing intra-class variations, and 4) placing greater emphasis on learning minority class features. We evaluated the performance of the proposed CFAL loss function on two publicly available breast and colon cancer datasets having varying levels of imbalanced classes. The proposed CFAL function shows better discrimination abilities as compared to the popular loss functions such as ArcFace, CosFace, and Focal loss. Moreover, it outperforms several SOTA methods for histology image classification across both datasets.


Subject(s)
Breast , Neoplasms , Humans , Breast/diagnostic imaging , Histological Techniques , Tumor Microenvironment , Neoplasms/diagnostic imaging
8.
IEEE Trans Image Process ; 33: 241-256, 2024.
Article in English | MEDLINE | ID: mdl-38064329

ABSTRACT

Accurate classification of nuclei communities is an important step towards timely treating the cancer spread. Graph theory provides an elegant way to represent and analyze nuclei communities within the histopathological landscape in order to perform tissue phenotyping and tumor profiling tasks. Many researchers have worked on recognizing nuclei regions within the histology images in order to grade cancerous progression. However, due to the high structural similarities between nuclei communities, defining a model that can accurately differentiate between nuclei pathological patterns still needs to be solved. To surmount this challenge, we present a novel approach, dubbed neural graph refinement, that enhances the capabilities of existing models to perform nuclei recognition tasks by employing graph representational learning and broadcasting processes. Based on the physical interaction of the nuclei, we first construct a fully connected graph in which nodes represent nuclei and adjacent nodes are connected to each other via an undirected edge. For each edge and node pair, appearance and geometric features are computed and are then utilized for generating the neural graph embeddings. These embeddings are used for diffusing contextual information to the neighboring nodes, all along a path traversing the whole graph to infer global information over an entire nuclei network and predict pathologically meaningful communities. Through rigorous evaluation of the proposed scheme across four public datasets, we showcase that learning such communities through neural graph refinement produces better results that outperform state-of-the-art methods.


Subject(s)
Cell Nucleus , Learning , Histological Techniques
9.
Artif Intell Med ; 149: 102782, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38462283

ABSTRACT

Diabetic retinopathy (DR) is the most prevalent cause of visual impairment in adults worldwide. Typically, patients with DR do not show symptoms until later stages, by which time it may be too late to receive effective treatment. DR Grading is challenging because of the small size and variation in lesion patterns. The key to fine-grained DR grading is to discover more discriminating elements such as cotton wool, hard exudates, hemorrhages, microaneurysms etc. Although deep learning models like convolutional neural networks (CNN) seem ideal for the automated detection of abnormalities in advanced clinical imaging, small-size lesions are very hard to distinguish by using traditional networks. This work proposes a bi-directional spatial and channel-wise parallel attention based network to learn discriminative features for diabetic retinopathy grading. The proposed attention block plugged with a backbone network helps to extract features specific to fine-grained DR-grading. This scheme boosts classification performance along with the detection of small-sized lesion parts. Extensive experiments are performed on four widely used benchmark datasets for DR grading, and performance is evaluated on different quality metrics. Also, for model interpretability, activation maps are generated using the LIME method to visualize the predicted lesion parts. In comparison with state-of-the-art methods, the proposed IDANet exhibits better performance for DR grading and lesion detection.


Subject(s)
Diabetes Mellitus , Diabetic Retinopathy , Adult , Humans , Diabetic Retinopathy/diagnostic imaging , Diabetic Retinopathy/pathology , Neural Networks, Computer , Image Interpretation, Computer-Assisted/methods
10.
Med Image Anal ; 96: 103203, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38810517

