Opportunities and obstacles for deep learning in biology and medicine

Neural network-assisted localization of clustered point spread functions in single-molecule localization microscopy

Single-molecule localization microscopy (SMLM), which has revolutionized nanoscale imaging, faces challenges in densely labelled samples due to fluorophore clustering, leading to compromised localization accuracy. In this paper, we propose a novel convolutional neural network (CNN)-assisted approach to address the issue of locating the clustered fluorophores. Our CNN is trained on a diverse data set of simulated SMLM images where it learns to predict point spread function (PSF) locations by generating Gaussian blobs as output. Through rigorous evaluation, we demonstrate significant improvements in PSF localization accuracy, especially in densely labelled samples where traditional methods struggle. In addition, we employ blob detection as a post-processing technique to refine the predicted PSF locations and enhance localization precision. Our study underscores the efficacy of CNN in addressing clustering challenges in SMLM, thereby advancing spatial resolution and enabling deeper insights into complex biological structures.

Generative Artificial Intelligence Use in Healthcare: Opportunities for Clinical Excellence and Administrative Efficiency

Generative Artificial Intelligence (Gen AI) has transformative potential in healthcare to enhance patient care, personalize treatment options, train healthcare professionals, and advance medical research. This paper examines various clinical and non-clinical applications of Gen AI. In clinical settings, Gen AI supports the creation of customized treatment plans, generation of synthetic data, analysis of medical images, nursing workflow management, risk prediction, pandemic preparedness, and population health management. By automating administrative tasks such as medical documentations, Gen AI has the potential to reduce clinician burnout, freeing more time for direct patient care. Furthermore, application of Gen AI may enhance surgical outcomes by providing real-time feedback and automation of certain tasks in operating rooms. The generation of synthetic data opens new avenues for model training for diseases and simulation, enhancing research capabilities and improving predictive accuracy. In non-clinical contexts, Gen AI improves medical education, public relations, revenue cycle management, healthcare marketing etc. Its capacity for continuous learning and adaptation enables it to drive ongoing improvements in clinical and operational efficiencies, making healthcare delivery more proactive, predictive, and precise.

Deep neural networks have an inbuilt Occam's razor

The remarkable performance of overparameterized deep neural networks (DNNs) must arise from an interplay between network architecture, training algorithms, and structure in the data. To disentangle these three components for supervised learning, we apply a Bayesian picture based on the functions expressed by a DNN. The prior over functions is determined by the network architecture, which we vary by exploiting a transition between ordered and chaotic regimes. For Boolean function classification, we approximate the likelihood using the error spectrum of functions on data. Combining this with the prior yields an accurate prediction for the posterior, measured for DNNs trained with stochastic gradient descent. This analysis shows that structured data, together with a specific Occam's razor-like inductive bias towards (Kolmogorov) simple functions that exactly counteracts the exponential growth of the number of functions with complexity, is a key to the success of DNNs.

Protocol for the development and validation of machine-learning models for predicting the risk of hypertriglyceridemia in critically ill patients receiving propofol sedation using retrospective data

Introduction

Propofol is a widely used sedative-hypnotic agent for critically-ill patients requiring invasive mechanical ventilation (IMV). Despite its clinical benefits, propofol is associated with increased risks of hypertriglyceridemia. Early identification of patients at risk for propofol-associated hypertriglyceridemia is crucial for optimizing sedation strategies and preventing adverse outcomes. Machine learning (ML) models offer a promising approach for predicting individualized patient risks of propofol-associated hypertriglyceridemia.

Methods and analysis

We propose the development of a ML model aimed at predicting the risk of propofol-associated hypertriglyceridemia in ICU patients receiving IMV. The study will utilize retrospective data from four Mayo Clinic sites. Nested cross-validation (CV) will be employed, with a 10-fold inner CV loop for model tuning and selection as well as an outer loop using leave-one-site-out CV for external validation. Feature selection will be conducted using Boruta and LASSO-penalized logistic regression. Data preprocessing steps include missing data imputation, feature scaling, and dimensionality reduction techniques. Six ML algorithms will be tuned and evaluated. Bayesian optimization will be used for hyperparameter selection. Global model explainability will be assessed using permutation importance, and local model explainability will be assessed using SHapley Additive exPlanations (SHAP).

Ethics and dissemination

The proposed ML model aims to provide a reliable and interpretable tool for clinicians to predict the risk of propofol-associated hypertriglyceridemia in ICU patients. The final model will be deployed in a web-based clinical risk calculator. The model development process and performance measures obtained during nested cross-validation will be described in a study publication to be disseminated in a peer-reviewed journal. The proposed study has received ethics approval from the Mayo Clinic Institutional Review Board (IRB #23-007416).

Strengths and limitations of this study

Robust external validation using a nested cross-validation (CV) framework will help assess the generalizability of models produced from the modeling pipeline across different hospital settings.A diverse set of machine learning (ML) algorithms and advanced hyperparameter tuning techniques will be employed to identify the most optimal model configuration.Integration of feature explainability will enhance the clinical applicability of the ML models by providing transparency in predictions, which can improve clinician trust and encourage adoption.Reliance on retrospective data may introduce biases due to inconsistent or erroneous data collection, and the computational intensity of the validation approach may limit replication and future model expansion in resource-constrained settings.

Researching public health datasets in the era of deep learning: a systematic literature review

Objective: Explore deep learning applications in predictive analytics for public health data, identify challenges and trends, and then understand the current landscape. Materials and Methods: A systematic literature review was conducted in June 2023 to search articles on public health data in the context of deep learning, published from the inception of medical and computer science databases through June 2023. The review focused on diverse datasets, abstracting applications, challenges, and advancements in deep learning. Results: 2004 articles were reviewed, identifying 14 disease categories. Observed trends include explainable-AI, patient embedding learning, and integrating different data sources and employing deep learning models in health informatics. Noted challenges were technical reproducibility and handling sensitive data. Discussion: There has been a notable surge in deep learning applications on public health data publications since 2015. Consistent deep learning applications and models continue to be applied across public health data. Despite the wide applications, a standard approach still does not exist for addressing the outstanding challenges and issues in this field. Conclusion: Guidelines are needed for applying deep learning and models in public health data to improve FAIRness, efficiency, transparency, comparability, and interoperability of research. Interdisciplinary collaboration among data scientists, public health experts, and policymakers is needed to harness the full potential of deep learning.

Brief Review and Primer of Key Terminology for Artificial Intelligence and Machine Learning in Hypertension

Recent breakthroughs in artificial intelligence (AI) have caught the attention of many fields, including health care. The vision for AI is that a computer model can process information and provide output that is indistinguishable from that of a human and, in specific repetitive tasks, outperform a human's capability. The 2 critical underlying technologies in AI are used for supervised and unsupervised machine learning. Machine learning uses neural networks and deep learning modeled after the human brain from structured or unstructured data sets to learn, make decisions, and continuously improve the model. Natural language processing, used for supervised learning, is understanding, interpreting, and generating information using human language in chatbots and generative and conversational AI. These breakthroughs result from increased computing power and access to large data sets, setting the stage for releasing large language models, such as ChatGPT and others, and new imaging models using computer vision. Hypertension management involves using blood pressure and other biometric data from connected devices and generative AI to communicate with patients and health care professionals. AI can potentially improve hypertension diagnosis and treatment through remote patient monitoring and digital therapeutics.

