Artificial Intelligence in Epigenetic Studies: Shedding Light on Rare Diseases.
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ABSTRACT:
SUBMITTER: Brasil S
PROVIDER: S-EPMC8131862 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The amount of data collected and managed in (bio)medicine is ever-increasing. Thus, there is a need to rapidly and efficiently collect, analyze, and characterize all this information. Artificial intelligence (AI), with an emphasis on deep learning, holds great promise in this area and is already being successfully applied to basic research, diagnosis, drug discovery, and clinical trials. Rare diseases (RDs), which are severely underrepresented in basic and clinical research, can particularly benefit from AI technologies. Of the more than 7000 RDs described worldwide, only 5% have a treatment. The ability of AI technologies to integrate and analyze data from different sources (e.g., multi-omics, patient registries, and so on) can be used to overcome RDs' challenges (e.g., low diagnostic rates, reduced number of patients, geographical dispersion, and so on). Ultimately, RDs' AI-mediated knowledge could significantly boost therapy development. Presently, there are AI approaches being used in RDs and this review aims to collect and summarize these advances. A section dedicated to congenital disorders of glycosylation (CDG), a particular group of orphan RDs that can serve as a potential study model for other common diseases and RDs, has also been included.
| S-EPMC6947640 | biostudies-literature
Project description:Artificial intelligence (AI) is a major branch of computer science that is fruitfully used for analyzing complex medical data and extracting meaningful relationships in datasets, for several clinical aims. Specifically, in the brain care domain, several innovative approaches have achieved remarkable results and open new perspectives in terms of diagnosis, planning, and outcome prediction. In this work, we present an overview of different artificial intelligent techniques used in the brain care domain, along with a review of important clinical applications. A systematic and careful literature search in major databases such as Pubmed, Scopus, and Web of Science was carried out using "artificial intelligence" and "brain" as main keywords. Further references were integrated by cross-referencing from key articles. 155 studies out of 2696 were identified, which actually made use of AI algorithms for different purposes (diagnosis, surgical treatment, intra-operative assistance, and postoperative assessment). Artificial neural networks have risen to prominent positions among the most widely used analytical tools. Classic machine learning approaches such as support vector machine and random forest are still widely used. Task-specific algorithms are designed for solving specific problems. Brain images are one of the most used data types. AI has the possibility to improve clinicians' decision-making ability in neuroscience applications. However, major issues still need to be addressed for a better practical use of AI in the brain. To this aim, it is important to both gather comprehensive data and build explainable AI algorithms.
| S-EPMC7556883 | biostudies-literature
Project description:Novel artificial intelligence techniques are emerging in all fields of healthcare, including gastroenterology. The aim of this review is to give an overview of artificial intelligence applications in the management of pancreatic diseases. We performed a systematic literature search in PubMed and Medline up to May 2020 to identify relevant articles. Our results showed that the development of machine-learning based applications is rapidly evolving in the management of pancreatic diseases, guiding precision medicine in clinical, endoscopic and radiologic settings. Before implementation into clinical practice, further research should focus on the external validation of novel techniques, clarifying the accuracy and robustness of these models.
| S-EPMC7898901 | biostudies-literature
Project description:Neuroinflammation is a common factor in neurodegenerative diseases, and it has been demonstrated that galectin-3 activates microglia and astrocytes, leading to inflammation. This means that inhibition of galectin-3 may become a new strategy for the treatment of neurodegenerative diseases. Based on this motivation, the objective of this study is to explore an integrated new approach for finding lead compounds that inhibit galectin-3, by combining universal artificial intelligence algorithms with traditional drug screening methods. Based on molecular docking method, potential compounds with high binding affinity were screened out from Chinese medicine database. Manifold artificial intelligence algorithms were performed to validate the docking results and further screen compounds. Among all involved predictive methods, the deep learning-based algorithm made 500 modeling attempts, and the square correlation coefficient of the best trained model on the test sets was 0.9. The XGBoost model reached a square correlation coefficient of 0.97 and a mean square error of only 0.01. We switched to the ZINC database and performed the same experiment, the results showed that the compounds in the former database showed stronger affinity. Finally, we further verified through molecular dynamics simulation that the complex composed of the candidate ligand and the target protein showed stable binding within 100 ns of simulation time. In summary, combined with the application based on artificial intelligence algorithms, we unearthed the active ingredients 1,2-Dimethylbenzene and Typhic acid contained in Crataegus pinnatifida and Typha angustata might be the effective inhibitors of neurodegenerative diseases. The high prediction accuracy of the models shows that it has practical application value on small sample data sets such as drug screening.