ABSTRACT

The classification of gigapixel Whole Slide Images (WSIs) is an important task in the emerging area of computational pathology. There has been a surge of interest in deep learning models for WSI classification with clinical applications such as cancer detection or prediction of cellular mutations. Most supervised methods require expensive and labor-intensive manual annotations by expert pathologists. Weakly supervised Multiple Instance Learning (MIL) methods have recently demonstrated excellent performance; however, they still require large-scale slide-level labeled training datasets that require a careful inspection of each slide by an expert pathologist. In this work, we propose a fully unsupervised WSI classification algorithm based on mutual transformer learning. The instances (i.e., patches) from gigapixel WSIs are transformed into a latent space and then inverse-transformed to the original space. Using the transformation loss, pseudo labels are generated and cleaned using a transformer label cleaner. The proposed transformer-based pseudo-label generator and cleaner modules mutually train each other iteratively in an unsupervised manner. A discriminative learning mechanism is introduced to improve normal versus cancerous instance labeling. In addition to the unsupervised learning, we demonstrate the effectiveness of the proposed framework for weakly supervised learning and cancer subtype classification as downstream analysis. Extensive experiments on four publicly available datasets show better performance of the proposed algorithm compared to the existing state-of-the-art methods.


Subject(s)
Algorithms , Image Interpretation, Computer-Assisted , Humans , Image Interpretation, Computer-Assisted/methods , Unsupervised Machine Learning , Deep Learning , Neoplasms/diagnostic imaging , Image Processing, Computer-Assisted/methods
11.
Article in English | MEDLINE | ID: mdl-38466603

ABSTRACT

Analysis of the 3-D texture is indispensable for various tasks, such as retrieval, segmentation, classification, and inspection of sculptures, knit fabrics, and biological tissues. A 3-D texture represents a locally repeated surface variation (SV) that is independent of the overall shape of the surface and can be determined using the local neighborhood and its characteristics. Existing methods mostly employ computer vision techniques that analyze a 3-D mesh globally, derive features, and then utilize them for classification or retrieval tasks. While several traditional and learning-based methods have been proposed in the literature, only a few have addressed 3-D texture analysis, and none have considered unsupervised schemes so far. This article proposes an original framework for the unsupervised segmentation of 3-D texture on the mesh manifold. The problem is approached as a binary surface segmentation task, where the mesh surface is partitioned into textured and nontextured regions without prior annotation. The proposed method comprises a mutual transformer-based system consisting of a label generator (LG) and a label cleaner (LC). Both models take geometric image representations of the surface mesh facets and label them as texture or nontexture using an iterative mutual learning scheme. Extensive experiments on three publicly available datasets with diverse texture patterns demonstrate that the proposed framework outperforms standard and state-of-the-art unsupervised techniques and performs reasonably well compared to supervised methods.

12.
Sci Data ; 11(1): 15, 2024 Jan 02.
Article in English | MEDLINE | ID: mdl-38167525

ABSTRACT

Drone-person tracking in uniform appearance crowds poses unique challenges due to the difficulty in distinguishing individuals with similar attire and multi-scale variations. To address this issue and facilitate the development of effective tracking algorithms, we present a novel dataset named D-PTUAC (Drone-Person Tracking in Uniform Appearance Crowd). The dataset comprises 138 sequences comprising over 121 K frames, each manually annotated with bounding boxes and attributes. During dataset creation, we carefully consider 18 challenging attributes encompassing a wide range of viewpoints and scene complexities. These attributes are annotated to facilitate the analysis of performance based on specific attributes. Extensive experiments are conducted using 44 state-of-the-art (SOTA) trackers, and the performance gap between the visual object trackers on existing benchmarks compared to our proposed dataset demonstrate the need for a dedicated end-to-end aerial visual object tracker that accounts the inherent properties of aerial environment.

