Opportunities and obstacles for deep learning in biology and medicine

Publicly available datasets of breast histopathology H&E whole-slide images: A scoping review

Advancements in digital pathology and computing resources have made a significant impact in the field of computational pathology for breast cancer diagnosis and treatment. However, access to high-quality labeled histopathological images of breast cancer is a big challenge that limits the development of accurate and robust deep learning models. In this scoping review, we identified the publicly available datasets of breast H&E-stained whole-slide images (WSIs) that can be used to develop deep learning algorithms. We systematically searched 9 scientific literature databases and 9 research data repositories and found 17 publicly available datasets containing 10 385 H&E WSIs of breast cancer. Moreover, we reported image metadata and characteristics for each dataset to assist researchers in selecting proper datasets for specific tasks in breast cancer computational pathology. In addition, we compiled 2 lists of breast H&E patches and private datasets as supplementary resources for researchers. Notably, only 28% of the included articles utilized multiple datasets, and only 14% used an external validation set, suggesting that the performance of other developed models may be susceptible to overestimation. The TCGA-BRCA was used in 52% of the selected studies. This dataset has a considerable selection bias that can impact the robustness and generalizability of the trained algorithms. There is also a lack of consistent metadata reporting of breast WSI datasets that can be an issue in developing accurate deep learning models, indicating the necessity of establishing explicit guidelines for documenting breast WSI dataset characteristics and metadata.

Simulated gastrointestinal digestion of walnut protein yields anti-inflammatory peptides

The impact of the simulated gastrointestinal digestion process on walnut protein and the potential anti-inflammatory properties of its metabolites was studied. Structural changes induced by digestion, notably in α-Helix, β-Turn, and Random Coil configurations, were unveiled. Proteins over 10,000 Da significantly decreased by 35.6 %. Antioxidant activity in these metabolites paralleled increased amino acid content. Molecular docking identified three walnut polypeptides-IPAGTPVYLINR, FQGQLPR, and VVYVLR-with potent anti-inflammatory properties. RMSD and RMSF analysis demonstrated the stable and flexible interaction of these polypeptides with their target proteins. In lipopolysaccharide (LPS)-induced inflammation in normal human colon mucosal epithelial NCM460 cells, these peptides decreased 5-hydroxytryptamine (5-HT), tumor necrosis factor-alpha (TNF-α), and vascular endothelial growth factor (VEGF) expression, while mitigating cell apoptosis and inflammation. Our study offers valuable insights into walnut protein physiology, shedding light on its potential health benefits.

A prediction model based on digital breast pathology image information

BACKGROUND

The workload of breast cancer pathological diagnosis is very heavy. The purpose of this study is to establish a nomogram model based on pathological images to predict the benign and malignant nature of breast diseases and to validate its predictive performance.

METHODS

In retrospect, a total of 2,723 H&E-stained pathological images were collected from 1,474 patients at Qingdao Central Hospital between 2019 and 2022. The dataset consisted of 509 benign tumor images (adenosis and fibroadenoma) and 2,214 malignant tumor images (infiltrating ductal carcinoma). The images were divided into a training set (1,907) and a validation set (816). Python3.7 was used to extract the values of the R channel, G channel, B channel, and one-dimensional information entropy from all images. Multivariable logistic regression was used to select variables and establish the breast tissue pathological image prediction model.

RESULTS

The R channel value, B channel value, and one-dimensional information entropy of the images were identified as independent predictive factors for the classification of benign and malignant pathological images (P < 0.05). The area under the curve (AUC) of the nomogram model in the training set was 0.889 (95% CI: 0.869, 0.909), and the AUC in the validation set was 0.838 (95% CI: 0.7980.877). The calibration curve results showed that the calibration curve of this nomogram model was close to the ideal curve. The decision curve results indicated that the predictive model curve had a high value for auxiliary diagnosis.

CONCLUSION

The nomogram model for the prediction of benign and malignant breast diseases based on pathological images demonstrates good predictive performance. This model can assist in the diagnosis of breast tissue pathological images.

Deep Learning for Elucidating Modifications to RNA-Status and Challenges Ahead

RNA-binding proteins and chemical modifications to RNA play vital roles in the co- and post-transcriptional regulation of genes. In order to fully decipher their biological roles, it is an essential task to catalogue their precise target locations along with their preferred contexts and sequence-based determinants. Recently, deep learning approaches have significantly advanced in this field. These methods can predict the presence or absence of modification at specific genomic regions based on diverse features, particularly sequence and secondary structure, allowing us to decipher the highly non-linear sequence patterns and structures that underlie site preferences. This article provides an overview of how deep learning is being applied to this area, with a particular focus on the problem of mRNA-RBP binding, while also considering other types of chemical modification to RNA. It discusses how different types of model can handle sequence-based and/or secondary-structure-based inputs, the process of model training, including choice of negative regions and separating sets for testing and training, and offers recommendations for developing biologically relevant models. Finally, it highlights four key areas that are crucial for advancing the field.

FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology

In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. In recent years, two computational techniques, machine learning (ML) and physics-based methods, have evolved substantially and are now frequently incorporated into the medicinal chemist's toolbox to enhance the efficiency of both hit optimization and candidate design. Both computational methods come with their own set of limitations, and they are often used independently of each other. ML's capability to screen extensive compound libraries expediently is tempered by its reliance on quality data, which can be scarce especially during early-stage optimization. Contrarily, physics-based approaches like free energy perturbation (FEP) are frequently constrained by low throughput and high cost by comparison; however, physics-based methods are capable of making highly accurate binding affinity predictions. In this study, we harnessed the strength of FEP to overcome data paucity in ML by generating virtual activity data sets which then inform the training of algorithms. Here, we show that ML algorithms trained with an FEP-augmented data set could achieve comparable predictive accuracy to data sets trained on experimental data from biological assays. Throughout the paper, we emphasize key mechanistic considerations that must be taken into account when aiming to augment data sets and lay the groundwork for successful implementation. Ultimately, the study advocates for the synergy of physics-based methods and ML to expedite the lead optimization process. We believe that the physics-based augmentation of ML will significantly benefit drug discovery, as these techniques continue to evolve.

Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning

BACKGROUND

The prediction of drug sensitivity plays a crucial role in improving the therapeutic effect of drugs. However, testing the effectiveness of drugs is challenging due to the complex mechanism of drug reactions and the lack of interpretability in most machine learning and deep learning methods. Therefore, it is imperative to establish an interpretable model that receives various cell line and drug feature data to learn drug response mechanisms and achieve stable predictions between available datasets.

RESULTS

This study proposes a new and interpretable deep learning model, DrugGene, which integrates gene expression, gene mutation, gene copy number variation of cancer cells, and chemical characteristics of anticancer drugs to predict their sensitivity. This model comprises two different branches of neural networks, where the first involves a hierarchical structure of biological subsystems that uses the biological processes of human cells to form a visual neural network (VNN) and an interpretable deep neural network for human cancer cells. DrugGene receives genotype input from the cell line and detects changes in the subsystem states. We also employ a traditional artificial neural network (ANN) to capture the chemical structural features of drugs. DrugGene generates final drug response predictions by combining VNN and ANN and integrating their outputs into a fully connected layer. The experimental results using drug sensitivity data extracted from the Cancer Drug Sensitivity Genome Database and the Cancer Treatment Response Portal v2 reveal that the proposed model is better than existing prediction methods. Therefore, our model achieves higher accuracy, learns the reaction mechanisms between anticancer drugs and cell lines from various features, and interprets the model's predicted results.

CONCLUSIONS

Our method utilizes biological pathways to construct neural networks, which can use genotypes to monitor changes in the state of network subsystems, thereby interpreting the prediction results in the model and achieving satisfactory prediction accuracy. This will help explore new directions in cancer treatment. More available code resources can be downloaded for free from GitHub ( https://github.com/pangweixiong/DrugGene ).