| S-EPMC7783404 | biostudies-literature
Project description:ImportanceRecent studies have demonstrated the successful application of artificial intelligence (AI) for automated retinal disease diagnostics but have not addressed a fundamental challenge for deep learning systems: the current need for large, criterion standard-annotated retinal data sets for training. Low-shot learning algorithms, aiming to learn from a relatively low number of training data, may be beneficial for clinical situations involving rare retinal diseases or when addressing potential bias resulting from data that may not adequately represent certain groups for training, such as individuals older than 85 years.ObjectiveTo evaluate whether low-shot deep learning methods are beneficial when using small training data sets for automated retinal diagnostics.Design, setting, and participantsThis cross-sectional study, conducted from July 1, 2019, to June 21, 2020, compared different diabetic retinopathy classification algorithms, traditional and low-shot, for 2-class designations (diabetic retinopathy warranting referral vs not warranting referral). The public domain EyePACS data set was used, which originally included 88 692 fundi from 44 346 individuals. Statistical analysis was performed from February 1 to June 21, 2020.Main outcomes and measuresThe performance (95% CIs) of the various AI algorithms was measured via receiver operating curves and their area under the curve (AUC), precision recall curves, accuracy, and F1 score, evaluated for different training data sizes, ranging from 5120 to 10 samples per class.ResultsDeep learning algorithms, when trained with sufficiently large data sets (5120 samples per class), yielded comparable performance, with an AUC of 0.8330 (95% CI, 0.8140-0.8520) for a traditional approach (eg, fined-tuned ResNet), compared with low-shot methods (AUC, 0.8348 [95% CI, 0.8159-0.8537]) (using self-supervised Deep InfoMax [our method denoted as DIM]). However, when far fewer training images were available (n = 160), the traditional deep learning approach had an AUC decreasing to 0.6585 (95% CI, 0.6332-0.6838) and was outperformed by a low-shot method using self-supervision with an AUC of 0.7467 (95% CI, 0.7239-0.7695). At very low shots (n = 10), the traditional approach had performance close to chance, with an AUC of 0.5178 (95% CI, 0.4909-0.5447) compared with the best low-shot method (AUC, 0.5778 [95% CI, 0.5512-0.6044]).Conclusions and relevanceThese findings suggest the potential benefits of using low-shot methods for AI retinal diagnostics when a limited number of annotated training retinal images are available (eg, with rare ophthalmic diseases or when addressing potential AI bias).
| S-EPMC7489388 | biostudies-literature
Project description:We propose a model of a learning agent whose interaction with the environment is governed by a simulation-based projection, which allows the agent to project itself into future situations before it takes real action. Projective simulation is based on a random walk through a network of clips, which are elementary patches of episodic memory. The network of clips changes dynamically, both due to new perceptual input and due to certain compositional principles of the simulation process. During simulation, the clips are screened for specific features which trigger factual action of the agent. The scheme is different from other, computational, notions of simulation, and it provides a new element in an embodied cognitive science approach to intelligent action and learning. Our model provides a natural route for generalization to quantum-mechanical operation and connects the fields of reinforcement learning and quantum computation.
| S-EPMC3351754 | biostudies-other
Project description:BackgroundArtificial intelligence (AI) has recently been applied to endoscopy and questionnaires for the evaluation of oesophageal diseases (ODs).AimWe performed a systematic review with meta-analysis to evaluate the performance of AI in the diagnosis of malignant and benign OD.MethodsWe searched MEDLINE, EMBASE, EMBASE Classic and the Cochrane Library. A bivariate random-effect model was used to calculate pooled diagnostic efficacy of AI models and endoscopists. The reference tests were histology for neoplasms and the clinical and instrumental diagnosis for gastro-oesophageal reflux disease (GERD). The pooled area under the summary receiver operating characteristic (AUROC), sensitivity, specificity, positive and negative likelihood ratio (PLR and NLR) and diagnostic odds ratio (DOR) were estimated.ResultsFor the diagnosis of Barrett's neoplasia, AI had AUROC of 0.90, sensitivity 0.89, specificity 0.86, PLR 6.50, NLR 0.13 and DOR 50.53. AI models' performance was comparable with that of endoscopists (P = 0.35). For the diagnosis of oesophageal squamous cell carcinoma, the AUROC, sensitivity, specificity, PLR, NLR and DOR were 0.97, 0.95, 0.92, 12.65, 0.05 and DOR 258.36, respectively. In this task, AI performed better than endoscopists although without statistically significant differences. In the detection of abnormal intrapapillary capillary loops, the performance of AI was: AUROC 0.98, sensitivity 0.94, specificity 0.94, PLR 14.75, NLR 0.07 and DOR 225.83. For the diagnosis of GERD based on questionnaires, the AUROC, sensitivity, specificity, PLR, NLR and DOR were 0.99, 0.97, 0.97, 38.26, 0.03 and 1159.6, respectively.ConclusionsAI demonstrated high performance in the clinical and endoscopic diagnosis of OD.