13.
Article in English | MEDLINE | ID: mdl-39298306

ABSTRACT

Retinopathy is a group of retinal disabilities that causes severe visual impairments or complete blindness. Due to the capability of optical coherence tomography to reveal early retinal abnormalities, many researchers have utilized it to develop autonomous retinal screening systems. However, to the best of our knowledge, most of these systems rely only on mathematical features, which might not be helpful to clinicians since they do not encompass the clinical manifestations of screening the underlying diseases. Such clinical manifestations are critically important to be considered within the autonomous screening systems to match the grading of ophthalmologists within the clinical settings. To overcome these limitations, we present a novel framework that exploits the fusion of vision language correlation between the retinal imagery and the set of clinical prompts to recognize the different types of retinal disabilities. The proposed framework is rigorously tested on six public datasets, where, across each dataset, the proposed framework outperformed state-of-the-art methods in various metrics. Moreover, the clinical significance of the proposed framework is also tested under strict blind testing experiments, where the proposed system achieved a statistically significant correlation coefficient of 0.9185 and 0.9529 with the two expert clinicians. These blind test experiments highlight the potential of the proposed framework to be deployed in the real world for accurate screening of retinal diseases.

14.
PLoS One ; 19(9): e0308658, 2024.
Article in English | MEDLINE | ID: mdl-39269959

ABSTRACT

Spectral Photon Counting Computed Tomography (SPCCT), a ground-breaking development in CT technology, has immense potential to address the persistent problem of metal artefacts in CT images. This study aims to evaluate the potential of Mars photon-counting CT technology in reducing metal artefacts. It focuses on identifying and quantifying clinically significant materials in the presence of metal objects. A multi-material phantom was used, containing inserts of varying concentrations of hydroxyapatite (a mineral present in teeth, bones, and calcified plaque), iodine (used as a contrast agent), CT water (to mimic soft tissue), and adipose (as a fat substitute). Three sets of scans were acquired: with aluminium, with stainless steel, and without a metal insert as a reference dataset. Data acquisition was performed using a Mars SPCCT scanner (Microlab 5×120); operated at 118 kVp and 80 µA. The images were subsequently reconstructed into five energy bins: 7-40, 40-50, 50-60, 60-79, and 79-118 keV. Evaluation metrics including signal-to-noise ratio (SNR), linearity of attenuation profiles, root mean square error (RMSE), and area under the curve (AUC) were employed to assess the energy and material-density images with and without metal inserts. Results show decreased metal artefacts and a better signal-to-noise ratio (up to 25%) with increased energy bins as compared to reference data. The attenuation profile also demonstrated high linearity (R2 >0.95) and lower RMSE across all material concentrations, even in the presence of aluminium and steel. Material identification accuracy for iodine and hydroxyapatite (with and without metal inserts) remained consistent, minimally impacting AUC values. For demonstration purposes, the biological sample was also scanned with the stainless steel volar implant and cortical bone screw, and the images were objectively assessed to indicate the potential effectiveness of SPCCT in replicating real-world clinical scenarios.


Subject(s)
Metals , Phantoms, Imaging , Photons , Tomography, X-Ray Computed , Tomography, X-Ray Computed/methods , Metals/analysis , Metals/chemistry , Humans , Signal-To-Noise Ratio , Artifacts , Iodine/analysis , Durapatite/analysis
15.
Article in English | MEDLINE | ID: mdl-37021915

ABSTRACT

Automatic tissue classification is a fundamental task in computational pathology for profiling tumor micro-environments. Deep learning has advanced tissue classification performance at the cost of significant computational power. Shallow networks have also been end-to-end trained using direct supervision however their performance degrades because of the lack of capturing robust tissue heterogeneity. Knowledge distillation has recently been employed to improve the performance of the shallow networks used as student networks by using additional supervision from deep neural networks used as teacher networks. In the current work, we propose a novel knowledge distillation algorithm to improve the performance of shallow networks for tissue phenotyping in histology images. For this purpose, we propose multi-layer feature distillation such that a single layer in the student network gets supervision from multiple teacher layers. In the proposed algorithm, the size of the feature map of two layers is matched by using a learnable multi-layer perceptron. The distance between the feature maps of the two layers is then minimized during the training of the student network. The overall objective function is computed by summation of the loss over multiple layers combination weighted with a learnable attention-based parameter. The proposed algorithm is named as Knowledge Distillation for Tissue Phenotyping (KDTP). Experiments are performed on five different publicly available histology image classification datasets using several teacher-student network combinations within the KDTP algorithm. Our results demonstrate a significant performance increase in the student networks by using the proposed KDTP algorithm compared to direct supervision-based training methods.