Current perspectives on the use of artificial intelligence in critical patient safety

Intensive Care Units (ICUs) have undergone enhancements in patient safety, and artificial intelligence (AI) emerges as a disruptive technology offering novel opportunities. While the published evidence is limited and presents methodological issues, certain areas show promise, such as decision support systems, detection of adverse events, and prescription error identification. The application of AI in safety may pursue predictive or diagnostic objectives. Implementing AI-based systems necessitates procedures to ensure secure assistance, addressing challenges including trust in such systems, biases, data quality, scalability, and ethical and confidentiality considerations. The development and application of AI demand thorough testing, encompassing retrospective data assessments, real-time validation with prospective cohorts, and efficacy demonstration in clinical trials. Algorithmic transparency and explainability are essential, with active involvement of clinical professionals being crucial in the implementation process.

Inference of drug off-target effects on cellular signaling using interactome-based deep learning

Many diseases emerge from dysregulated cellular signaling, and drugs are often designed to target specific signaling proteins. Off-target effects are, however, common and may ultimately result in failed clinical trials. Here we develop a computer model of the cell's transcriptional response to drugs for improved understanding of their mechanisms of action. The model is based on ensembles of artificial neural networks and simultaneously infers drug-target interactions and their downstream effects on intracellular signaling. With this, it predicts transcription factors' activities, while recovering known drug-target interactions and inferring many new ones, which we validate with an independent dataset. As a case study, we analyze the effects of the drug Lestaurtinib on downstream signaling. Alongside its intended target, FLT3, the model predicts an inhibition of CDK2 that enhances the downregulation of the cell cycle-critical transcription factor FOXM1. Our approach can therefore enhance our understanding of drug signaling for therapeutic design.

Pathophysiologic Mapping of Chronic Liver Diseases With Longitudinal Multiparametric MRI in Animal Models

OBJECTIVES

Chronic liver diseases (CLDs) have diverse etiologies. To better classify CLDs, we explored the ability of longitudinal multiparametric MRI (magnetic resonance imaging) in depicting alterations in liver morphology, inflammation, and hepatocyte and macrophage activity in murine high-fat diet (HFD)- and carbon tetrachloride (CCl4)-induced CLD models.

MATERIALS AND METHODS

Mice were either untreated, fed an HFD for 24 weeks, or injected with CCl4 for 8 weeks. Longitudinal multiparametric MRI was performed every 4 weeks using a 7 T MRI scanner, including T1/T2 relaxometry, morphological T1/T2-weighted imaging, and fat-selective imaging. Diffusion-weighted imaging was applied to assess fibrotic remodeling and T1-weighted and T2*-weighted dynamic contrast-enhanced MRI and dynamic susceptibility contrast MRI using gadoxetic acid and ferucarbotran to target hepatocytes and the mononuclear phagocyte system, respectively. Imaging data were associated with histopathological and serological analyses. Principal component analysis and clustering were used to reveal underlying disease patterns.

RESULTS

The MRI parameters significantly correlated with histologically confirmed steatosis, fibrosis, and liver damage, with varying importance. No single MRI parameter exclusively correlated with 1 pathophysiological feature, underscoring the necessity for using parameter patterns. Clustering revealed early-stage, model-specific patterns. Although the HFD model exhibited pronounced liver fat content and fibrosis, the CCl4 model indicated reduced liver fat content and impaired hepatocyte and macrophage function. In both models, MRI biomarkers of inflammation were elevated.

CONCLUSIONS

Multiparametric MRI patterns can be assigned to pathophysiological processes and used for murine CLD classification and progression tracking. These MRI biomarker patterns can directly be explored clinically to improve early CLD detection and differentiation and to refine treatments.

AI in cellular engineering and reprogramming

During the last decade, artificial intelligence (AI) has increasingly been applied in biophysics and related fields, including cellular engineering and reprogramming, offering novel approaches to understand, manipulate, and control cellular function. The potential of AI lies in its ability to analyze complex datasets and generate predictive models. AI algorithms can process large amounts of data from single-cell genomics and multiomic technologies, allowing researchers to gain mechanistic insights into the control of cell identity and function. By integrating and interpreting these complex datasets, AI can help identify key molecular events and regulatory pathways involved in cellular reprogramming. This knowledge can inform the design of precision engineering strategies, such as the development of new transcription factor and signaling molecule cocktails, to manipulate cell identity and drive authentic cell fate across lineage boundaries. Furthermore, when used in combination with computational methods, AI can accelerate and improve the analysis and understanding of the intricate relationships between genes, proteins, and cellular processes. In this review article, we explore the current state of AI applications in biophysics with a specific focus on cellular engineering and reprogramming. Then, we showcase a couple of recent applications where we combined machine learning with experimental and computational techniques. Finally, we briefly discuss the challenges and prospects of AI in cellular engineering and reprogramming, emphasizing the potential of these technologies to revolutionize our ability to engineer cells for a variety of applications, from disease modeling and drug discovery to regenerative medicine and biomanufacturing.

A novel deep generative model for mRNA vaccine development: Designing 5' UTRs with N1-methyl-pseudouridine modification

Efficient translation mediated by the 5' untranslated region (5' UTR) is essential for the robust efficacy of mRNA vaccines. However, the N1-methyl-pseudouridine (m1Ψ) modification of mRNA can impact the translation efficiency of the 5' UTR. We discovered that the optimal 5' UTR for m1Ψ-modified mRNA (m1Ψ-5' UTR) differs significantly from its unmodified counterpart, highlighting the need for a specialized tool for designing m1Ψ-5' UTRs rather than directly utilizing high-expression endogenous gene 5' UTRs. In response, we developed a novel machine learning-based tool, Smart5UTR, which employs a deep generative model to identify superior m1Ψ-5' UTRs in silico. The tailored loss function and network architecture enable Smart5UTR to overcome limitations inherent in existing models. As a result, Smart5UTR can successfully design superior 5' UTRs, greatly benefiting mRNA vaccine development. Notably, Smart5UTR-designed superior 5' UTRs significantly enhanced antibody titers induced by COVID-19 mRNA vaccines against the Delta and Omicron variants of SARS-CoV-2, surpassing the performance of vaccines using high-expression endogenous gene 5' UTRs.

Prediction of preeclampsia from retinal fundus images via deep learning in singleton pregnancies: a prospective cohort study

INTRODUCTION

Early prediction of preeclampsia (PE) is of universal importance in controlling the disease process. Our study aimed to assess the feasibility of using retinal fundus images to predict preeclampsia via deep learning in singleton pregnancies.

METHODS

This prospective cohort study was conducted at Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine. Eligible participants included singleton pregnancies who presented for prenatal visits before 14 weeks of gestation from September 1, 2020, to February 1, 2022. Retinal fundus images were obtained using a nonmydriatic digital retinal camera during their initial prenatal visit upon admission before 20 weeks of gestation. In addition, we generated fundus scores, which indicated the predictive value of hypertension, using a hypertension detection model. To evaluate the predictive value of the retinal fundus image-based deep learning algorithm for preeclampsia, we conducted stratified analyses and measured the area under the curve (AUC), sensitivity, and specificity. We then conducted sensitivity analyses for validation.

RESULTS

Our study analyzed a total of 1138 women, 92 pregnancies developed into hypertension disorders of pregnancy (HDP), including 26 cases of gestational hypertension and 66 cases of preeclampsia. The adjusted odds ratio (aOR) of the fundus scores was 2.582 (95% CI, 1.883-3.616; P  < 0.001). Otherwise, in the categories of prepregnancy BMI less than 28.0 and at least 28.0, the aORs were 3.073 (95%CI, 2.265-4.244; P  < 0.001) and 5.866 (95% CI, 3.292-11.531; P  < 0.001). In the categories of maternal age less than 35.0 and at least 35.0, the aORs were 2.845 (95% CI, 1.854-4.463; P  < 0.001) and 2.884 (95% CI, 1.794-4.942; P  < 0.001). The AUC of the fundus score combined with risk factors was 0.883 (sensitivity, 0.722; specificity, 0.934; 95% CI, 0.834-0.932) for predicting preeclampsia.

