An automatic approach for classification and categorisation of lip morphological traits.
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ABSTRACT:
SUBMITTER: Abbas HH
PROVIDER: S-EPMC6818784 | biostudies-literature | 2019
REPOSITORIES: biostudies-literature
Publications
An automatic approach for classification and categorisation of lip morphological traits.
Abbas Hawraa H HH Hicks Yulia Y Zhurov Alexei A Marshall David D Claes Peter P Wilson-Nagrani Caryl C Richmond Stephen S
PloS one 20191029 10
Classification of facial traits (e.g., lip shape) is an important area of medical research, for example, in determining associations between lip traits and genetic variants which may lead to a cleft lip. In clinical situations, classification of facial traits is usually performed subjectively directly on the individual or recorded later from a three-dimensional image, which is time consuming and prone to operator errors. The present study proposes, for the first time, an automatic approach for t ...[more]
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Project description:ObjectiveTo apply an automated computerised method to categorise and determine the prevalence of different types of lip traits, and to explore associations between lip traits and sex differences.DesignObservational descriptive study utilising an automated method of facial assessment.Setting and participantsA total of 4747 children from the Avon Longitudinal Study of Parents and Children (ALSPAC) who each had 3D facial scans carried out at 15 years of age.MethodsEach of the participants was automatically categorised regarding predetermined lip morphological traits. Descriptive statistics were applied to report the prevalence of the different types of each trait, and chi-square tests were used to investigate sex differences and associations between traits.ResultsA total of 4730 individuals were assessed (47% male, 53% female). Eight predetermined lip traits have been reported previously. There were differences in prevalence for all lip traits in male and female patients (all P ⩽ 0.0002), with differences between the sexes described for each trait. For example, a deeply grooved philtrum of average width was more prevalent in boys, and an indentation near the upper vermilion border was more prevalent in girls. Each of the traits was significantly associated with the other traits (all P < 0.0001), with particularly strong associations seen between traits in the same region (e.g. upper lip). Individual associations between traits are reported; for example, a straight lip contour was found to be associated with no true vermilion border in both the upper and lower lip regions.ConclusionThe automated computerised method described is an invaluable tool for the categorisation of lip morphological traits. The prevalence of various types of traits has been described. Sexual dimorphism exists for all the lip traits assessed. Generally, each of the traits are associated with all other traits, with individual associations reported.
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Project description:Infertility has become a common problem in global health, and unsurprisingly, many couples need medical assistance to achieve reproduction. Many human behaviors can lead to infertility, which is none other than unhealthy sperm. The important thing is that assisted reproductive techniques require selecting healthy sperm. Hence, machine learning algorithms are presented as the subject of this research to effectively modernize and make accurate standards and decisions in classifying sperm. In this study, we developed a deep learning fusion architecture called SwinMobile that combines the Shifted Windows Vision Transformer (Swin) and MobileNetV3 into a unified feature space and classifies sperm from impurities in the SVIA Subset-C. Swin Transformer provides long-range feature extraction, while MobileNetV3 is responsible for extracting local features. We also explored incorporating an autoencoder into the architecture for an automatic noise-removing model. Our model was tested on SVIA, HuSHem, and SMIDS. Comparison to the state-of-the-art models was based on F1-score and accuracy. Our deep learning results accurately classified sperm and performed well in direct comparisons with previous approaches despite the datasets' different characteristics. We compared the model from Xception on the SVIA dataset, the MC-HSH model on the HuSHem dataset, and Ilhan et al.'s model on the SMIDS dataset and the astonishing results given by our model. The proposed model, especially SwinMobile-AE, has strong classification capabilities that enable it to function with high classification results on three different datasets. We propose that our deep learning approach to sperm classification is suitable for modernizing the clinical world. Our work leverages the potential of artificial intelligence technologies to rival humans in terms of accuracy, reliability, and speed of analysis. The SwinMobile-AE method we provide can achieve better results than state-of-the-art, even for three different datasets. Our results were benchmarked by comparisons with three datasets, which included SVIA, HuSHem, and SMIDS, respectively (95.4% vs. 94.9%), (97.6% vs. 95.7%), and (91.7% vs. 90.9%). Thus, the proposed model can realize technological advances in classifying sperm morphology based on the evidential results with three different datasets, each having its characteristics related to data size, number of classes, and color space.