A new risk assessment model of venous thromboembolism by considering fuzzy population

BACKGROUND

Inpatients with high risk of venous thromboembolism (VTE) usually face serious threats to their health and economic conditions. Many studies using machine learning (ML) models to predict VTE risk overlook the impact of class-imbalance problem due to the low incidence rate of VTE, resulting in inferior and unstable model performance, which hinders their ability to replace the Padua model, a widely used linear weighted model in clinic. Our study aims to develop a new VTE risk assessment model suitable for Chinese medical inpatients.

METHODS

3284 inpatients in the medical department of Peking Union Medical College Hospital (PUMCH) from January 2014 to June 2016 were collected. The training and test set were divided based on the admission time and inpatients from May 2016 to June 2016 were included as the test dataset. We explained the class imbalance problem from a clinical perspective and defined a new term, "fuzzy population", to elaborate and model this phenomenon. By considering the "fuzzy population", a new ML VTE risk assessment model was built through population splitting. Sensitivity and specificity of our method was compared with five ML models (support vector machine (SVM), random forest (RF), gradient boosting decision tree (GBDT), logistic regression (LR), and XGBoost) and the Padua model.

RESULTS

The 'fuzzy population' phenomenon was explained and verified on the VTE dataset. The proposed model achieved higher specificity (64.94% vs. 63.30%) and the same sensitivity (90.24% vs. 90.24%) on test data than the Padua model. Other five ML models couldn't simultaneously surpass the Padua's sensitivity and specificity. Besides, our model was more robust than five ML models and its standard deviations of sensitivities and specificities were smaller. Adjusting the distribution of negative samples in the training set based on the 'fuzzy population' would exacerbate the instability of performance of five ML models, which limited the application of ML methods in clinic.

CONCLUSIONS

The proposed model achieved higher sensitivity and specificity than the Padua model, and better robustness than traditional ML models. This study built a population-split-based ML model of VTE by modeling the class-imbalance problem and it can be applied more broadly in risk assessment of other diseases.

Automatic ovarian follicle detection using object detection models

Ovaries are of paramount importance in reproduction as they produce female gametes through a complex developmental process known as folliculogenesis. In the prospect of better understanding the mechanisms of folliculogenesis and of developing novel pharmacological approaches to control it, it is important to accurately and quantitatively assess the later stages of ovarian folliculogenesis (i.e. the formation of antral follicles and corpus lutea). Manual counting from histological sections is commonly employed to determine the number of these follicular structures, however it is a laborious and error prone task. In this work, we show the benefits of deep learning models for counting antral follicles and corpus lutea in ovarian histology sections. Here, we use various backbone architectures to build two one-stage object detection models, i.e. YOLO and RetinaNet. We employ transfer learning, early stopping, and data augmentation approaches to improve the generalizability of the object detectors. Furthermore, we use sampling strategy to mitigate the foreground-foreground class imbalance and focal loss to reduce the imbalance between the foreground-background classes. Our models were trained and validated using a dataset containing only 1000 images. With RetinaNet, we achieved a mean average precision of 83% whereas with YOLO of 75% on the testing dataset. Our results demonstrate that deep learning methods are useful to speed up the follicle counting process and improve accuracy by correcting manual counting errors.

AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images

Visual analysis of peripheral blood smear slides using medical image analysis is required to diagnose red blood cell (RBC) morphological deformities caused by anemia. The absence of a complete anaemic RBC dataset has hindered the training and testing of deep convolutional neural networks (CNNs) for computer-aided analysis of RBC morphology. We introduce a benchmark RBC image dataset named Anemic RBC (AneRBC) to overcome this problem. This dataset is divided into two versions: AneRBC-I and AneRBC-II. AneRBC-I contains 1000 microscopic images, including 500 healthy and 500 anaemic images with 1224 × 960 pixel resolution, along with manually generated ground truth of each image. Each image contains approximately 1550 RBC elements, including normocytes, microcytes, macrocytes, elliptocytes, and target cells, resulting in a total of approximately 1 550 000 RBC elements. The dataset also includes each image's complete blood count and morphology reports to validate the CNN model results with clinical data. Under the supervision of a team of expert pathologists, the annotation, labeling, and ground truth for each image were generated. Due to the high resolution, each image was divided into 12 subimages with ground truth and incorporated into AneRBC-II. AneRBC-II comprises a total of 12 000 images, comprising 6000 original and 6000 anaemic RBC images. Four state-of-the-art CNN models were applied for segmentation and classification to validate the proposed dataset. Database URL: https://data.mendeley.com/preview/hms3sjzt7f?a=4d0ba42a-cc6f-4777-adc4-2552e80db22b.

Artificial intelligence in pediatric allergy research

Atopic dermatitis, food allergy, allergic rhinitis, and asthma are among the most common diseases in childhood. They are heterogeneous diseases, can co-exist in their development, and manifest complex associations with other disorders and environmental and hereditary factors. Elucidating these intricacies by identifying clinically distinguishable groups and actionable risk factors will allow for better understanding of the diseases, which will enhance clinical management and benefit society and affected individuals and families. Artificial intelligence (AI) is a promising tool in this context, enabling discovery of meaningful patterns in complex data. Numerous studies within pediatric allergy have and continue to use AI, primarily to characterize disease endotypes/phenotypes and to develop models to predict future disease outcomes. However, most implementations have used relatively simplistic data from one source, such as questionnaires. In addition, methodological approaches and reporting are lacking. This review provides a practical hands-on guide for conducting AI-based studies in pediatric allergy, including (1) an introduction to essential AI concepts and techniques, (2) a blueprint for structuring analysis pipelines (from selection of variables to interpretation of results), and (3) an overview of common pitfalls and remedies. Furthermore, the state-of-the art in the implementation of AI in pediatric allergy research, as well as implications and future perspectives are discussed.

CONCLUSION

AI-based solutions will undoubtedly transform pediatric allergy research, as showcased by promising findings and innovative technical solutions, but to fully harness the potential, methodologically robust implementation of more advanced techniques on richer data will be needed.

WHAT IS KNOWN

• Pediatric allergies are heterogeneous and common, inflicting substantial morbidity and societal costs. • The field of artificial intelligence is undergoing rapid development, with increasing implementation in various fields of medicine and research.

WHAT IS NEW

• Promising applications of AI in pediatric allergy have been reported, but implementation largely lags behind other fields, particularly in regard to use of advanced algorithms and non-tabular data. Furthermore, lacking reporting on computational approaches hampers evidence synthesis and critical appraisal. • Multi-center collaborations with multi-omics and rich unstructured data as well as utilization of deep learning algorithms are lacking and will likely provide the most impactful discoveries.

Machine Learning-Engineered Nanozyme System for Synergistic Anti-Tumor Ferroptosis/Apoptosis Therapy

Nanozymes with multienzyme-like activity have sparked significant interest in anti-tumor therapy via responding to the tumor microenvironment (TME). However, the consequent induction of protective autophagy substantially compromises the therapeutic efficacy. Here, a targeted nanozyme system (Fe-Arg-CDs@ZIF-8/HAD, FZH) is shown, which enhances synergistic anti-tumor ferroptosis/apoptosis therapy by leveraging machine learning (ML). A novel ML model, termed the sequential backward Tree-Classifier for Gaussian Process Regression (TCGPR), is proposed to improve data pattern recognition following the divide-and-conquer principle. Based on this, a Bayesian optimization algorithm is employed to select candidates from the extensive search space. Leveraging this fresh material discovery framework, a novel strategy for enhancing nanozyme-based tumor therapy, has been developed. The results reveal that FZH effectively exerts anti-tumor effects by sequentially responding to the TME, having a cascade reaction to induce ferroptosis. Moreover, the endogenous elevation of high concentration nitric oxide (NO) serves as a direct mechanism for killing tumor cells while concurrently suppressing the protective autophagy induced by oxidative stress (OS), enhancing synergistic ferroptosis/apoptosis therapy. Overall, a novel strategy for improving nanozyme-based tumor therapy has been proposed, underlying the integration of ML, experiments, and biological applications.

