A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease

Automated inflammatory bowel disease detection using wearable bowel sound event spotting

Introduction

Inflammatory bowel disorders may result in abnormal Bowel Sound (BS) characteristics during auscultation. We employ pattern spotting to detect rare bowel BS events in continuous abdominal recordings using a smart T-shirt with embedded miniaturised microphones. Subsequently, we investigate the clinical relevance of BS spotting in a classification task to distinguish patients diagnosed with inflammatory bowel disease (IBD) and healthy controls.

Methods

Abdominal recordings were obtained from 24 patients with IBD with varying disease activity and 21 healthy controls across different digestive phases. In total, approximately 281 h of audio data were inspected by expert raters and thereof 136 h were manually annotated for BS events. A deep-learning-based audio pattern spotting algorithm was trained to retrieve BS events. Subsequently, features were extracted around detected BS events and a Gradient Boosting Classifier was trained to classify patients with IBD vs. healthy controls. We further explored classification window size, feature relevance, and the link between BS-based IBD classification performance and IBD activity.

Results

Stratified group K-fold cross-validation experiments yielded a mean area under the receiver operating characteristic curve ≥0.83 regardless of whether BS were manually annotated or detected by the BS spotting algorithm.

Discussion

Automated BS retrieval and our BS event classification approach have the potential to support diagnosis and treatment of patients with IBD.

Advances in Inflammatory Bowel Disease Diagnostics: Machine Learning and Genomic Profiling Reveal Key Biomarkers for Early Detection

This study, utilizing high-throughput technologies and Machine Learning (ML), has identified gene biomarkers and molecular signatures in Inflammatory Bowel Disease (IBD). We could identify significant upregulated or downregulated genes in IBD patients by comparing gene expression levels in colonic specimens from 172 IBD patients and 22 healthy individuals using the GSE75214 microarray dataset. Our ML techniques and feature selection methods revealed six Differentially Expressed Gene (DEG) biomarkers (VWF, IL1RL1, DENND2B, MMP14, NAAA, and PANK1) with strong diagnostic potential for IBD. The Random Forest (RF) model demonstrated exceptional performance, with accuracy, F1-score, and AUC values exceeding 0.98. Our findings were rigorously validated with independent datasets (GSE36807 and GSE10616), further bolstering their credibility and showing favorable performance metrics (accuracy: 0.841, F1-score: 0.734, AUC: 0.887). Our functional annotation and pathway enrichment analysis provided insights into crucial pathways associated with these dysregulated genes. DENND2B and PANK1 were identified as novel IBD biomarkers, advancing our understanding of the disease. The validation in independent cohorts enhances the reliability of these findings and underscores their potential for early detection and personalized treatment of IBD. Further exploration of these genes is necessary to fully comprehend their roles in IBD pathogenesis and develop improved diagnostic tools and therapies. This study significantly contributes to IBD research with valuable insights, potentially greatly enhancing patient care.

Pathway Activation Analysis for Pan-Cancer Personalized Characterization Based on Riemannian Manifold

The pathogenesis of carcinoma is believed to come from the combined effect of polygenic variation, and the initiation and progression of malignant tumors are closely related to the dysregulation of biological pathways. Quantifying the alteration in pathway activation and identifying coordinated patterns of pathway dysfunction are the imperative part of understanding the malignancy process and distinguishing different tumor stages or clinical outcomes of individual patients. In this study, we have conducted in silico pathway activation analysis using Riemannian manifold (RiePath) toward pan-cancer personalized characterization, which is the first attempt to apply the Riemannian manifold theory to measure the extent of pathway dysregulation in individual patient on the tangent space of the Riemannian manifold. RiePath effectively integrates pathway and gene expression information, not only generating a relatively low-dimensional and biologically relevant representation, but also identifying a robust panel of biologically meaningful pathway signatures as biomarkers. The pan-cancer analysis across 16 cancer types reveals the capability of RiePath to evaluate pathway activation accurately and identify clinical outcome-related pathways. We believe that RiePath has the potential to provide new prospects in understanding the molecular mechanisms of complex diseases and may find broader applications in predicting biomarkers for other intricate diseases.

Understanding gut microbiome-based machine learning platforms: A review on therapeutic approaches using deep learning

Human beings possess trillions of microbial cells in a symbiotic relationship. This relationship benefits both partners for a long time. The gut microbiota helps in many bodily functions from harvesting energy from digested food to strengthening biochemical barriers of the gut and intestine. But the changes in microbiota composition and bacteria that can enter the gastrointestinal tract can cause infection. Several approaches like culture-independent techniques such as high-throughput and meta-omics projects targeting 16S ribosomal RNA (rRNA) sequencing are popular methods to investigate the composition of the human gastrointestinal tract microbiota and taxonomically characterizing microbial communities. The microbiota conformation and diversity should be provided by whole-genome shotgun metagenomic sequencing of site-specific community DNA associating genome mapping, gene inventory, and metabolic remodelling and reformation, to ease the functional study of human microbiota. Preliminary examination of the therapeutic potency for dysbiosis-associated diseases permits investigation of pharmacokinetic-pharmacodynamic changes in microbial communities for escalation of treatment and dosage plan. Gut microbiome study is an integration of metagenomics which has influenced the field in the last two decades. And the incorporation of artificial intelligence and deep learning through "omics-based" methods and microfluidic evaluation enhanced the capability of identification of thousands of microbes.