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Project description:Introduction: Scientific articles serve as vital sources of biomedical information, but with the yearly growth in publication volume, processing such vast amounts of information has become increasingly challenging. This difficulty is particularly pronounced when it requires the expertise of highly qualified professionals. Our research focused on the domain-specific articles classification to determine whether they contain information about drug-induced liver injury (DILI). DILI is a clinically significant condition and one of the reasons for drug registration failures. The rapid and accurate identification of drugs that may cause such conditions can prevent side effects in millions of patients. Methods: Developing a text classification method can help regulators, such as the FDA, much faster at a massive scale identify facts of potential DILI of concrete drugs. In our study, we compared several text classification methodologies, including transformers, LSTMs, information theory, and statistics-based methods. We devised a simple and interpretable text classification method that is as fast as Naïve Bayes while delivering superior performance for topic-oriented text categorisation. Moreover, we revisited techniques and methodologies to handle the imbalance of the data. Results: Transformers achieve the best results in cases if the distribution of classes and semantics of test data matches the training set. But in cases of imbalanced data, simple statistical-information theory-based models can surpass complex transformers, bringing more interpretable results that are so important for the biomedical domain. As our results show, neural networks can achieve better results if they are pre-trained on domain-specific data, and the loss function was designed to reflect the class distribution. Discussion: Overall, transformers are powerful architecture, however, in certain cases, such as topic classification, its usage can be redundant and simple statistical approaches can achieve compatible results while being much faster and explainable. However, we see potential in combining results from both worlds. Development of new neural network architectures, loss functions and training procedures that bring stability to unbalanced data is a promising topic of development.
| S-EPMC10668010 | biostudies-literature
Project description:BackgroundDocument classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature.ResultsWe present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept.ConclusionWe have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept.
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Project description:The classification of neurons into types has been much debated since the inception of modern neuroscience. Recent experimental advances are accelerating the pace of data collection. The resulting growth of information about morphological, physiological, and molecular properties encourages efforts to automate neuronal classification by powerful machine learning techniques. We review state-of-the-art analysis approaches and the availability of suitable data and resources, highlighting prominent challenges and opportunities. The effective solution of the neuronal classification problem will require continuous development of computational methods, high-throughput data production, and systematic metadata organization to enable cross-laboratory integration.
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| S-EPMC9781146 | biostudies-literature
Project description:BackgroundIn high-dimensional data analysis, the complexity of predictive models can be reduced by selecting the most relevant features, which is crucial to reduce data noise and increase model accuracy and interpretability. Thus, in the field of clinical decision making, only the most relevant features from a set of medical descriptors should be considered when determining whether a patient is healthy or not. This statistical approach known as feature selection can be performed through regression or classification, in a supervised or unsupervised manner. Several feature selection approaches using different mathematical concepts have been described in the literature. In the field of classification, a new approach has recently been proposed that uses the [Formula: see text]-metric, an index measuring separability between different classes in heart rhythm characterization. The present study proposes a filter approach for feature selection in classification using this [Formula: see text]-metric, and evaluates its application to automatic atrial fibrillation detection.MethodsThe stability and prediction performance of the [Formula: see text]-metric feature selection approach was evaluated using the support vector machine model on two heart rhythm datasets, one extracted from the PhysioNet database and the other from the database of Marseille University Hospital Center, France (Timone Hospital). Both datasets contained electrocardiogram recordings grouped into two classes: normal sinus rhythm and atrial fibrillation. The performance of this feature selection approach was compared to that of three other approaches, with the first two based on the Random Forest technique and the other on receiver operating characteristic curve analysis.ResultsThe [Formula: see text]-metric approach showed satisfactory results, especially for models with a smaller number of features. For the training dataset, all prediction indicators were higher for our approach (accuracy greater than 99% for models with 5 to 17 features), as was stability (greater than 0.925 regardless of the number of features included in the model). For the validation dataset, the features selected with the [Formula: see text]-metric approach differed from those selected with the other approaches; sensitivity was higher for our approach, but other indicators were similar.ConclusionThis filter approach for feature selection in classification opens up new methodological avenues for atrial fibrillation detection using short electrocardiogram recordings.
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Project description:SummaryThe classification of transposable elements (TEs) is key step towards deciphering their potential impact on the genome. However, this process is often based on manual sequence inspection by TE experts. With the wealth of genomic sequences now available, this task requires automation, making it accessible to most scientists. We propose a new tool, PASTEC, which classifies TEs by searching for structural features and similarities. This tool outperforms currently available software for TE classification. The main innovation of PASTEC is the search for HMM profiles, which is useful for inferring the classification of unknown TE on the basis of conserved functional domains of the proteins. In addition, PASTEC is the only tool providing an exhaustive spectrum of possible classifications to the order level of the Wicker hierarchical TE classification system. It can also automatically classify other repeated elements, such as SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. Finally, the output of this new tool is designed to facilitate manual curation by providing to biologists with all the evidence accumulated for each TE consensus.AvailabilityPASTEC is available as a REPET module or standalone software (http://urgi.versailles.inra.fr/download/repet/REPET_linux-x64-2.2.tar.gz). It requires a Unix-like system. There are two standalone versions: one of which is parallelized (requiring Sun grid Engine or Torque), and the other of which is not.
| S-EPMC4008368 | biostudies-literature