MPCD: A Multitask Graph Transformer for Molecular Property Prediction by Integrating Common and Domain Knowledge

Molecular property prediction with deep learning often employs self-supervised learning techniques to learn common knowledge through masked atom prediction. However, the common knowledge gained by masked atom prediction dramatically differs from the graph-level optimization objective of downstream tasks, which results in suboptimal problems. Particularly for properties with limited data, the failure to consider domain knowledge results in a direct search in an immense common space, rendering it infeasible to identify the global optimum. To address this, we propose MPCD, which enhances pretraining transferability by aligning the optimization objectives between pretraining and fine-tuning with domain knowledge. MPCD also leverages multitask learning to improve data utilization and model robustness. Technically, MPCD employs a relation-aware self-attention mechanism to capture molecules' local and global structures comprehensively. Extensive validation demonstrates that MPCD outperforms state-of-the-art methods for absorption, distribution, metabolism, excretion, and toxicity (ADMET) and physicochemical prediction across various data sizes.

Time-Series Representation Feature Refinement with a Learnable Masking Augmentation Framework in Contrastive Learning

In this study, we propose a novel framework for time-series representation learning that integrates a learnable masking-augmentation strategy into a contrastive learning framework. Time-series data pose challenges due to their temporal dependencies and feature-extraction complexities. To address these challenges, we introduce a masking-based reconstruction approach within a contrastive learning context, aiming to enhance the model's ability to learn discriminative temporal features. Our method leverages self-supervised learning to effectively capture both global and local patterns by strategically masking segments of the time-series data and reconstructing them, which aids in revealing nuanced temporal dependencies. We utilize learnable masking as a dynamic augmentation technique, which enables the model to optimize contextual relationships in the data and extract meaningful representations that are both context-aware and robust. Extensive experiments were conducted on multiple time-series datasets, including SleepEDF-78, 20, UCI-HAR, achieving improvements of 2%, 2.55%, and 3.89% each and similar performance on Epilepsy in accuracy over baseline methods. Our results show significant performance gains compared to existing methods, highlighting the potential of our framework to advance the field of time-series analysis by improving the quality of learned representations and enhancing downstream task performance.

Three-Dimensional Bone-Image Synthesis with Generative Adversarial Networks

Medical image processing has been highlighted as an area where deep-learning-based models have the greatest potential. However, in the medical field, in particular, problems of data availability and privacy are hampering research progress and, thus, rapid implementation in clinical routine. The generation of synthetic data not only ensures privacy but also allows the drawing of new patients with specific characteristics, enabling the development of data-driven models on a much larger scale. This work demonstrates that three-dimensional generative adversarial networks (GANs) can be efficiently trained to generate high-resolution medical volumes with finely detailed voxel-based architectures. In addition, GAN inversion is successfully implemented for the three-dimensional setting and used for extensive research on model interpretability and applications such as image morphing, attribute editing, and style mixing. The results are comprehensively validated on a database of three-dimensional HR-pQCT instances representing the bone micro-architecture of the distal radius.

High-throughput platform for label-free sorting of 3D spheroids using deep learning

End-stage liver diseases have an increasing impact worldwide, exacerbated by the shortage of transplantable organs. Recognized as one of the promising solutions, tissue engineering aims at recreating functional tissues and organs in vitro. The integration of bioprinting technologies with biological 3D models, such as multi-cellular spheroids, has enabled the fabrication of tissue constructs that better mimic complex structures and in vivo functionality of organs. However, the lack of methods for large-scale production of homogeneous spheroids has hindered the upscaling of tissue fabrication. In this work, we introduce a fully automated platform, designed for high-throughput sorting of 3D spheroids based on label-free analysis of brightfield images. The compact platform is compatible with standard biosafety cabinets and includes a custom-made microscope and two fluidic systems that optimize single spheroid handling to enhance sorting speed. We use machine learning to classify spheroids based on their bioprinting compatibility. This approach enables complex morphological analysis, including assessing spheroid viability, without relying on invasive fluorescent labels. Furthermore, we demonstrate the efficacy of transfer learning for biological applications, for which acquiring large datasets remains challenging. Utilizing this platform, we efficiently sort mono-cellular and multi-cellular liver spheroids, the latter being used in bioprinting applications, and confirm that the sorting process preserves viability and functionality of the spheroids. By ensuring spheroid homogeneity, our sorting platform paves the way for standardized and scalable tissue fabrication, advancing regenerative medicine applications.

Systematic data analysis pipeline for quantitative morphological cell phenotyping

Quantitative morphological phenotyping (QMP) is an image-based method used to capture morphological features at both the cellular and population level. Its interdisciplinary nature, spanning from data collection to result analysis and interpretation, can lead to uncertainties, particularly among those new to this actively growing field. High analytical specificity for a typical QMP is achieved through sophisticated approaches that can leverage subtle cellular morphological changes. Here, we outline a systematic workflow to refine the QMP methodology. For a practical review, we describe the main steps of a typical QMP; in each step, we discuss the available methods, their applications, advantages, and disadvantages, along with the R functions and packages for easy implementation. This review does not cover theoretical backgrounds, but provides several references for interested researchers. It aims to broaden the horizons for future phenome studies and demonstrate how to exploit years of endeavors to achieve more with less.

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.

Multi-omics PGT: re-evaluation of euploid blastocysts for implantation potential based on RNA sequencing

STUDY QUESTION

In addition to chromosomal euploidy, can the transcriptome of blastocysts be used as a novel predictor of embryo implantation potential?

SUMMARY ANSWER

This retrospective analysis showed that based on differentially expressed genes (DEGs) between euploid blastocysts which resulted and did not result in a clinical pregnancy, machine learning models could help improve implantation rates by blastocyst optimization.

WHAT IS KNOWN ALREADY

Embryo implantation is a multifaceted process, with implantation loss and pregnancy failure related not only to blastocyst euploidy but also to the intricate dialog between blastocyst and endometrium. Although in vitro studies have revealed the characteristics of trophectoderm (TE) differentiation in implanted blastocysts and the function of TE placentation at the implantation site, the precise molecular mechanisms of embryo implantation and their clinical application remain to be fully elucidated.

STUDY DESIGN, SIZE, DURATION

This study involved 102 patients who underwent 111 cycles for preimplantation genetic testing for aneuploidies (PGT-A) between March 2022 and July 2023.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The study included 412 blastocysts biopsied at Day 5 [D5] or Day 6 [D6] for patients who underwent PGT-A. The biopsy lysates were split and subjected to DNA and RNA sequencing (DNA- and RNA-seq). One part was used for PGT-A to detect DNA copy number variations, whereas the other part was assessed simultaneously by RNA-seq to determine the transcriptome characteristics. To validate the reliability and accuracy of RNA-seq obtained from this strategy, we initially analyzed the transcriptome of blastocysts with chromosomal aneuploidies. Subsequently, we compared the transcriptomic features of blastocysts with different rates of formation (D5 vs D6) and investigated the network of interactions between key blastulation genes and the receptive endometrium. Then to evaluate the implantation potential of euploid blastocysts, we identified DEGs between euploid blastocysts that resulted in clinical pregnancy (defined as the presence of a gestational sac detected by ultrasound after 5 weeks) and those that did not. These DEGs were then employed to construct a predictive model for optimizing blastocyst selection.