| S-EPMC9305819 | biostudies-literature
Project description:With the aid of a plant disease forecasting model, the emergence of plant diseases in a given region can be predicted ahead of time. This makes it easier to take proactive steps to reduce losses before they occur. The proposed model attempts to find an association between agrometeorological parameters and the occurrence of the four types of rice diseases. Rice is the staple food of people in Maharashtra. The four major diseases that occur on rice crops are focused on this paper (namely Rice Blast, False Smut, Bacterial Blight and Brown Spot) as these diseases spread rapidly and lead to economic loss. This research paper demonstrates the usage of artificial neural network (ANN) to detect, classify and predict the occurrence of rice diseases based on diverse agro-meteorological conditions. The results were carried out on two cases of dataset split that is 70-30% and 80-20%. The various types of activation function (AF) such as sigmoid, tanH, ReLU and softmax are implemented and compared based on various evaluation metrics such as overall Accuracy, Precision, Recall and F1 score. It can be concluded that the softmax AF applied to 70-30% split of dataset gives the highest accuracy of 92.15% in rice disease prediction.
| S-EPMC8444092 | biostudies-literature
Project description:Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) plays a pivotal role in preventing autoimmunity and fostering anticancer immunity by interacting with B7 proteins CD80 and CD86. CTLA-4 is the first immune checkpoint targeted with a monoclonal antibody inhibitor. Checkpoint inhibitors have generated durable responses in many cancer patients, representing a revolutionary milestone in cancer immunotherapy. However, therapeutic efficacy is limited to a small portion of patients, and immune-related adverse events are noteworthy, especially for monoclonal antibodies directed against CTLA-4. Previously, small molecules have been developed to impair the CTLA-4: CD80 interaction; however, they directly targeted CD80 and not CTLA-4. In this study, we performed artificial intelligence (AI)-powered virtual screening of approximately ten million compounds to target CTLA-4. We validated primary hits with biochemical, biophysical, immunological, and experimental animal assays. We then optimized lead compounds and obtained inhibitors with an inhibitory concentration of 1 micromole in disrupting the interaction between CTLA-4 and CD80. Unlike ipilimumab, these small molecules did not degrade CTLA-4. Several compounds inhibited tumor development prophylactically and therapeutically in syngeneic and CTLA-4-humanized mice. This project supports an AI-based framework in designing small molecules targeting immune checkpoints for cancer therapy.
2024-02-15 | GSE228560 | GEO
Project description:BackgroundThe gold standard for the diagnosis of liver fibrosis and nonalcoholic fatty liver disease (NAFLD) is liver biopsy. Various noninvasive modalities, e.g., ultrasonography, elastography and clinical predictive scores, have been used as alternatives to liver biopsy, with limited performance. Recently, artificial intelligence (AI) models have been developed and integrated into noninvasive diagnostic tools to improve their performance.MethodsWe systematically searched for studies on AI-assisted diagnosis of liver fibrosis and NAFLD on MEDLINE, Scopus, Web of Science and Google Scholar. The pooled sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and diagnostic odds ratio (DOR) with their 95% confidence intervals (95% CIs) were calculated using a random effects model. A summary receiver operating characteristic curve and the area under the curve was generated to determine the diagnostic accuracy of the AI-assisted system. Subgroup analyses by diagnostic modalities, population and AI classifiers were performed.ResultsWe included 19 studies reporting the performances of AI-assisted ultrasonography, elastrography, computed tomography, magnetic resonance imaging and clinical parameters for the diagnosis of liver fibrosis and steatosis. For the diagnosis of liver fibrosis, the pooled sensitivity, specificity, PPV, NPV and DOR were 0.78 (0.71-0.85), 0.89 (0.81-0.94), 0.72 (0.58-0.83), 0.92 (0.88-0.94) and 31.58 (11.84-84.25), respectively, for cirrhosis; 0.86 (0.80-0.90), 0.87 (0.80-0.92), 0.85 (0.75-0.91), 0.88 (0.82-0.92) and 37.79 (16.01-89.19), respectively; for advanced fibrosis; and 0.86 (0.78-0.92), 0.81 (0.77-0.84), 0.88 (0.80-0.93), 0.77 (0.58-0.89) and 26.79 (14.47-49.62), respectively, for significant fibrosis. Subgroup analyses showed significant differences in performance for the diagnosis of fibrosis among different modalities. The pooled sensitivity, specificity, PPV, NPV and DOR were 0.97 (0.76-1.00), 0.91 (0.78-0.97), 0.95 (0.87-0.98), 0.93 (0.80-0.98) and 191.52 (38.82-944.81), respectively, for the diagnosis of liver steatosis.ConclusionsAI-assisted systems have promising potential for the diagnosis of liver fibrosis and NAFLD. Validations of their performances are warranted before implementing these AI-assisted systems in clinical practice.Trial registrationThe protocol was registered with PROSPERO (CRD42020183295).
| S-EPMC7788739 | biostudies-literature