16.
Comput Biol Med ; 164: 107302, 2023 09.
Article in English | MEDLINE | ID: mdl-37572443

ABSTRACT

Automated demarcation of stoke lesions from monospectral magnetic resonance imaging scans is extremely useful for diverse research and clinical applications, including lesion-symptom mapping to explain deficits and predict recovery. There is a significant surge of interest in the development of supervised artificial intelligence (AI) methods for that purpose, including deep learning, with a performance comparable to trained experts. Such AI-based methods, however, require copious amounts of data. Thanks to the availability of large datasets, the development of AI-based methods for lesion segmentation has immensely accelerated in the last decade. One of these datasets is the Anatomical Tracings of Lesions After Stroke (ATLAS) dataset which includes T1-weighted images from hundreds of chronic stroke survivors with their manually traced lesions. This systematic review offers an appraisal of the impact of the ATLAS dataset in promoting the development of AI-based segmentation of stroke lesions. An examination of all published studies, that used the ATLAS dataset to both train and test their methods, highlighted an overall moderate performance (median Dice index = 59.40%) and a huge variability across studies in terms of data preprocessing, data augmentation, AI architecture, and the mode of operation (two-dimensional versus three-dimensional methods). Perhaps most importantly, almost all AI tools were borrowed from existing AI architectures in computer vision, as 90% of all selected studies relied on conventional convolutional neural network-based architectures. Overall, current research has not led to the development of robust AI architectures than can handle spatially heterogenous lesion patterns. This review also highlights the difficulty of gauging the performance of AI tools in the presence of uncertainties in the definition of the ground truth.


Subject(s)
Artificial Intelligence , Stroke , Humans , Stroke/diagnostic imaging , Magnetic Resonance Imaging/methods , Neural Networks, Computer , Uncertainty , Image Processing, Computer-Assisted/methods
17.
Brain Inform ; 10(1): 25, 2023 Sep 09.
Article in English | MEDLINE | ID: mdl-37689601

ABSTRACT

Early identification of mental disorders, based on subjective interviews, is extremely challenging in the clinical setting. There is a growing interest in developing automated screening tools for potential mental health problems based on biological markers. Here, we demonstrate the feasibility of an AI-powered diagnosis of different mental disorders using EEG data. Specifically, this work aims to classify different mental disorders in the following ecological context accurately: (1) using raw EEG data, (2) collected during rest, (3) during both eye open, and eye closed conditions, (4) at short 2-min duration, (5) on participants with different psychiatric conditions, (6) with some overlapping symptoms, and (7) with strongly imbalanced classes. To tackle this challenge, we designed and optimized a transformer-based architecture, where class imbalance is addressed through focal loss and class weight balancing. Using the recently released TDBRAIN dataset (n= 1274 participants), our method classifies each participant as either a neurotypical or suffering from major depressive disorder (MDD), attention deficit hyperactivity disorder (ADHD), subjective memory complaints (SMC), or obsessive-compulsive disorder (OCD). We evaluate the performance of the proposed architecture on both the window-level and the patient-level. The classification of the 2-min raw EEG data into five classes achieved a window-level accuracy of 63.2% and 65.8% for open and closed eye conditions, respectively. When the classification is limited to three main classes (MDD, ADHD, SMC), window level accuracy improved to 75.1% and 69.9% for eye open and eye closed conditions, respectively. Our work paves the way for developing novel AI-based methods for accurately diagnosing mental disorders using raw resting-state EEG data.