MAIN RESULTS AND THE ROLE OF CHANCE

The successful detection rate of PGT-A was remarkably high at 99.8%. The RNA data may infer aneuploidy for both trisomy and monosomy. Between the euploid blastocysts that formed on D5 and D6, 187 DEGs were predominantly involved in cell differentiation for embryonic placenta development, the PPAR signaling pathway, and the Notch signaling pathway. These D5/D6 DEGs also exhibited a functional dialog with the receptive phase endometrium-specific genes through protein-protein interaction networks, indicating that the embryo undergoes further differentiation for post-implantation development. Furthermore, a modeling strategy using 280 DEGs between blastocysts leading to successful clinical pregnancies or failing to produce clinical pregnancies was implemented to refine the euploid embryo optimization, achieving areas under the curves of 0.88, 0.71, and 0.84 for the random forest (RF), support vector machine, and linear discriminant analysis models, respectively. Finally, a retrospective analysis of 83 transferred euploid blastocysts using the RF model identified three types of euploid embryos with a decreasing trend in implantation potential. Notably, the implantation rate of the good group was significantly higher than that of the moderate group (88.6% vs 50.0% P = 0.001) and that of the moderate group was higher than that of the poor group (50.0% vs 20.8%, P = 0.035).

LIMITATIONS, REASONS FOR CAUTION

The sample size was insufficient; thus, a prospective study is needed to verify the clinical effectiveness of the above model. Because we did not analyze blastocysts that led only to biochemical pregnancies but failed clinical pregnancies separately, our classification system still must be modified to screen these embryos.

WIDER IMPLICATIONS OF THE FINDINGS

Transcriptomic analysis of blastocysts offers a novel approach for predicting embryo implantation potential, which can be utilized to optimize clinical embryo selection. The ranking system may be effective in reducing the times and costs involved in achieving a clinical pregnancy.

STUDY FUNDING/COMPETING INTEREST(S)

This study was funded by the "Pioneer" and "Leading Goose" R&D Program of Zhejiang (No. 2023C03034), the National Natural Science Foundation of China (82101709), and the National Key Research and Development Program for Young Scientists of China (No. 2022YFC2702300). The authors state no competing interests.

TRIAL REGISTRATION NUMBER

N/A.

Cancer molecular subtyping using limited multi-omics data with missingness

Diagnosing cancer subtypes is a prerequisite for precise treatment. Existing multi-omics data fusion-based diagnostic solutions build on the requisite of sufficient samples with complete multi-omics data, which is challenging to obtain in clinical applications. To address the bottleneck of collecting sufficient samples with complete data in clinical applications, we proposed a flexible integrative model (CancerSD) to diagnose cancer subtype using limited samples with incomplete multi-omics data. CancerSD designs contrastive learning tasks and masking-and-reconstruction tasks to reliably impute missing omics, and fuses available omics data with the imputed ones to accurately diagnose cancer subtypes. To address the issue of limited clinical samples, it introduces a category-level contrastive loss to extend the meta-learning framework, effectively transferring knowledge from external datasets to pretrain the diagnostic model. Experiments on benchmark datasets show that CancerSD not only gives accurate diagnosis, but also maintains a high authenticity and good interpretability. In addition, CancerSD identifies important molecular characteristics associated with cancer subtypes, and it defines the Integrated CancerSD Score that can serve as an independent predictive factor for patient prognosis.

Harnessing Bioluminescence: A Comprehensive Review of In Vivo Imaging for Disease Monitoring and Therapeutic Intervention

The technique of using naturally occurring light-emitting reactants (photoproteins and luciferases] that have been extracted from a wide range of animals is known as bioluminescence imaging, or BLI. This imaging offers important details on the location and functional state of regenerative cells inserted into various disease-modeling animals. Reports on gene expression patterns, cell motions, and even the actions of individual biomolecules in whole tissues and live animals have all been made possible by bioluminescence. Generally speaking, bioluminescent light in animals may be found down to a few centimetres, while the precise limit depends on the signal's brightness and the detector's sensitivity. We can now spatiotemporally visualize cell behaviors in any body region of a living animal in a time frame process, including proliferation, apoptosis, migration, and immunological responses, thanks to BLI. The biological applications of in vivo BLI in nondestructively monitoring biological processes in intact small animal models are reviewed in this work, along with some of the advancements that will make BLI a more versatile molecular imaging tool.

Artificial Intelligence-Driven Precision Medicine: Multi-Omics and Spatial Multi-Omics Approaches in Diffuse Large B-Cell Lymphoma (DLBCL)

In this comprehensive review, we delve into the transformative role of artificial intelligence (AI) in refining the application of multi-omics and spatial multi-omics within the realm of diffuse large B-cell lymphoma (DLBCL) research. We scrutinized the current landscape of multi-omics and spatial multi-omics technologies, accentuating their combined potential with AI to provide unparalleled insights into the molecular intricacies and spatial heterogeneity inherent to DLBCL. Despite current progress, we acknowledge the hurdles that impede the full utilization of these technologies, such as the integration and sophisticated analysis of complex datasets, the necessity for standardized protocols, the reproducibility of findings, and the interpretation of their biological significance. We proceeded to pinpoint crucial research voids and advocated for a trajectory that incorporates the development of advanced AI-driven data integration and analytical frameworks. The evolution of these technologies is crucial for enhancing resolution and depth in multi-omics studies. We also emphasized the importance of amassing extensive, meticulously annotated multi-omics datasets and fostering translational research efforts to connect laboratory discoveries with clinical applications seamlessly. Our review concluded that the synergistic integration of multi-omics, spatial multi-omics, and AI holds immense promise for propelling precision medicine forward in DLBCL. By surmounting the present challenges and steering towards the outlined futuristic pathways, we can harness these potent investigative tools to decipher the molecular and spatial conundrums of DLBCL. This will pave the way for refined diagnostic precision, nuanced risk stratification, and individualized therapeutic regimens, ushering in a new era of patient-centric oncology care.

Artificial Neural Networks: A New Frontier in Dental Tissue Regeneration

In the realm of dental tissue regeneration research, various constraints exist such as the potential variance in cell quality, potency arising from differences in donor tissue and tissue microenvironment, the difficulties associated with sustaining long-term and large-scale cell expansion while preserving stemness and therapeutic attributes, as well as the need for extensive investigation into the enduring safety and effectiveness in clinical settings. The adoption of artificial intelligence (AI) technologies has been suggested as a means to tackle these challenges. This is because, tissue regeneration research could be advanced through the use of diagnostic systems that incorporate mining methods such as neural networks (NN), fuzzy, predictive modeling, genetic algorithms, machine learning (ML), cluster analysis, and decision trees. This article seeks to offer foundational insights into a subset of AI referred to as artificial neural networks (ANNs) and assess their potential applications as essential decision-making support tools in the field of dentistry, with a particular focus on tissue engineering research. Although ANNs may initially appear complex and resource intensive, they have proven to be effective in laboratory and therapeutic settings. This expert system can be trained using clinical data alone, enabling their deployment in situations where rule-based decision-making is impractical. As ANNs progress further, it is likely to play a significant role in revolutionizing dental tissue regeneration research, providing promising results in streamlining dental procedures and improving patient outcomes in the clinical setting.

Classification and detection of dental images using meta-learning

Meta-learning of dental X-rays is a machine learning technique that can be used to train models to perform new tasks quickly and with minimal input. Instead of just memorizing a task, this is accomplished through teaching a model how to learn. Algorithms for meta-learning are typically trained on a collection of training problems, each of which has a limited number of labelled instances. Multiple X-ray classification tasks, including the detection of pneumonia, coronavirus disease 2019, and other disorders, have demonstrated the effectiveness of meta-learning. Meta-learning has the benefit of allowing models to be trained on dental X-ray datasets that are too few for more conventional machine learning methods. Due to the high cost and lengthy collection process associated with dental imaging datasets, this is significant for dental X-ray classification jobs. The ability to train models that are more resistant to fresh input is another benefit of meta-learning.