CONCLUSION

Our study demonstrates that the use of deep learning algorithm-based retinal fundus images offers promising predictive value for the early detection of preeclampsia.

Integrating clinical pharmacology and artificial intelligence: potential benefits, challenges, and role of clinical pharmacologists

INTRODUCTION

The integration of artificial intelligence (AI) into clinical pharmacology could be a potential approach for accelerating drug discovery and development, improving patient care, and streamlining medical research processes.

AREAS COVERED

We reviewed the current state of AI applications in clinical pharmacology, focusing on drug discovery and development, precision medicine, pharmacovigilance, and other ventures. Key AI applications in clinical pharmacology are examined, including machine learning, natural language processing, deep learning, and reinforcement learning etc. Additionally, the evolving role of clinical pharmacologists, ethical considerations, and challenges in implementing AI in clinical pharmacology are discussed.

EXPERT OPINION

The AI could be instrumental in accelerating drug discovery, predicting drug safety and efficacy, and optimizing clinical trial designs. It can play a vital role in precision medicine by helping in personalized drug dosing, treatment selection, and predicting drug response based on genetic, clinical, and environmental factors. The role of AI in pharmacovigilance, such as signal detection and adverse event prediction, is also promising. The collaboration between clinical pharmacologists and AI experts also poses certain ethical and practical challenges. Clinical pharmacologists can be instrumental in shaping the future of AI-driven clinical pharmacology and contribute to the improvement of healthcare systems.

Clinical knowledge-guided deep reinforcement learning for sepsis antibiotic dosing recommendations

Sepsis is the third leading cause of death worldwide. Antibiotics are an important component in the treatment of sepsis. The use of antibiotics is currently facing the challenge of increasing antibiotic resistance (Evans et al., 2021). Sepsis medication prediction can be modeled as a Markov decision process, but existing methods fail to integrate with medical knowledge, making the decision process potentially deviate from medical common sense and leading to underperformance. (Wang et al., 2021). In this paper, we use Deep Q-Network (DQN) to construct a Sepsis Anti-infection DQN (SAI-DQN) model to address the challenge of determining the optimal combination and duration of antibiotics in sepsis treatment. By setting sepsis clinical knowledge as reward functions to guide DQN complying with medical guidelines, we formed personalized treatment recommendations for antibiotic combinations. The results showed that our model had a higher average value for decision-making than clinical decisions. For the test set of patients, our model predicts that 79.07% of patients will achieve a favorable prognosis with the recommended combination of antibiotics. By statistically analyzing decision trajectories and drug action selection, our model was able to provide reasonable medication recommendations that comply with clinical practices. Our model was able to improve patient outcomes by recommending appropriate antibiotic combinations in line with certain clinical knowledge.

Second mesiobuccal canal segmentation with YOLOv5 architecture using cone beam computed tomography images

The objective of this study is to use a deep-learning model based on CNN architecture to detect the second mesiobuccal (MB2) canals, which are seen as a variation in maxillary molars root canals. In the current study, 922 axial sections from 153 patients' cone beam computed tomography (CBCT) images were used. The segmentation method was employed to identify the MB2 canals in maxillary molars that had not previously had endodontic treatment. Labeled images were divided into training (80%), validation (10%) and testing (10%) groups. The artificial intelligence (AI) model was trained using the You Only Look Once v5 (YOLOv5x) architecture with 500 epochs and a learning rate of 0.01. Confusion matrix and receiver-operating characteristic (ROC) analysis were used in the statistical evaluation of the results. The sensitivity of the MB2 canal segmentation model was 0.92, the precision was 0.83, and the F1 score value was 0.87. The area under the curve (AUC) in the ROC graph of the model was 0.84. The mAP value at 0.5 inter-over union (IoU) was found as 0.88. The deep-learning algorithm used showed a high success in the detection of the MB2 canal. The success of the endodontic treatment can be increased and clinicians' time can be preserved using the newly created artificial intelligence-based models to identify variations in root canal anatomy before the treatment.

Deep learning in structural bioinformatics: current applications and future perspectives

In this review article, we explore the transformative impact of deep learning (DL) on structural bioinformatics, emphasizing its pivotal role in a scientific revolution driven by extensive data, accessible toolkits and robust computing resources. As big data continue to advance, DL is poised to become an integral component in healthcare and biology, revolutionizing analytical processes. Our comprehensive review provides detailed insights into DL, featuring specific demonstrations of its notable applications in bioinformatics. We address challenges tailored for DL, spotlight recent successes in structural bioinformatics and present a clear exposition of DL-from basic shallow neural networks to advanced models such as convolution, recurrent, artificial and transformer neural networks. This paper discusses the emerging use of DL for understanding biomolecular structures, anticipating ongoing developments and applications in the realm of structural bioinformatics.

Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design

Inter-residue interactions in protein structures provide valuable insights into protein folding and stability. Understanding these interactions can be helpful in many crucial applications, including rational design of therapeutic small molecules and biologics, locating functional protein sites, and predicting protein-protein and protein-ligand interactions. The process of developing machine learning models incorporating inter-residue interactions has been improved recently. This review highlights the theoretical models incorporating inter-residue interactions in predicting folding and unfolding rates of proteins. Utilizing contact maps to depict inter-residue interactions aids researchers in developing computer models for detecting remote homologs and interface residues within protein-protein complexes which, in turn, enhances our knowledge of the relationship between sequence and structure of proteins. Further, the application of contact maps derived from inter-residue interactions is highlighted in the field of drug discovery. Overall, this review presents an extensive assessment of the significant models that use inter-residue interactions to investigate folding rates, unfolding rates, remote homology, and drug development, providing potential future advancements in constructing efficient computational models in structural biology.

GPDminer: a tool for extracting named entities and analyzing relations in biological literature

PURPOSE

The expansion of research across various disciplines has led to a substantial increase in published papers and journals, highlighting the necessity for reliable text mining platforms for database construction and knowledge acquisition. This abstract introduces GPDMiner(Gene, Protein, and Disease Miner), a platform designed for the biomedical domain, addressing the challenges posed by the growing volume of academic papers.

METHODS

GPDMiner is a text mining platform that utilizes advanced information retrieval techniques. It operates by searching PubMed for specific queries, extracting and analyzing information relevant to the biomedical field. This system is designed to discern and illustrate relationships between biomedical entities obtained from automated information extraction.

RESULTS

The implementation of GPDMiner demonstrates its efficacy in navigating the extensive corpus of biomedical literature. It efficiently retrieves, extracts, and analyzes information, highlighting significant connections between genes, proteins, and diseases. The platform also allows users to save their analytical outcomes in various formats, including Excel and images.

CONCLUSION

GPDMiner offers a notable additional functionality among the array of text mining tools available for the biomedical field. This tool presents an effective solution for researchers to navigate and extract relevant information from the vast unstructured texts found in biomedical literature, thereby providing distinctive capabilities that set it apart from existing methodologies. Its application is expected to greatly benefit researchers in this domain, enhancing their capacity for knowledge discovery and data management.

Conditional generative adversarial network driven radiomic prediction of mutation status based on magnetic resonance imaging of breast cancer

BACKGROUND

Breast Cancer (BC) is a highly heterogeneous and complex disease. Personalized treatment options require the integration of multi-omic data and consideration of phenotypic variability. Radiogenomics aims to merge medical images with genomic measurements but encounter challenges due to unpaired data consisting of imaging, genomic, or clinical outcome data. In this study, we propose the utilization of a well-trained conditional generative adversarial network (cGAN) to address the unpaired data issue in radiogenomic analysis of BC. The generated images will then be used to predict the mutations status of key driver genes and BC subtypes.