Development of a 32-gene signature using machine learning for accurate prediction of inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic inflammatory condition caused by multiple genetic and environmental factors. Numerous genes are implicated in the etiology of IBD, but the diagnosis of IBD is challenging. Here, XGBoost, a machine learning prediction model, has been used to distinguish IBD from healthy cases following elaborative feature selection. Using combined unsupervised clustering analysis and the XGBoost feature selection method, we successfully identified a 32-gene signature that can predict IBD occurrence in new cohorts with 0.8651 accuracy. The signature shows enrichment in neutrophil extracellular trap formation and cytokine signaling in the immune system. The probability threshold of the XGBoost-based classification model can be adjusted to fit personalized lifestyle and health status. Therefore, this study reveals potential IBD-related biomarkers that facilitate an effective personalized diagnosis of IBD.

"Technology Proficiency" in Medical Education: Worthiness for Worldwide Wonderful Competency and Sophistication

PURPOSE

Advances in bioinformatics, information technology, advanced computing, imaging techniques are changing fundamentally the way physicians define, diagnose, treat, and prevent disease. New disciplines - Artificial Intelligence, Machine Learning, Computational Biology - are improving healthcare. Digital health solutions have immense scope. Education and practice need to keep pace.

METHODS

We aimed at assessment of "Technology proficiency" required by medical graduates and its implementation, if found useful. All this in a conceptual framework of "TP" model, having categories (a) proper assessment (b) pertinent treatment (c) progress monitoring (d) prevention applications (e) professional standards. A search of the literature was performed using MedLine & Cochrane Central Register of Controlled Trials databases, for systematic reviews and meta-analysis articles published in the last five years using keyword "technology". Analysis of those relevant to the role all medical graduates should play. An analysis of worldwide statutory medical institutions guidelines.

RESULTS

Twenty-three systematic studies and meta-analysis were studied. Eighteen show clear evidence for 'Technology proficiency", while 5 recommend further studies. The findings are discussed suiting the roles of doctors in the "TP" model. Medical institutions guidelines worldwide diligence suggests need of including "Technology proficiency" as a definite and distinct strategic plan. Medical Council of India mandates "use information technology for appropriate patient care and continued learning". General Medical Council, UK and Medical Council India have been proactive in technology training. GMC recommends technology use for learning, prescribing, communication, and interpersonal skills. It should be expanding technology proficiency in practice as an essential professional capability.

CONCLUSION

"Technology proficiency" is found pertinently fruitful. It should be included as a definitive requirement and a distinct strategic plan worldwide. Modern curriculum development is proposed (i) Educational goals and objectives as the proposed Conceptual framework "Technology proficiency" model (ii) Instructional strategies 'Five Bs' (iii) Implementation 'Five Ms'.

A Systematic Review of Artificial Intelligence and Machine Learning Applications to Inflammatory Bowel Disease, with Practical Guidelines for Interpretation

BACKGROUND

Inflammatory bowel disease (IBD) is a gastrointestinal chronic disease with an unpredictable disease course. Computational methods such as machine learning (ML) have the potential to stratify IBD patients for the provision of individualized care. The use of ML methods for IBD was surveyed, with an additional focus on how the field has changed over time.

METHODS

On May 6, 2021, a systematic review was conducted through a search of MEDLINE and Embase databases, with the search structure ("machine learning" OR "artificial intelligence") AND ("Crohn* Disease" OR "Ulcerative Colitis" OR "Inflammatory Bowel Disease"). Exclusion criteria included studies not written in English, no human patient data, publication before 2001, studies that were not peer reviewed, nonautoimmune disease comorbidity research, and record types that were not primary research.

RESULTS

Seventy-eight (of 409) records met the inclusion criteria. Random forest methods were most prevalent, and there was an increase in neural networks, mainly applied to imaging data sets. The main applications of ML to clinical tasks were diagnosis (18 of 78), disease course (22 of 78), and disease severity (16 of 78). The median sample size was 263. Clinical and microbiome-related data sets were most popular. Five percent of studies used an external data set after training and testing for additional model validation.

DISCUSSION

Availability of longitudinal and deep phenotyping data could lead to better modeling. Machine learning pipelines that consider imbalanced data and that feature selection only on training data will generate more generalizable models. Machine learning models are increasingly being applied to more complex clinical tasks for specific phenotypes, indicating progress towards personalized medicine for IBD.