An explainable longitudinal multi-modal fusion model for predicting neoadjuvant therapy response in women with breast cancer

Multi-modal image analysis using deep learning (DL) lays the foundation for neoadjuvant treatment (NAT) response monitoring. However, existing methods prioritize extracting multi-modal features to enhance predictive performance, with limited consideration on real-world clinical applicability, particularly in longitudinal NAT scenarios with multi-modal data. Here, we propose the Multi-modal Response Prediction (MRP) system, designed to mimic real-world physician assessments of NAT responses in breast cancer. To enhance feasibility, MRP integrates cross-modal knowledge mining and temporal information embedding strategy to handle missing modalities and remain less affected by different NAT settings. We validated MRP through multi-center studies and multinational reader studies. MRP exhibited comparable robustness to breast radiologists, outperforming humans in predicting pathological complete response in the Pre-NAT phase (ΔAUROC 14% and 10% on in-house and external datasets, respectively). Furthermore, we assessed MRP's clinical utility impact on treatment decision-making. MRP may have profound implications for enrolment into NAT trials and determining surgery extensiveness.

Compare three deep learning-based artificial intelligence models for classification of calcified lumbar disc herniation: a multicenter diagnostic study

Objective

To develop and validate an artificial intelligence diagnostic model for identifying calcified lumbar disc herniation based on lateral lumbar magnetic resonance imaging(MRI).

Methods

During the period from January 2019 to March 2024, patients meeting the inclusion criteria were collected. All patients had undergone both lumbar spine MRI and computed tomography(CT) examinations, with regions of interest (ROI) clearly marked on the lumbar sagittal MRI images. The participants were then divided into separate sets for training, testing, and external validation. Ultimately, we developed a deep learning model using the ResNet-34 algorithm model and evaluated its diagnostic efficacy.

Results

A total of 1,224 eligible patients were included in this study, consisting of 610 males and 614 females, with an average age of 53.34 ± 10.61 years. Notably, the test datasets displayed an impressive classification accuracy rate of 91.67%, whereas the external validation datasets achieved a classification accuracy rate of 88.76%. Among the test datasets, the ResNet34 model outperformed other models, yielding the highest area under the curve (AUC) of 0.96 (95% CI: 0.93, 0.99). Additionally, the ResNet34 model also exhibited superior performance in the external validation datasets, exhibiting an AUC of 0.88 (95% CI: 0.80, 0.93).

Conclusion

In this study, we established a deep learning model with excellent performance in identifying calcified intervertebral discs, thereby offering a valuable and efficient diagnostic tool for clinical surgeons.

The Co-Piloting Model for Using Artificial Intelligence Systems in Medicine: Implementing the Constrained-Disorder-Principle-Based Second-Generation System

The development of artificial intelligence (AI) and machine learning (ML)-based systems in medicine is growing, and these systems are being used for disease diagnosis, drug development, and treatment personalization. Some of these systems are designed to perform activities that demand human cognitive function. However, use of these systems in routine care by patients and caregivers lags behind expectations. This paper reviews several challenges that healthcare systems face and the obstacles of integrating digital systems into routine care. This paper focuses on integrating digital systems with human physicians. It describes second-generation AI systems designed to move closer to biology and reduce complexity, augmenting but not replacing physicians to improve patient outcomes. The constrained disorder principle (CDP) defines complex biological systems by their degree of regulated variability. This paper describes the CDP-based second-generation AI platform, which is the basis for the Digital Pill that is humanizing AI by moving closer to human biology via using the inherent variability of biological systems for improving outcomes. This system augments physicians, assisting them in decision-making to improve patients' responses and adherence but not replacing healthcare providers. It restores the efficacy of chronic drugs and improves adherence while generating data-driven therapeutic regimens. While AI can substitute for many medical activities, it is unlikely to replace human physicians. Human doctors will continue serving patients with capabilities augmented by AI. The described co-piloting model better reflects biological pathways and provides assistance to physicians for better care.

Exploring the Trade-Off between generalist and specialized Models: A center-based comparative analysis for glioblastoma segmentation

INTRODUCTION

Inherent variations between inter-center data can undermine the robustness of segmentation models when applied at a specific center (dataset shift). We investigated whether specialized center-specific models are more effective compared to generalist models based on multi-center data, and how center-specific data could enhance the performance of generalist models within a particular center using a fine-tuning transfer learning approach. For this purpose, we studied the dataset shift at center level and conducted a comparative analysis to assess the impact of data source on glioblastoma segmentation models.

METHODS & MATERIALS

The three key components of dataset shift were studied: prior probability shift-variations in tumor size or tissue distribution among centers; covariate shift-inter-center MRI alterations; and concept shift-different criteria for tumor segmentation. BraTS 2021 dataset was used, which includes 1251 cases from 23 centers. Thereafter, 155 deep-learning models were developed and compared, including 1) generalist models trained with multi-center data, 2) specialized models using only center-specific data, and 3) fine-tuned generalist models using center-specific data.

RESULTS

The three key components of dataset shift were characterized. The amount of covariate shift was substantial, indicating large variations in MR imaging between different centers. Glioblastoma segmentation models tend to perform best when using data from the application center. Generalist models, trained with over 700 samples, achieved a median Dice score of 88.98%. Specialized models surpassed this with 200 cases, while fine-tuned models outperformed with 50 cases.

CONCLUSIONS

The influence of dataset shift on model performance is evident. Fine-tuned and specialized models, utilizing data from the evaluated center, outperform generalist models, which rely on data from other centers. These approaches could encourage medical centers to develop customized models for their local use, enhancing the accuracy and reliability of glioblastoma segmentation in a context where dataset shift is inevitable.

Data-driven toxicity prediction in drug discovery: Current status and future directions

Early toxicity assessment plays a vital role in the drug discovery process on account of its significant influence on the attrition rate of candidates. Recently, constant upgrading of information technology has greatly promoted the continuous development of toxicity prediction. To give an overview of the current state of data-driven toxicity prediction, we reviewed relevant studies and summarized them in three main respects: the features and difficulties of toxicity prediction, the evolution of modeling approaches, and the available tools for toxicity prediction. For each part, we expound the research status, existing challenges, and feasible solutions. Finally, several new directions and suggestions for toxicity prediction are also put forward.

A deep learning approach to prediction of blood group antigens from genomic data

BACKGROUND

Deep learning methods are revolutionizing natural science. In this study, we aim to apply such techniques to develop blood type prediction models based on cheap to analyze and easily scalable screening array genotyping platforms.

METHODS

Combining existing blood types from blood banks and imputed screening array genotypes for ~111,000 Danish and 1168 Finnish blood donors, we used deep learning techniques to train and validate blood type prediction models for 36 antigens in 15 blood group systems. To account for missing genotypes a denoising autoencoder initial step was utilized, followed by a convolutional neural network blood type classifier.

RESULTS

Two thirds of the trained blood type prediction models demonstrated an F1-accuracy above 99%. Models for antigens with low or high frequencies like, for example, Cw, low training cohorts like, for example, Cob, or very complicated genetic underpinning like, for example, RhD, proved to be more challenging for high accuracy (>99%) DL modeling. However, in the Danish cohort only 4 out of 36 models (Cob, Cw, D-weak, Kpa) failed to achieve a prediction F1-accuracy above 97%. This high predictive performance was replicated in the Finnish cohort.