METHODS

We integrated the paired MRI and multi-omic (mRNA gene expression, DNA methylation, and copy number variation) profiles of 61 BC patients from The Cancer Imaging Archive (TCIA) and The Cancer Genome Atlas (TCGA). To facilitate this integration, we employed a Bayesian Tensor Factorization approach to factorize the multi-omic data into 17 latent features. Subsequently, a cGAN model was trained based on the matched side-view patient MRIs and their corresponding latent features to predict MRIs for BC patients who lack MRIs. Model performance was evaluated by calculating the distance between real and generated images using the Fréchet Inception Distance (FID) metric. BC subtype and mutation status of driver genes were obtained from the cBioPortal platform, where 3 genes were selected based on the number of mutated patients. A convolutional neural network (CNN) was constructed and trained using the generated MRIs for mutation status prediction. Receiver operating characteristic area under curve (ROC-AUC) and precision-recall area under curve (PR-AUC) were used to evaluate the performance of the CNN models for mutation status prediction. Precision, recall and F1 score were used to evaluate the performance of the CNN model in subtype classification.

RESULTS

The FID of the images from the well-trained cGAN model based on the test set is 1.31. The CNN for TP53, PIK3CA, and CDH1 mutation prediction yielded ROC-AUC values 0.9508, 0.7515, and 0.8136 and PR-AUC are 0.9009, 0.7184, and 0.5007, respectively for the three genes. Multi-class subtype prediction achieved precision, recall and F1 scores of 0.8444, 0.8435 and 0.8336 respectively. The source code and related data implemented the algorithms can be found in the project GitHub at https://github.com/mattthuang/BC_RadiogenomicGAN .

CONCLUSION

Our study establishes cGAN as a viable tool for generating synthetic BC MRIs for mutation status prediction and subtype classification to better characterize the heterogeneity of BC in patients. The synthetic images also have the potential to significantly augment existing MRI data and circumvent issues surrounding data sharing and patient privacy for future BC machine learning studies.

Noninvasive Nonlinear Optical Computational Histology

Cancer remains a global health challenge, demanding early detection and accurate diagnosis for improved patient outcomes. An intelligent paradigm is introduced that elevates label-free nonlinear optical imaging with contrastive patch-wise learning, yielding stain-free nonlinear optical computational histology (NOCH). NOCH enables swift, precise diagnostic analysis of fresh tissues, reducing patient anxiety and healthcare costs. Nonlinear modalities are evaluated, including stimulated Raman scattering and multiphoton imaging, for their ability to enhance tumor microenvironment sensitivity, pathological analysis, and cancer examination. Quantitative analysis confirmed that NOCH images accurately reproduce nuclear morphometric features across different cancer stages. Key diagnostic features, such as nuclear morphology, size, and nuclear-cytoplasmic contrast, are well preserved. NOCH models also demonstrate promising generalization when applied to other pathological tissues. The study unites label-free nonlinear optical imaging with histopathology using contrastive learning to establish stain-free computational histology. NOCH provides a rapid, non-invasive, and precise approach to surgical pathology, holding immense potential for revolutionizing cancer diagnosis and surgical interventions.

Toward Robust Self-Training Paradigm for Molecular Prediction Tasks

Molecular prediction tasks normally demand a series of professional experiments to label the target molecule, which suffers from the limited labeled data problem. One of the semisupervised learning paradigms, known as self-training, utilizes both labeled and unlabeled data. Specifically, a teacher model is trained using labeled data and produces pseudo labels for unlabeled data. These labeled and pseudo-labeled data are then jointly used to train a student model. However, the pseudo labels generated from the teacher model are generally not sufficiently accurate. Thus, we propose a robust self-training strategy by exploring robust loss function to handle such noisy labels in two paradigms, that is, generic and adaptive. We have conducted experiments on three molecular biology prediction tasks with four backbone models to gradually evaluate the performance of the proposed robust self-training strategy. The results demonstrate that the proposed method enhances prediction performance across all tasks, notably within molecular regression tasks, where there has been an average enhancement of 41.5%. Furthermore, the visualization analysis confirms the superiority of our method. Our proposed robust self-training is a simple yet effective strategy that efficiently improves molecular biology prediction performance. It tackles the labeled data insufficient issue in molecular biology by taking advantage of both labeled and unlabeled data. Moreover, it can be easily embedded with any prediction task, which serves as a universal approach for the bioinformatics community.

RobOCTNet: Robotics and Deep Learning for Referable Posterior Segment Pathology Detection in an Emergency Department Population

Purpose

To evaluate the diagnostic performance of a robotically aligned optical coherence tomography (RAOCT) system coupled with a deep learning model in detecting referable posterior segment pathology in OCT images of emergency department patients.

Methods

A deep learning model, RobOCTNet, was trained and internally tested to classify OCT images as referable versus non-referable for ophthalmology consultation. For external testing, emergency department patients with signs or symptoms warranting evaluation of the posterior segment were imaged with RAOCT. RobOCTNet was used to classify the images. Model performance was evaluated against a reference standard based on clinical diagnosis and retina specialist OCT review.

Results

We included 90,250 OCT images for training and 1489 images for internal testing. RobOCTNet achieved an area under the curve (AUC) of 1.00 (95% confidence interval [CI], 0.99-1.00) for detection of referable posterior segment pathology in the internal test set. For external testing, RAOCT was used to image 72 eyes of 38 emergency department patients. In this set, RobOCTNet had an AUC of 0.91 (95% CI, 0.82-0.97), a sensitivity of 95% (95% CI, 87%-100%), and a specificity of 76% (95% CI, 62%-91%). The model's performance was comparable to two human experts' performance.

Conclusions

A robotically aligned OCT coupled with a deep learning model demonstrated high diagnostic performance in detecting referable posterior segment pathology in a cohort of emergency department patients.

Translational Relevance

Robotically aligned OCT coupled with a deep learning model may have the potential to improve emergency department patient triage for ophthalmology referral.

Natural Language Processing for Radiation Oncology: Personalizing Treatment Pathways

Natural language processing (NLP), a technology that translates human language into machine-readable data, is revolutionizing numerous sectors, including cancer care. This review outlines the evolution of NLP and its potential for crafting personalized treatment pathways for cancer patients. Leveraging NLP's ability to transform unstructured medical data into structured learnable formats, researchers can tap into the potential of big data for clinical and research applications. Significant advancements in NLP have spurred interest in developing tools that automate information extraction from clinical text, potentially transforming medical research and clinical practices in radiation oncology. Applications discussed include symptom and toxicity monitoring, identification of social determinants of health, improving patient-physician communication, patient education, and predictive modeling. However, several challenges impede the full realization of NLP's benefits, such as privacy and security concerns, biases in NLP models, and the interpretability and generalizability of these models. Overcoming these challenges necessitates a collaborative effort between computer scientists and the radiation oncology community. This paper serves as a comprehensive guide to understanding the intricacies of NLP algorithms, their performance assessment, past research contributions, and the future of NLP in radiation oncology research and clinics.