18.
Genes (Basel) ; 14(1)2023 01 03.
Article in English | MEDLINE | ID: mdl-36672878

ABSTRACT

The rapid improvements in identifying the genetic factors contributing to facial morphology have enabled the early identification of craniofacial syndromes. Similarly, this technology can be vital in forensic cases involving human identification from biological traces or human remains, especially when reference samples are not available in the deoxyribose nucleic acid (DNA) database. This review summarizes the currently used methods for predicting human phenotypes such as age, ancestry, pigmentation, and facial features based on genetic variations. To identify the facial features affected by DNA, various two-dimensional (2D)- and three-dimensional (3D)-scanning techniques and analysis tools are reviewed. A comparison between the scanning technologies is also presented in this review. Face-landmarking techniques and face-phenotyping algorithms are discussed in chronological order. Then, the latest approaches in genetic to 3D face shape analysis are emphasized. A systematic review of the current markers that passed the threshold of a genome-wide association (GWAS) of single nucleotide polymorphism (SNP)-face traits from the GWAS Catalog is also provided using the preferred reporting items for systematic reviews and meta-analyses (PRISMA), approach. Finally, the current challenges in forensic DNA phenotyping are analyzed and discussed.


Subject(s)
Nucleic Acids , Humans , Genome-Wide Association Study , Phenotype , Pigmentation , DNA/genetics
19.
Sci Rep ; 13(1): 22885, 2023 Dec 21.
Article in English | MEDLINE | ID: mdl-38129680

ABSTRACT

Tomatoes are a major crop worldwide, and accurately classifying their maturity is important for many agricultural applications, such as harvesting, grading, and quality control. In this paper, the authors propose a novel method for tomato maturity classification using a convolutional transformer. The convolutional transformer is a hybrid architecture that combines the strengths of convolutional neural networks (CNNs) and transformers. Additionally, this study introduces a new tomato dataset named KUTomaData, explicitly designed to train deep-learning models for tomato segmentation and classification. KUTomaData is a compilation of images sourced from a greenhouse in the UAE, with approximately 700 images available for training and testing. The dataset is prepared under various lighting conditions and viewing perspectives and employs different mobile camera sensors, distinguishing it from existing datasets. The contributions of this paper are threefold: firstly, the authors propose a novel method for tomato maturity classification using a modular convolutional transformer. Secondly, the authors introduce a new tomato image dataset that contains images of tomatoes at different maturity levels. Lastly, the authors show that the convolutional transformer outperforms state-of-the-art methods for tomato maturity classification. The effectiveness of the proposed framework in handling cluttered and occluded tomato instances was evaluated using two additional public datasets, Laboro Tomato and Rob2Pheno Annotated Tomato, as benchmarks. The evaluation results across these three datasets demonstrate the exceptional performance of our proposed framework, surpassing the state-of-the-art by 58.14%, 65.42%, and 66.39% in terms of mean average precision scores for KUTomaData, Laboro Tomato, and Rob2Pheno Annotated Tomato, respectively. This work can potentially improve the efficiency and accuracy of tomato harvesting, grading, and quality control processes.

20.
Comput Biol Med ; 143: 105281, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35139456

ABSTRACT

Nucleus detection is an important step for the analysis of histology images in the field of computational pathology. Pathologists use quantitative nuclear morphology for better cancer grading and prognostication. The nucleus detection becomes very challenging because of the large morphological variations across different types of nuclei, nuclei clutter, and heterogeneity. To address these challenges, we aim to improve the nucleus detection using multi-level feature fusion based on discriminative correlation filters. The proposed algorithm employs multiple features pool, based on varying features combinations. Early fusion is employed to integrate multi-feature information within a pool and inter-pool fusion is proposed to fuse information across multiple pools. Inter-pool consistency is proposed to find the pools which are consistent and complement each other to improve performance. For this purpose, the relative standard deviation is used as an inter-pool consistency measure. Pool robustness to noise is also estimated using relative standard deviation as a robustness measure. High-level pool fusion is proposed using inter-pool consistency and pool-robustness scores. The proposed algorithm facilitates a robust and reliable appearance model for nucleus detection. The proposed algorithm is evaluated on three publicly available datasets and compared with several existing state-of-the-art methods. Our proposed algorithm has consistently outperformed existing methods on a wide range of experiments.

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