DISCUSSION

High accuracy in a variety of blood groups proves viability of deep learning-based blood type prediction using array chip genotypes, even in blood groups with nontrivial genetic underpinnings. These techniques are suitable for aiding in identifying blood donors with rare blood types by greatly narrowing down the potential pool of candidate donors before clinical grade confirmation.

Ethical Challenges of Artificial Intelligence in Medicine

Artificial intelligence (AI) and machine learning (ML) have become critical components in the transformation of healthcare. They offer enhanced diagnostic accuracy, personalized treatment plans, and support for clinical decision-making. However, with these advancements come significant ethical challenges, including concerns around transparency, bias, data privacy, and the potential displacement of healthcare professionals. This review delves into these ethical concerns, issues of transparency, data privacy, bias, and the moral responsibility of decision-making with a particular focus on the role of AI in new drug/genetic treatment discovery, exploring how AI models are employed in protein, RNA, and DNA structural prediction to accelerate drug development. Addressing these challenges is crucial for ensuring that AI is used responsibly, benefiting patients while maintaining trust in the healthcare system.

Multimodal Approaches Based on Microbial Data for Accurate Postmortem Interval Estimation

Accurate postmortem interval (PMI) estimation is critical for forensic investigations, aiding case classification and providing vital trial evidence. Early postmortem signs, such as body temperature and rigor mortis, are reliable for estimating PMI shortly after death. However, these indicators become less useful as decomposition progresses, making late-stage PMI estimation a significant challenge. Decomposition involves predictable microbial activity, which may serve as an objective criterion for PMI estimation. During decomposition, anaerobic microbes metabolize body tissues, producing gases and organic acids, leading to significant changes in skin and soil microbial communities. These shifts, especially the transition from anaerobic to aerobic microbiomes, can objectively segment decomposition into pre- and post-rupture stages according to rupture point. Microbial communities change markedly after death, with anaerobic bacteria dominating early stages and aerobic bacteria prevalent post-rupture. Different organs exhibit distinct microbial successions, providing valuable PMI insights. Alongside microbial changes, metabolic and volatile organic compound (VOC) profiles also shift, reflecting the body's biochemical environment. Due to insufficient information, unimodal models could not comprehensively reflect the PMI, so a muti-modal model should be used to estimate the PMI. Machine learning (ML) offers promising methods for integrating these multimodal data sources, enabling more accurate PMI predictions. Despite challenges such as data quality and ethical considerations, developing human-specific multimodal databases and exploring microbial-insect interactions can significantly enhance PMI estimation accuracy, advancing forensic science.

In silico prediction of drug-induced nephrotoxicity: current progress and pitfalls

INTRODUCTION

Due to its role in absorption and metabolism, the kidney is an important target for drug toxicity. Drug-induced nephrotoxicity (DIN) presents a significant challenge in clinical practice and drug development. Conventional methods for assessing nephrotoxicity have limitations, highlighting the need for innovative approaches. In recent years, in silico methods have emerged as promising tools for predicting DIN.

AREAS COVERED

A literature search was performed using PubMed and Web of Science, from 2013 to February 2023 for this review. This review provides an overview of the current progress and pitfalls in the in silico prediction of DIN, which discusses the principles and methodologies of computational models.

EXPERT OPINION

Despite significant advancements, this review identified issues accentuates the pivotal imperatives of data fidelity, model optimization, interdisciplinary collaboration, and mechanistic comprehension in sculpting the vista of DIN prediction. Integration of multiple data sources and collaboration between disciplines are essential for improving predictive models. Ultimately, a holistic approach combining computational, experimental, and clinical methods will enhance our understanding and management of DIN.

Application of machine learning based genome sequence analysis in pathogen identification

Infectious diseases caused by pathogenic microorganisms pose a serious threat to human health. Despite advances in molecular biology, genetics, computation, and medicinal chemistry, infectious diseases remain a significant public health concern. Addressing the challenges posed by pathogen outbreaks, pandemics, and antimicrobial resistance requires concerted interdisciplinary efforts. With the development of computer technology and the continuous exploration of artificial intelligence(AI)applications in the biomedical field, the automatic morphological recognition and image processing of microbial images under microscopes have advanced rapidly. The research team of Institute of Microbiology, Chinese Academy of Sciences has developed a single cell microbial identification technology combining Raman spectroscopy and artificial intelligence. Through laser Raman acquisition system and convolutional neural network analysis, the average accuracy rate of 95.64% has been achieved, and the identification can be completed in only 5 min. These technologies have shown substantial advantages in the visible morphological detection of pathogenic microorganisms, expanding anti-infective drug discovery, enhancing our understanding of infection biology, and accelerating the development of diagnostics. In this review, we discuss the application of AI-based machine learning in image analysis, genome sequencing data analysis, and natural language processing (NLP) for pathogen identification, highlighting the significant role of artificial intelligence in pathogen diagnosis. AI can improve the accuracy and efficiency of diagnosis, promote early detection and personalized treatment, and enhance public health safety.

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 (CCl 4 )-induced CLD models.

MATERIALS AND METHODS

Mice were either untreated, fed an HFD for 24 weeks, or injected with CCl 4 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 CCl 4 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.

Deep reinforcement learning control of combined chemotherapy and anti-angiogenic drug delivery for cancerous tumor treatment

By virtue of the chronic and dangerous nature of cancer, researchers have explored various approaches to managing the abnormal cell growth associated with this disease using novel treatment methods. This study introduces a control system based on normalized advantage function reinforcement learning. It aims to boost the body's immune response against cancer cell proliferation. This control approach is applied to provide a combination of both chemotherapy and anti-angiogenic drugs for the first time without the need for complex, predefined mathematical models. It employs a model-free reinforcement learning technique that adaptively adjusts to individual patients to determine optimal drug administration with minimum injection rates. In this regard, a comprehensive and realistic simulation and training environment is employed, with the concentrations of normal cells, cancer cells, and endothelial cells, as well as the levels of chemotherapy and anti-angiogenic agents, as state variables. Furthermore, high levels of disturbances are considered in the simulation to investigate the robustness of the proposed method against probable uncertainties in the treatment process or patient parameters. A practical reward function has also been devised in alignment with medical objectives to ensure effective and safe treatment outcomes. The results demonstrate robustness and superior performance compared to the existing methods. Simulations show that the proposed approach is a dependable strategy for effectively reducing the concentration of cancer cells in the shortest duration using minimal doses of chemotherapy and anti-angiogenic drugs.

Reproducibility and explainability in digital pathology: The need to make black-box artificial intelligence systems more transparent

Artificial intelligence (AI), and more specifically Machine Learning (ML) and Deep learning (DL), has permeated the digital pathology field in recent years, with many algorithms successfully applied as new advanced tools to analyze pathological tissues. The introduction of high-resolution scanners in histopathology services has represented a real revolution for pathologists, allowing the analysis of digital whole-slide images (WSI) on a screen without a microscope at hand. However, it means a transition from microscope to algorithms in the absence of specific training for most pathologists involved in clinical practice. The WSI approach represents a major transformation, even from a computational point of view. The multiple ML and DL tools specifically developed for WSI analysis may enhance the diagnostic process in many fields of human pathology. AI-driven models allow the achievement of more consistent results, providing valid support for detecting, from H&E-stained sections, multiple biomarkers, including microsatellite instability, that are missed by expert pathologists.