Prediction of xerostomia in elderly based on clinical characteristics and salivary flow rate with machine learning

Xerostomia may be accompanied by changes in salivary flow rate and the incidence increases in elderly. We aimed to use machine learning algorithms, to identify significant predictors for the presence of xerostomia. This study is the first to predict xerostomia with salivary flow rate in elderly based on artificial intelligence. In a cross-sectional study, 829 patients with oral discomfort were enrolled, and six features (sex, age, unstimulated and stimulated salivary flow rates (UFR and SFR, respectively), number of systemic diseases, and medication usage) were used in four machine learning algorithms to predict the presence of xerostomia. The incidence of xerostomia increased with age. The SFR was significantly higher than the UFR, and the UFR and SFR were significantly correlated. The UFR, but not SFR, decreased with age significantly. In patients more than 60 years of age, the UFR had a significantly higher predictive accuracy for xerostomia than the SFR. Using machine learning algorithms with tenfold cross-validation, the prediction accuracy increased significantly. In particular, the prediction accuracy of the multilayer perceptron (MLP) algorithm that combined UFR and SFR data was significantly better than either UFR or SFR individually. Moreover, when sex, age, number of systemic diseases, and number of medications were added to the MLP model, the prediction accuracy increased from 56 to 68%.

Early Detection of Oral Potentially Malignant Disorders: A Review on Prospective Screening Methods with Regard to Global Challenges

Oral cancer is a cancer type that is widely prevalent in low-and middle-income countries with a high mortality rate, and poor quality of life for patients after treatment. Early treatment of cancer increases patient survival, improves quality of life and results in less morbidity and a better prognosis. To reach this goal, early detection of malignancies using technologies that can be used in remote and low resource areas is desirable. Such technologies should be affordable, accurate, and easy to use and interpret. This review surveys different technologies that have the potentials of implementation in primary health and general dental practice, considering global perspectives and with a focus on the population in India, where oral cancer is highly prevalent. The technologies reviewed include both sample-based methods, such as saliva and blood analysis and brush biopsy, and more direct screening of the oral cavity including fluorescence, Raman techniques, and optical coherence tomography. Digitalisation, followed by automated artificial intelligence based analysis, are key elements in facilitating wide access to these technologies, to non-specialist personnel and in rural areas, increasing quality and objectivity of the analysis while simultaneously reducing the labour and need for highly trained specialists.

A primer on the use of machine learning to distil knowledge from data in biological psychiatry

Applications of machine learning in the biomedical sciences are growing rapidly. This growth has been spurred by diverse cross-institutional and interdisciplinary collaborations, public availability of large datasets, an increase in the accessibility of analytic routines, and the availability of powerful computing resources. With this increased access and exposure to machine learning comes a responsibility for education and a deeper understanding of its bases and bounds, borne equally by data scientists seeking to ply their analytic wares in medical research and by biomedical scientists seeking to harness such methods to glean knowledge from data. This article provides an accessible and critical review of machine learning for a biomedically informed audience, as well as its applications in psychiatry. The review covers definitions and expositions of commonly used machine learning methods, and historical trends of their use in psychiatry. We also provide a set of standards, namely Guidelines for REporting Machine Learning Investigations in Neuropsychiatry (GREMLIN), for designing and reporting studies that use machine learning as a primary data-analysis approach. Lastly, we propose the establishment of the Machine Learning in Psychiatry (MLPsych) Consortium, enumerate its objectives, and identify areas of opportunity for future applications of machine learning in biological psychiatry. This review serves as a cautiously optimistic primer on machine learning for those on the precipice as they prepare to dive into the field, either as methodological practitioners or well-informed consumers.

LVONet: automatic classification model for large vessel occlusion based on the difference information between left and right hemispheres

Objective.Stroke is a highly lethal condition, with intracranial vessel occlusion being one of its primary causes. Intracranial vessel occlusion can typically be categorized into four types, each requiring different intervention measures. Therefore, the automatic and accurate classification of intracranial vessel occlusions holds significant clinical importance for assessing vessel occlusion conditions. However, due to the visual similarities in shape and size among different vessels and variations in the degree of vessel occlusion, the automated classification of intracranial vessel occlusions remains a challenging task. Our study proposes an automatic classification model for large vessel occlusion (LVO) based on the difference information between the left and right hemispheres.Approach.Our approach is as follows. We first introduce a dual-branch attention module to learn long-range dependencies through spatial and channel attention, guiding the model to focus on vessel-specific features. Subsequently, based on the symmetry of vessel distribution, we design a differential information classification module to dynamically learn and fuse the differential information of vessel features between the two hemispheres, enhancing the sensitivity of the classification model to occluded vessels. To optimize the feature differential information among similar vessels, we further propose a novel cooperative learning loss function to minimize changes within classes and similarities between classes.Main results.We evaluate our proposed model on an intracranial LVO data set. Compared to state-of-the-art deep learning models, our model performs optimally, achieving a classification sensitivity of 93.73%, precision of 83.33%, accuracy of 89.91% and Macro-F1 score of 87.13%.Significance.This method can adaptively focus on occluded vessel regions and effectively train in scenarios with high inter-class similarity and intra-class variability, thereby improving the performance of LVO classification.

AutoTransOP: translating omics signatures without orthologue requirements using deep learning

The development of therapeutics and vaccines for human diseases requires a systematic understanding of human biology. Although animal and in vitro culture models can elucidate some disease mechanisms, they typically fail to adequately recapitulate human biology as evidenced by the predominant likelihood of clinical trial failure. To address this problem, we developed AutoTransOP, a neural network autoencoder framework, to map omics profiles from designated species or cellular contexts into a global latent space, from which germane information for different contexts can be identified without the typically imposed requirement of matched orthologues. This approach was found in general to perform at least as well as current alternative methods in identifying animal/culture-specific molecular features predictive of other contexts-most importantly without requiring homology matching. For an especially challenging test case, we successfully applied our framework to a set of inter-species vaccine serology studies, where 1-to-1 mapping between human and non-human primate features does not exist.

Antimicrobial resistance crisis: could artificial intelligence be the solution?

Antimicrobial resistance is a global public health threat, and the World Health Organization (WHO) has announced a priority list of the most threatening pathogens against which novel antibiotics need to be developed. The discovery and introduction of novel antibiotics are time-consuming and expensive. According to WHO's report of antibacterial agents in clinical development, only 18 novel antibiotics have been approved since 2014. Therefore, novel antibiotics are critically needed. Artificial intelligence (AI) has been rapidly applied to drug development since its recent technical breakthrough and has dramatically improved the efficiency of the discovery of novel antibiotics. Here, we first summarized recently marketed novel antibiotics, and antibiotic candidates in clinical development. In addition, we systematically reviewed the involvement of AI in antibacterial drug development and utilization, including small molecules, antimicrobial peptides, phage therapy, essential oils, as well as resistance mechanism prediction, and antibiotic stewardship.

Exploring the Potential of Artificial Intelligence in Adolescent Suicide Prevention: Current Applications, Challenges, and Future Directions

ObjectiveThe global surge in adolescent suicide necessitates the development of innovative and efficacious preventive measures. Traditionally, various approaches have been used, but with limited success. However, with the rapid advancements in artificial intelligence (AI), new possibilities have emerged. This paper reviews the potentials and challenges of integrating AI into suicide prevention strategies, focusing on adolescents. Method: This narrative review assesses the impact of AI on suicide prevention strategies, the strategies and cases of AI applications in adolescent suicide prevention, as well as the challenges faced. Through searches on the PubMed, web of science, PsycINFO, and EMBASE databases, 19 relevant articles were included in the review. Results: AI has significantly improved risk assessment and predictive modeling for identifying suicidal behavior. It has enabled the analysis of textual data through natural language processing and fostered novel intervention strategies. Although AI applications, such as chatbots and monitoring systems, show promise, they must navigate challenges like data privacy and ethical considerations. The research underscores the potential of AI to enhance future suicide prevention efforts through personalized interventions and integration with emerging technologies. Conclusion: AI possesses transformative potential for adolescent suicide prevention by offering targeted and adaptive solutions, while they also raise crucial ethical and practical considerations. Looking forward, AI can play a critical role in mitigating adolescent suicide rates, marking a new frontier in mental health care.