Exploring the Artificial Intelligence and Its Impact in Pharmaceutical Sciences: Insights Toward the Horizons Where Technology Meets Tradition

The technological revolutions in computers and the advancement of high-throughput screening technologies have driven the application of artificial intelligence (AI) for faster discovery of drug molecules with more efficiency, and cost-friendly finding of hit or lead molecules. The ability of software and network frameworks to interpret molecular structures' representations and establish relationships/correlations has enabled various research teams to develop numerous AI platforms for identifying new lead molecules or discovering new targets for already established drug molecules. The prediction of biological activity, ADME properties, and toxicity parameters in early stages have reduced the chances of failure and associated costs in later clinical stages, which was observed at a high rate in the tedious, expensive, and laborious drug discovery process. This review focuses on the different AI and machine learning (ML) techniques with their applications mainly focused on the pharmaceutical industry. The applications of AI frameworks in the identification of molecular target, hit identification/hit-to-lead optimization, analyzing drug-receptor interactions, drug repurposing, polypharmacology, synthetic accessibility, clinical trial design, and pharmaceutical developments are discussed in detail. We have also compiled the details of various startups in AI in this field. This review will provide a comprehensive analysis and outline various state-of-the-art AI/ML techniques to the readers with their framework applications. This review also highlights the challenges in this field, which need to be addressed for further success in pharmaceutical applications.

Structural and biochemical insights of xylose MFS and SWEET transporters in microbial cell factories: challenges to lignocellulosic hydrolysates fermentation

The production of bioethanol from lignocellulosic biomass requires the efficient conversion of glucose and xylose to ethanol, a process that depends on the ability of microorganisms to internalize these sugars. Although glucose transporters exist in several species, xylose transporters are less common. Several types of transporters have been identified in diverse microorganisms, including members of the Major Facilitator Superfamily (MFS) and Sugars Will Eventually be Exported Transporter (SWEET) families. Considering that Saccharomyces cerevisiae lacks an effective xylose transport system, engineered yeast strains capable of efficiently consuming this sugar are critical for obtaining high ethanol yields. This article reviews the structure-function relationship of sugar transporters from the MFS and SWEET families. It provides information on several tools and approaches used to identify and characterize them to optimize xylose consumption and, consequently, second-generation ethanol production.

An interpretable deep learning framework identifies proteomic drivers of Alzheimer's disease

Alzheimer's disease (AD) is the leading neurodegenerative pathology in aged individuals, but many questions remain on its pathogenesis, and a cure is still not available. Recent research efforts have generated measurements of multiple omics in individuals that were healthy or diagnosed with AD. Although machine learning approaches are well-suited to handle the complexity of omics data, the models typically lack interpretability. Additionally, while the genetic landscape of AD is somewhat more established, the proteomic landscape of the diseased brain is less well-understood. Here, we establish a deep learning method that takes advantage of an ensemble of autoencoders (AEs) - EnsembleOmicsAE-to reduce the complexity of proteomics data into a reduced space containing a small number of latent features. We combine brain proteomic data from 559 individuals across three AD cohorts and demonstrate that the ensemble autoencoder models generate stable latent features which are well-suited for downstream biological interpretation. We present an algorithm to calculate feature importance scores based on the iterative scrambling of individual input features (i.e., proteins) and show that the algorithm identifies signaling modules (AE signaling modules) that are significantly enriched in protein-protein interactions. The molecular drivers of AD identified within the AE signaling modules derived with EnsembleOmicsAE were missed by linear methods, including integrin signaling and cell adhesion. Finally, we characterize the relationship between the AE signaling modules and the age of death of the patients and identify a differential regulation of vimentin and MAPK signaling in younger compared with older AD patients.

An artificial intelligence-based model exploiting H&E images to predict recurrence in negative sentinel lymph-node melanoma patients

BACKGROUND

Risk stratification and treatment benefit prediction models are urgent to improve negative sentinel lymph node (SLN-) melanoma patient selection, thus avoiding costly and toxic treatments in patients at low risk of recurrence. To this end, the application of artificial intelligence (AI) could help clinicians to better calculate the recurrence risk and choose whether to perform adjuvant therapy.

METHODS

We made use of AI to predict recurrence-free status (RFS) within 2-years from diagnosis in 94 SLN- melanoma patients. In detail, we detected quantitative imaging information from H&E slides of a cohort of 71 SLN- melanoma patients, who registered at Istituto Tumori "Giovanni Paolo II" in Bari, Italy (investigational cohort, IC). For each slide, two expert pathologists firstly annotated two Regions of Interest (ROIs) containing tumor cells alone (TUMOR ROI) or with infiltrating cells (TUMOR + INF ROI). In correspondence of the two kinds of ROIs, two AI-based models were developed to extract information directly from the tiles in which each ROI was automatically divided. This information was then used to predict RFS. Performances of the models were computed according to a 5-fold cross validation scheme. We further validated the prediction power of the two models on an independent external validation cohort of 23 SLN- melanoma patients (validation cohort, VC).

RESULTS

The TUMOR ROIs have revealed more informative than the TUMOR + INF ROIs. An Area Under the Curve (AUC) value of 79.1% and 62.3%, a sensitivity value of 81.2% and 76.9%, a specificity value of 70.0% and 43.3%, an accuracy value of 73.2% and 53.4%, were achieved on the TUMOR and TUMOR + INF ROIs extracted for the IC cohort, respectively. An AUC value of 76.5% and 65.2%, a sensitivity value of 66.7% and 41.6%, a specificity value of 70.0% and 55.9%, an accuracy value of 70.0% and 56.5%, were achieved on the TUMOR and TUMOR + INF ROIs extracted for the VC cohort, respectively.

CONCLUSIONS

Our approach represents a first effort to develop a non-invasive prognostic method to better define the recurrence risk and improve the management of SLN- melanoma patients.

Machine learning reveals the rules governing the efficacy of mesenchymal stromal cells in septic preclinical models

BACKGROUND

Mesenchymal Stromal Cells (MSCs) are the preferred candidates for therapeutics as they possess multi-directional differentiation potential, exhibit potent immunomodulatory activity, are anti-inflammatory, and can function like antimicrobials. These capabilities have therefore encouraged scientists to undertake numerous preclinical as well as a few clinical trials to access the translational potential of MSCs in disease therapeutics. In spite of these efforts, the efficacy of MSCs has not been consistent-as is reflected in the large variation in the values of outcome measures like survival rates. Survival rate is a resultant of complex cascading interactions that not only depends upon upstream experimental factors like dosage, time of infusion, type of transplant, etc.; but is also dictated, post-infusion, by intrinsic host specific attributes like inflammatory microniche including proinflammatory cytokines and alarmins released by the damaged host cells. These complex interdependencies make a researcher's task of designing MSC transfusion experiments challenging.

METHODS

In order to identify the rules and associated attributes that influence the final outcome (survival rates) of MSC transfusion experiments, we decided to apply machine learning techniques on manually curated data collected from available literature. As sepsis is a multi-faceted condition that involves highly dysregulated immune response, inflammatory environment and microbial invasion, sepsis can be an efficient model to verify the therapeutic effects of MSCs. We therefore decided to implement rule-based classification models on data obtained from studies involving interventions of MSCs in sepsis preclinical models.

RESULTS

The rules from the generated graph models indicated that survival rates, post-MSC-infusion, are influenced by factors like source, dosage, time of infusion, pre-Interleukin-6 (IL-6)/ Tumour Necrosis Factor- alpha (TNF-α levels, etc. CONCLUSION: This approach provides important information for optimization of MSCs based treatment strategies that may help the researchers design their experiments.

Comprehensive detection and characterization of human druggable pockets through binding site descriptors

Druggable pockets are protein regions that have the ability to bind organic small molecules, and their characterization is essential in target-based drug discovery. However, deriving pocket descriptors is challenging and existing strategies are often limited in applicability. We introduce PocketVec, an approach to generate pocket descriptors via inverse virtual screening of lead-like molecules. PocketVec performs comparably to leading methodologies while addressing key limitations. Additionally, we systematically search for druggable pockets in the human proteome, using experimentally determined structures and AlphaFold2 models, identifying over 32,000 binding sites across 20,000 protein domains. We then generate PocketVec descriptors for each site and conduct an extensive similarity search, exploring over 1.2 billion pairwise comparisons. Our results reveal druggable pocket similarities not detected by structure- or sequence-based methods, uncovering clusters of similar pockets in proteins lacking crystallized inhibitors and opening the door to strategies for prioritizing chemical probe development to explore the druggable space.

Evaluating the Alignment of Artificial Intelligence-Generated Recommendations With Clinical Guidelines Focused on Soft Tissue Tumors

BACKGROUND

The integration of artificial intelligence (AI), particularly, in oncology, has significantly shifted the paradigms of medical diagnostics and treatment planning. However, the utility of AI, specifically OpenAI's ChatGPT, in soft tissue sarcoma treatment, remains unclear.

METHODS

We evaluated ChatGPT's alignment with the Japanese Orthopaedic Association (JOA) clinical practice guidelines on the management of soft tissue tumors 2020. Twenty-two clinical questions (CQs) were formulated to encompass various aspects of sarcoma diagnosis, treatment, and management. ChatGPT's responses were classified into "Complete Alignment," "Partial Alignment," or "Nonalignment" based on the recommendation and strength of evidence.

RESULTS

ChatGPT demonstrated an 86% alignment rate with the JOA guidelines. The AI provided two instances of complete alignment and 17 instances of partial alignment, indicating a strong capability to match guideline criteria for most questions. However, three discrepancies were identified in areas concerning the treatment of atypical lipomatous tumors, perioperative chemotherapy for synovial sarcoma, and treatment strategies for elderly patients with malignant soft tissue tumors. Reassessment with guideline input led to some adjustments, revealing both the potential and limitations of AI in complex sarcoma care.

CONCLUSION

Our study demonstrates that AI, specifically ChatGPT, can align with clinical guidelines for soft tissue sarcoma treatment. It also underscores the need for continuous refinement and cautious integration of AI in medical decision-making, particularly in the context of treatment for soft tissue sarcoma.

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.

Prediction of inhibitor development in previously untreated and minimally treated children with severe and moderately severe hemophilia A using a machine-learning network

BACKGROUND

Prediction of inhibitor development in patients with hemophilia A (HA) remains a challenge.

OBJECTIVES

To construct a predictive model for inhibitor development in HA using a network of clinical variables and biomarkers based on the individual similarity network.

METHODS

Previously untreated and minimally treated children with severe/moderately severe HA, participants of the HEMFIL Cohort Study, were followed up until reaching 75 exposure days (EDs) without inhibitor (INH-) or upon inhibitor development (INH+). Clinical data and biological samples were collected before the start of factor (F)VIII replacement (T0). A predictive model (HemfilNET) was built to compare the networks and potential global topological differences between INH- and INH+ at T0, considering the network robustness. For validation, the "leave-one-out" cross-validation technique was employed. Accuracy, precision, recall, and F1-score were used as evaluation metrics for the machine-learning model.

RESULTS

We included 95 children with HA (CHA), of whom 31 (33%) developed inhibitors. The algorithm, featuring 37 variables, identified distinct patterns of networks at T0 for INH+ and INH-. The accuracy of the model was 74.2% for CHA INH+ and 98.4% for INH-. By focusing the analysis on CHA with high-risk F8 mutations for inhibitor development, the accuracy in identifying CHA INH+ increased to 82.1%.

CONCLUSION

Our machine-learning algorithm demonstrated an overall accuracy of 90.5% for predicting inhibitor development in CHA, which further improved when restricting the analysis to CHA with a high-risk F8 genotype. However, our model requires validation in other cohorts. Yet, missing data for some variables hindered more precise predictions.

Recent advances in artificial intelligent strategies for tissue engineering and regenerative medicine

BACKGROUND

Tissue engineering and regenerative medicine (TERM) aim to repair or replace damaged or lost tissues or organs due to accidents, diseases, or aging, by applying different sciences. For this purpose, an essential part of TERM is the designing, manufacturing, and evaluating of scaffolds, cells, tissues, and organs. Artificial intelligence (AI) or the intelligence of machines or software can be effective in all areas where computers play a role.

METHODS

The "artificial intelligence," "machine learning," "tissue engineering," "clinical evaluation," and "scaffold" keywords used for searching in various databases and articles published from 2000 to 2024 were evaluated.

RESULTS

The combination of tissue engineering and AI has created a new generation of technological advancement in the biomedical industry. Experience in TERM has been refined using advanced design and manufacturing techniques. Advances in AI, particularly deep learning, offer an opportunity to improve scientific understanding and clinical outcomes in TERM.

CONCLUSION

The findings of this research show the high potential of AI, machine learning, and robots in the selection, design, and fabrication of scaffolds, cells, tissues, or organs, and their analysis, characterization, and evaluation after their implantation. AI can be a tool to accelerate the introduction of tissue engineering products to the bedside.

HIGHLIGHTS

The capabilities of artificial intelligence (AI) can be used in different ways in all the different stages of TERM and not only solve the existing limitations, but also accelerate the processes, increase efficiency and precision, reduce costs, and complications after transplantation. ML predicts which technologies have the most efficient and easiest path to enter the market and clinic. The use of AI along with these imaging techniques can lead to the improvement of diagnostic information, the reduction of operator errors when reading images, and the improvement of image analysis (such as classification, localization, regression, and segmentation).

Current strategies to address data scarcity in artificial intelligence-based drug discovery: A comprehensive review

Artificial intelligence (AI) has played a vital role in computer-aided drug design (CADD). This development has been further accelerated with the increasing use of machine learning (ML), mainly deep learning (DL), and computing hardware and software advancements. As a result, initial doubts about the application of AI in drug discovery have been dispelled, leading to significant benefits in medicinal chemistry. At the same time, it is crucial to recognize that AI is still in its infancy and faces a few limitations that need to be addressed to harness its full potential in drug discovery. Some notable limitations are insufficient, unlabeled, and non-uniform data, the resemblance of some AI-generated molecules with existing molecules, unavailability of inadequate benchmarks, intellectual property rights (IPRs) related hurdles in data sharing, poor understanding of biology, focus on proxy data and ligands, lack of holistic methods to represent input (molecular structures) to prevent pre-processing of input molecules (feature engineering), etc. The major component in AI infrastructure is input data, as most of the successes of AI-driven efforts to improve drug discovery depend on the quality and quantity of data, used to train and test AI algorithms, besides a few other factors. Additionally, data-gulping DL approaches, without sufficient data, may collapse to live up to their promise. Current literature suggests a few methods, to certain extent, effectively handle low data for better output from the AI models in the context of drug discovery. These are transferring learning (TL), active learning (AL), single or one-shot learning (OSL), multi-task learning (MTL), data augmentation (DA), data synthesis (DS), etc. One different method, which enables sharing of proprietary data on a common platform (without compromising data privacy) to train ML model, is federated learning (FL). In this review, we compare and discuss these methods, their recent applications, and limitations while modeling small molecule data to get the improved output of AI methods in drug discovery. Article also sums up some other novel methods to handle inadequate data.