Research on breast cancer pathological image classification method based on wavelet transform and YOLOv8

 Breast cancer is one of the cancers with high morbidity and mortality in the world, which is a serious threat to the health of women. With the development of deep learning, the recognition about computer-aided diagnosis technology is getting higher and higher. And the traditional data feature extraction technology has been gradually replaced by the feature extraction technology based on convolutional neural network which helps to realize the automatic recognition and classification of pathological images. In this paper, a novel method based on deep learning and wavelet transform is proposed to classify the pathological images of breast cancer. Firstly, the image flip technique is used to expand the data set, then the two-level wavelet decomposition and reconfiguration technology is used to sharpen and enhance the pathological images. Secondly, the processed data set is divided into the training set and the test set according to 8:2 and 7:3, and the YOLOv8 network model is selected to perform the eight classification tasks of breast cancer pathological images. Finally, the classification accuracy of the proposed method is compared with the classification accuracy obtained by YOLOv8 for the original BreaKHis dataset, and it is found that the algorithm can improve the classification accuracy of images with different magnifications, which proves the effectiveness of combining two-level wavelet decomposition and reconfiguration with YOLOv8 network model.

Artificial intelligence for segmentation and classification of lobar, lobular, and interstitial pneumonia using case-specific CT information

Background

Pneumonia can be anatomically classified into lobar, lobular, and interstitial types, with each type associated with different pathogens. Utilizing artificial intelligence (AI) to determine the anatomical classifications of pneumonia and assist in refining the differential diagnosis may offer a more viable and clinically relevant solution. This study aimed to develop a multi-classification model capable of identifying the occurrence of pneumonia in patients by utilizing case-specific computed tomography (CT) information, categorizing the pneumonia type (lobar, lobular, and interstitial pneumonia), and performing segmentation of the associated lesions.

Methods

A total of 61 lobar pneumonia patients, 60 lobular pneumonia patients, and 60 interstitial pneumonia patients were consecutively enrolled at our local hospital from June 2020 and May 2022. All selected cases were divided into a training cohort (n=135) and an independent testing cohort (n=46). To generate the ground truth labels for the training process, manual segmentation and labeling were performed by three junior radiologists. Subsequently, the segmentations were manually reviewed and edited by a senior radiologist. AI models were developed to automatically segment the infected lung regions and classify the pneumonia. The accuracy of pneumonia lesion segmentation was analyzed and evaluated using the Dice coefficient. Receiver operating characteristic curves were plotted, and the area under the curve (AUC), accuracy, precision, sensitivity, and specificity were calculated to assess the efficacy of pneumonia classification.

Results

Our AI model achieved a Dice coefficient of 0.743 [95% confidence interval (CI): 0.657-0.826] for lesion segmentation in the training set and 0.723 (95% CI: 0.602-0.845) in the test set. In the test set, our model achieved an accuracy of 0.927 (95% CI: 0.876-0.978), precision of 0.889 (95% CI: 0.827-0.951), sensitivity of 0.889 (95% CI: 0.827-0.951), specificity of 0.946 (95% CI: 0.902-0.990), and AUC of 0.989 (95% CI: 0.969-1.000) for pneumonia classification. We trained the model using labels annotated by senior physicians and compared it to a model trained using labels annotated by junior physicians. The Dice coefficient of the model's segmentation improved by 0.014, increasing from 0.709 (95% CI: 0.589-0.830) to 0.723 (95% CI: 0.602-0.845), and the AUC improved by 0.042, rising from 0.947 to 0.989.

Conclusions

Our study presents a robust multi-task learning model with substantial promise in enhancing the segmentation and classification of pneumonia in medical imaging.

Multiple-instance learning of somatic mutations for the classification of tumour type and the prediction of microsatellite status

Large-scale genomic data are well suited to analysis by deep learning algorithms. However, for many genomic datasets, labels are at the level of the sample rather than for individual genomic measures. Machine learning models leveraging these datasets generate predictions by using statically encoded measures that are then aggregated at the sample level. Here we show that a single weakly supervised end-to-end multiple-instance-learning model with multi-headed attention can be trained to encode and aggregate the local sequence context or genomic position of somatic mutations, hence allowing for the modelling of the importance of individual measures for sample-level classification and thus providing enhanced explainability. The model solves synthetic tasks that conventional models fail at, and achieves best-in-class performance for the classification of tumour type and for predicting microsatellite status. By improving the performance of tasks that require aggregate information from genomic datasets, multiple-instance deep learning may generate biological insight.

Artificial Intelligence: Singularity Approaches

SUMMARY

Artificial intelligence (AI) has been a disruptive technology within health care, from the development of simple care algorithms to complex deep-learning models. AI has the potential to reduce the burden of administrative tasks, advance clinical decision-making, and improve patient outcomes. Unlocking the full potential of AI requires the analysis of vast quantities of clinical information. Although AI holds tremendous promise, widespread adoption within plastic surgery remains limited. Understanding the basics is essential for plastic surgeons to evaluate the potential uses of AI. This review provides an introduction of AI, including the history of AI, key concepts, applications of AI in plastic surgery, and future implications.

Big Data Analysis in Computational Biology and Bioinformatics

Advancements in high-throughput technologies, genomics, transcriptomics, and metabolomics play an important role in obtaining biological information about living organisms. The field of computational biology and bioinformatics has experienced significant growth with the advent of high-throughput sequencing technologies and other high-throughput techniques. The resulting large amounts of data present both opportunities and challenges for data analysis. Big data analysis has become essential for extracting meaningful insights from the massive amount of data. In this chapter, we provide an overview of the current status of big data analysis in computational biology and bioinformatics. We discuss the various aspects of big data analysis, including data acquisition, storage, processing, and analysis. We also highlight some of the challenges and opportunities of big data analysis in this area of research. Despite the challenges, big data analysis presents significant opportunities like development of efficient and fast computing algorithms for advancing our understanding of biological processes, identifying novel biomarkers for breeding research and developments, predicting disease, and identifying potential drug targets for drug development programs.

Application of machine learning in the management of lymphoma: Current practice and future prospects

In the past decade, digitization of medical records and multiomics data analysis in lymphoma has led to the accessibility of high-dimensional records. The digitization of medical records, the visualization of extensive volume data extracted from medical images, and the integration of multiomics methods into clinical decision-making have produced many datasets. As a promising auxiliary tool, machine learning (ML) intends to extract homologous features in large-scale data sets and encode them into various patterns to complete complicated tasks. At present, artificial intelligence and digital mining have shown promising prospects in the field of lymphoma pathological image analysis. The paradigm shift from qualitative analysis to quantitative analysis makes the pathological diagnosis more intelligent and the results more accurate and objective. ML can promote accurate lymphoma diagnosis and provide patients with prognostic information and more individualized treatment options. Based on the above, this comprehensive review of the general workflow of ML highlights recent advances in ML techniques in the diagnosis, treatment, and prognosis of lymphoma, and clarifies the boundedness and future orientation of the ML technique in the clinical practice of lymphoma.

Metabolomic-Based Approaches for Endometrial Cancer Diagnosis and Prognosis: A Review

Endometrial cancer, the most prevalent gynecological malignancy in developed countries, is experiencing a sustained rise in both its incidence and mortality rates, primarily attributed to extended life expectancy and lifestyle factors. Currently, the absence of precise diagnostic tools hampers the effective management of the expanding population of women at risk of developing this disease. Furthermore, patients diagnosed with endometrial cancer require precise risk stratification to align with optimal treatment planning. Metabolomics technology offers a unique insight into the molecular landscape of endometrial cancer, providing a promising approach to address these unmet needs. This comprehensive literature review initiates with an overview of metabolomic technologies and their intrinsic workflow components, aiming to establish a fundamental understanding for the readers. Subsequently, a detailed exploration of the existing body of research is undertaken with the objective of identifying metabolite biomarkers capable of enhancing current strategies for endometrial cancer diagnosis, prognosis, and recurrence monitoring. Metabolomics holds vast potential to revolutionize the management of endometrial cancer by providing accuracy and valuable insights into crucial aspects.

Computer-Aided Drug Design and Drug Discovery: A Prospective Analysis

In the dynamic landscape of drug discovery, Computer-Aided Drug Design (CADD) emerges as a transformative force, bridging the realms of biology and technology. This paper overviews CADDs historical evolution, categorization into structure-based and ligand-based approaches, and its crucial role in rationalizing and expediting drug discovery. As CADD advances, incorporating diverse biological data and ensuring data privacy become paramount. Challenges persist, demanding the optimization of algorithms and robust ethical frameworks. Integrating Machine Learning and Artificial Intelligence amplifies CADDs predictive capabilities, yet ethical considerations and scalability challenges linger. Collaborative efforts and global initiatives, exemplified by platforms like Open-Source Malaria, underscore the democratization of drug discovery. The convergence of CADD with personalized medicine offers tailored therapeutic solutions, though ethical dilemmas and accessibility concerns must be navigated. Emerging technologies like quantum computing, immersive technologies, and green chemistry promise to redefine the future of CADD. The trajectory of CADD, marked by rapid advancements, anticipates challenges in ensuring accuracy, addressing biases in AI, and incorporating sustainability metrics. This paper concludes by highlighting the need for proactive measures in navigating the ethical, technological, and educational frontiers of CADD to shape a healthier, brighter future in drug discovery.

Do neutrophil extracellular traps implicate in atheromatous plaques from carotid endarterectomy? Re-analyzes of cDNA microarray data by surgeons

Background

Carotid artery stenosis is the cause of 15% of strokes. Neutrophil extracellular traps (NETs) and peptidyl arginine deiminase 4 (PAD4) are believed to be involved in thrombosis. This pilot study described the differential expression profile of NETs between atheromatous plaques and surrounding tissues.

Methods

Microarray datasets of carotid plaques were obtained from Gene Expression Omnibus. The normalized data were processed into comma-separated value matrix files using spreadsheet software. Analyzes of microarray data were conducted using integrated differential expression and pathway analysis.

Result

The clustering results illustrated that the classifications of plaque and control had reasonable biological validity. Pathway analysis revealed the relevance of immune response, cell signaling, and other pathways. Differentially expressed genes were detected between carotid plaques and control specimens. However, enrichment analyzes did not reveal a difference in PAD4 expression between the groups and that NET implication was only found in one cDNA microarray dataset.

Discussion

This pilot study does not necessarily dismiss the possibility of a relationship between NETs and atherothrombotic stroke. Gene expression could differ between endothelial cells and atheromas, and further studies are needed.

Deep learning in bioinformatics

Deep learning is a powerful machine learning technique that can learn from large amounts of data using multiple layers of artificial neural networks. This paper reviews some applications of deep learning in bioinformatics, a field that deals with analyzing and interpreting biological data. We first introduce the basic concepts of deep learning and then survey the recent advances and challenges of applying deep learning to various bioinformatics problems, such as genome sequencing, gene expression analysis, protein structure prediction, drug discovery, and disease diagnosis. We also discuss future directions and opportunities for deep learning in bioinformatics. We aim to provide an overview of deep learning so that bioinformaticians applying deep learning models can consider all critical technical and ethical aspects. Thus, our target audience is biomedical informatics researchers who use deep learning models for inference. This review will inspire more bioinformatics researchers to adopt deep-learning methods for their research questions while considering fairness, potential biases, explainability, and accountability.

Self-Supervised Contrastive Representation Learning for Semi-Supervised Time-Series Classification

Learning time-series representations when only unlabeled data or few labeled samples are available can be a challenging task. Recently, contrastive self-supervised learning has shown great improvement in extracting useful representations from unlabeled data via contrasting different augmented views of data. In this work, we propose a novel Time-Series representation learning framework via Temporal and Contextual Contrasting (TS-TCC) that learns representations from unlabeled data with contrastive learning. Specifically, we propose time-series-specific weak and strong augmentations and use their views to learn robust temporal relations in the proposed temporal contrasting module, besides learning discriminative representations by our proposed contextual contrasting module. Additionally, we conduct a systematic study of time-series data augmentation selection, which is a key part of contrastive learning. We also extend TS-TCC to the semi-supervised learning settings and propose a Class-Aware TS-TCC (CA-TCC) that benefits from the available few labeled data to further improve representations learned by TS-TCC. Specifically, we leverage the robust pseudo labels produced by TS-TCC to realize a class-aware contrastive loss. Extensive experiments show that the linear evaluation of the features learned by our proposed framework performs comparably with the fully supervised training. Additionally, our framework shows high efficiency in few labeled data and transfer learning scenarios.

Artificial intelligence for dementia genetics and omics

Genetics and omics studies of Alzheimer's disease and other dementia subtypes enhance our understanding of underlying mechanisms and pathways that can be targeted. We identified key remaining challenges: First, can we enhance genetic studies to address missing heritability? Can we identify reproducible omics signatures that differentiate between dementia subtypes? Can high-dimensional omics data identify improved biomarkers? How can genetics inform our understanding of causal status of dementia risk factors? And which biological processes are altered by dementia-related genetic variation? Artificial intelligence (AI) and machine learning approaches give us powerful new tools in helping us to tackle these challenges, and we review possible solutions and examples of best practice. However, their limitations also need to be considered, as well as the need for coordinated multidisciplinary research and diverse deeply phenotyped cohorts. Ultimately AI approaches improve our ability to interrogate genetics and omics data for precision dementia medicine. HIGHLIGHTS: We have identified five key challenges in dementia genetics and omics studies. AI can enable detection of undiscovered patterns in dementia genetics and omics data. Enhanced and more diverse genetics and omics datasets are still needed. Multidisciplinary collaborative efforts using AI can boost dementia research.

Deep Learning Model for Predicting Airway Organoid Differentiation

BACKGROUND

Organoids are self-organized three-dimensional culture systems and have the advantages of both in vitro and in vivo experiments. However, each organoid has a different degree of self-organization, and methods such as immunofluorescence staining are required for confirmation. Therefore, we established a system to select organoids with high tissue-specific similarity using deep learning without relying on staining by acquiring bright-field images in a non-destructive manner.

METHODS

We identified four biomarkers in RNA extracted from airway organoids. We also predicted biomarker expression by image-based analysis of organoids by convolution neural network, a deep learning method.

RESULTS

We predicted airway organoid-specific marker expression from bright-field images of organoids. Organoid differentiation was verified by immunofluorescence staining of the same organoid after predicting biomarker expression in bright-field images.

CONCLUSION

Our study demonstrates the potential of imaging and deep learning to distinguish organoids with high human tissue similarity in disease research and drug screening.

Artificial intelligence revolutionizing drug development: Exploring opportunities and challenges

By harnessing artificial intelligence (AI) algorithms and machine learning techniques, the entire drug discovery process stands to undergo a profound transformation, offering a myriad of advantages. Foremost among these is the ability of AI to conduct swift and efficient screenings of expansive compound libraries, significantly augmenting the identification of potential drug candidates. Moreover, AI algorithms can prove instrumental in predicting the efficacy and safety profiles of candidate compounds, thus endowing invaluable insights and reducing reliance on extensive preclinical and clinical testing. This predictive capacity of AI has the potential to streamline the drug development pipeline and enhance the success rate of clinical trials, ultimately resulting in the emergence of more efficacious and safer therapeutic agents. However, the deployment of AI in drug discovery introduces certain challenges that warrant attention. A primary hurdle entails the imperative acquisition of high-quality and diverse data. Furthermore, ensuring the interpretability of AI models assumes critical importance in securing regulatory endorsement and cultivating trust within scientific and medical communities. Addressing ethical considerations, including data privacy and mitigating bias, represents an additional momentous challenge, requiring assiduous navigation. In this review, we provide an intricate and comprehensive overview of the multifaceted challenges intrinsic to conventional drug development paradigms, while simultaneously interrogating the efficacy of AI in effectively surmounting these formidable obstacles.

Computational approaches for modeling and structural design of biological systems: A comprehensive review

The convergence of biology and computational science has ushered in a revolutionary era, revolutionizing our understanding of biological systems and providing novel solutions to global problems. The field of genetic engineering has facilitated the manipulation of genetic codes, thus providing opportunities for the advancement of innovative disease therapies and environmental enhancements. The emergence of bio-molecular simulation represents a significant advancement in this particular field, as it offers the ability to gain microscopic insights into molecular-level biological processes over extended periods. Biomolecular simulation plays a crucial role in advancing our comprehension of organismal mechanisms by establishing connections between molecular structures, interactions, and biological functions. The field of computational biology has demonstrated its significance in deciphering intricate biological enigmas through the utilization of mathematical models and algorithms. The process of decoding the human genome has resulted in the advancement of therapies for a wide range of genetic disorders, while the simulation of biological systems contributes to the identification of novel pharmaceutical compounds. The potential of biomolecular simulation and computational biology is vast and limitless. As the exploration of the underlying principles that govern living organisms progresses, the potential impact of this understanding on cancer treatment, environmental restoration, and other domains is anticipated to be transformative. This review examines the notable advancements achieved in the field of computational biology, emphasizing its potential to revolutionize the comprehension and enhancement of biological systems.

Interpretable neural architecture search and transfer learning for understanding CRISPR-Cas9 off-target enzymatic reactions

Finely tuned enzymatic pathways control cellular processes, and their dysregulation can lead to disease. Developing predictive and interpretable models for these pathways is challenging because of the complexity of the pathways and of the cellular and genomic contexts. Here we introduce Elektrum, a deep learning framework that addresses these challenges with data-driven and biophysically interpretable models for determining the kinetics of biochemical systems. First, it uses in vitro kinetic assays to rapidly hypothesize an ensemble of high-quality kinetically interpretable neural networks (KINNs) that predict reaction rates. It then employs a transfer learning step, where the KINNs are inserted as intermediary layers into deeper convolutional neural networks, fine-tuning the predictions for reaction-dependent in vivo outcomes. We apply Elektrum to predict CRISPR-Cas9 off-target editing probabilities and demonstrate that Elektrum achieves improved performance, regularizes neural network architectures and maintains physical interpretability.

Advancing Computational Toxicology by Interpretable Machine Learning

Chemical toxicity evaluations for drugs, consumer products, and environmental chemicals have a critical impact on human health. Traditional animal models to evaluate chemical toxicity are expensive, time-consuming, and often fail to detect toxicants in humans. Computational toxicology is a promising alternative approach that utilizes machine learning (ML) and deep learning (DL) techniques to predict the toxicity potentials of chemicals. Although the applications of ML- and DL-based computational models in chemical toxicity predictions are attractive, many toxicity models are "black boxes" in nature and difficult to interpret by toxicologists, which hampers the chemical risk assessments using these models. The recent progress of interpretable ML (IML) in the computer science field meets this urgent need to unveil the underlying toxicity mechanisms and elucidate the domain knowledge of toxicity models. In this review, we focused on the applications of IML in computational toxicology, including toxicity feature data, model interpretation methods, use of knowledge base frameworks in IML development, and recent applications. The challenges and future directions of IML modeling in toxicology are also discussed. We hope this review can encourage efforts in developing interpretable models with new IML algorithms that can assist new chemical assessments by illustrating toxicity mechanisms in humans.

Screening for Psychological Distress in Healthcare Workers Using Machine Learning: A Proof of Concept

The purpose of this study was to train and test preliminary models using two machine learning algorithms to identify healthcare workers at risk of developing anxiety, depression, and post-traumatic stress disorder. The study included data from a prospective cohort study of 816 healthcare workers collected using a mobile application during the first two waves of COVID-19. Each week, the participants responded to 11 questions and completed three screening questionnaires (one for anxiety, one for depression, and one for post-traumatic stress disorder). Then, the research team selected two questions (out of the 11), which were used with biological sex to identify whether scores on each screening questionnaire would be positive or negative. The analyses involved a fivefold cross-validation to test the accuracy of models based on logistic regression and support vector machines using cross-sectional and cumulative measures. The findings indicated that the models derived from the two questions and biological sex accurately identified screening scores for anxiety, depression, and post-traumatic stress disorders in 70% to 80% of cases. However, the positive predictive value never exceeded 50%, underlining the importance of collecting more data to train better models. Our proof of concept demonstrates the feasibility of using machine learning to develop novel models to screen for psychological distress in at-risk healthcare workers. Developing models with fewer questions may reduce burdens of active monitoring in practical settings by decreasing the weekly assessment duration.

Disability risk prediction model based on machine learning among Chinese healthy older adults: results from the China Health and Retirement Longitudinal Study

Background

Predicting disability risk in healthy older adults in China is essential for timely preventive interventions, improving their quality of life, and providing scientific evidence for disability prevention. Therefore, developing a machine learning model capable of evaluating disability risk based on longitudinal research data is crucial.

Methods

We conducted a prospective cohort study of 2,175 older adults enrolled in the China Health and Retirement Longitudinal Study (CHARLS) between 2015 and 2018 to develop and validate this prediction model. Several machine learning algorithms (logistic regression, k-nearest neighbors, naive Bayes, multilayer perceptron, random forest, and XGBoost) were used to assess the 3-year risk of developing disability. The optimal cutoff points and adjustment parameters are explored in the training set, the prediction accuracy of the models is compared in the testing set, and the best-performing models are further interpreted.

Results

During a 3-year follow-up period, a total of 505 (23.22%) healthy older adult individuals developed disabilities. Among the 43 features examined, the LASSO regression identified 11 features as significant for model establishment. When comparing six different machine learning models on the testing set, the XGBoost model demonstrated the best performance across various evaluation metrics, including the highest area under the ROC curve (0.803), accuracy (0.757), sensitivity (0.790), and F1 score (0.789), while its specificity was 0.712. The decision curve analysis (DCA) indicated showed that XGBoost had the highest net benefit in most of the threshold ranges. Based on the importance of features determined by SHAP (model interpretation method), the top five important features were identified as right-hand grip strength, depressive symptoms, marital status, respiratory function, and age. Moreover, the SHAP summary plot was used to illustrate the positive or negative effects attributed to the features influenced by XGBoost. The SHAP dependence plot explained how individual features affected the output of the predictive model.

Conclusion

Machine learning-based prediction models can accurately evaluate the likelihood of disability in healthy older adults over a period of 3 years. A combination of XGBoost and SHAP can provide clear explanations for personalized risk prediction and offer a more intuitive understanding of the effect of key features in the model.

Biomolecular NMR spectroscopy in the era of artificial intelligence

Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence (AI) have a burgeoning synergy. Deep learning-based structural predictors have forever changed structural biology, yet these tools currently face limitations in accurately characterizing protein dynamics, allostery, and conformational heterogeneity. We begin by highlighting the unique abilities of biomolecular NMR spectroscopy to complement AI-based structural predictions toward addressing these knowledge gaps. We then highlight the direct integration of deep learning approaches into biomolecular NMR methods. AI-based tools can dramatically improve the acquisition and analysis of NMR spectra, enhancing the accuracy and reliability of NMR measurements, thus streamlining experimental processes. Additionally, deep learning enables the development of novel types of NMR experiments that were previously unattainable, expanding the scope and potential of biomolecular NMR spectroscopy. Ultimately, a combination of AI and NMR promises to further revolutionize structural biology on several levels, advance our understanding of complex biomolecular systems, and accelerate drug discovery efforts.