Comparing Bayesian-Based Reconstruction Strategies in Topology-Based Pathway Enrichment Analysis

The development of high-throughput omics technologies has enabled the quantification of vast amounts of genes and gene products in the whole genome. Pathway enrichment analysis (PEA) provides an intuitive solution for extracting biological insights from massive amounts of data. Topology-based pathway analysis (TPA) represents the latest generation of PEA methods, which exploit pathway topology in addition to lists of differentially expressed genes and their expression profiles. A subset of these TPA methods, such as BPA, BNrich, and PROPS, reconstruct pathway structures by training Bayesian networks (BNs) from canonical biological pathways, providing superior representations that explain causal relationships between genes. However, these methods have never been compared for their differences in the PEA and their different topology reconstruction strategies. In this study, we aim to compare the BN reconstruction strategies of the BPA, BNrich, PROPS, Clipper, and Ensemble methods and their PEA and performance on tumor and non-tumor classification based on gene expression data. Our results indicate that they performed equally well in distinguishing tumor and non-tumor samples (AUC > 0.95) yet with a varying ranking of pathways, which can be attributed to the different BN structures resulting from the different cyclic structure removal strategies. This can be clearly seen from the reconstructed JAK-STAT networks by different strategies. In a nutshell, BNrich, which relies on expert intervention to remove loops and cyclic structures, produces BNs that best fit the biological facts. The plausibility of the Clipper strategy can also be partially explained by intuitive biological rules and theorems. Our results may offer an informed reference for the proper method for a given data analysis task.

Detection and Classification of Colorectal Polyp Using Deep Learning

Colorectal Cancer (CRC) is the third most dangerous cancer in the world and also increasing day by day. So, timely and accurate diagnosis is required to save the life of patients. Cancer grows from polyps which can be either cancerous or noncancerous. So, if the cancerous polyps are detected accurately and removed on time, then the dangerous consequences of cancer can be reduced to a large extent. The colonoscopy is used to detect the presence of colorectal polyps. However, manual examinations performed by experts are prone to various errors. Therefore, some researchers have utilized machine and deep learning-based models to automate the diagnosis process. However, existing models suffer from overfitting and gradient vanishing problems. To overcome these problems, a convolutional neural network- (CNN-) based deep learning model is proposed. Initially, guided image filter and dynamic histogram equalization approaches are used to filter and enhance the colonoscopy images. Thereafter, Single Shot MultiBox Detector (SSD) is used to efficiently detect and classify colorectal polyps from colonoscopy images. Finally, fully connected layers with dropouts are used to classify the polyp classes. Extensive experimental results on benchmark dataset show that the proposed model achieves significantly better results than the competitive models. The proposed model can detect and classify colorectal polyps from the colonoscopy images with 92% accuracy.

SEPA: Signalling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data

MOTIVATION

Biomarkers with prognostic ability and biological interpretability can be used to support decision-making in the survival analysis. Genes usually form functional modules to play synergistic roles, such as pathways. Predicting significant features from the functional level can effectively reduce the adverse effects of heterogeneity and obtain more reproducible and interpretable biomarkers. Personalized pathway activation inference can quantify the dysregulation of essential pathways involved in the initiation and progression of cancers, and can contribute to the development of personalized medical treatments.

RESULTS

In this study, we propose a novel method to evaluate personalized pathway activation based on signalling entropy for survival analysis (SEPA), which is a new attempt to introduce the information-theoretic entropy in generating pathway representation for each patient. SEPA effectively integrates pathway-level information into gene expression data, converting the high-dimensional gene expression data into the low-dimensional biological pathway activation scores. SEPA shows its classification power on the prognostic pan-cancer genomic data, and the potential pathway markers identified based on SEPA have statistical significance in the discrimination of high-risk and low-risk cohorts and are likely to be associated with the initiation and progress of cancers. The results show that SEPA scores can be used as an indicator to precisely distinguish cancer patients with different clinical outcomes, and identify important pathway features with strong discriminative power and biological interpretability.

AVAILABILITY

The MATLAB-package for SEPA is freely available from https://github.com/xingyili/SEPA.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Artificial Intelligence for Inflammatory Bowel Diseases (IBD); Accurately Predicting Adverse Outcomes Using Machine Learning

BACKGROUND

Inflammatory Bowel Diseases with its complexity and heterogeneity could benefit from the increased application of Artificial Intelligence in clinical management.

AIM

To accurately predict adverse outcomes in patients with IBD using advanced computational models in a nationally representative dataset for potential use in clinical practice.

METHODS

We built a training model cohort and validated our result in a separate cohort. We used LASSO and Ridge regressions, Support Vector Machines, Random Forests and Neural Networks to balance between complexity and interpretability and analyzed their relative performances and reported the strongest predictors to the respective models. The participants in our study were patients with IBD selected from The OptumLabs® Data Warehouse (OLDW), a longitudinal, real-world data asset with de-identified administrative claims and electronic health record (EHR) data.

RESULTS

We included 72,178 and 69,165 patients in the training and validation set, respectively. In total, 4.1% of patients in the validation set were hospitalized, 2.9% needed IBD-related surgeries, 17% used long-term steroids and 13% of patients were initiated with biological therapy. Of the AI models we tested, the Random Forest and LASSO resulted in high accuracies (AUCs 0.70-0.92). Our artificial neural network performed similarly well in most of the models (AUCs 0.61-0.90).

CONCLUSIONS

This study demonstrates feasibility of accurately predicting adverse outcomes using complex and novel AI models on large longitudinal data sets of patients with IBD. These models could be applied for risk stratification and implementation of preemptive measures to avoid adverse outcomes in a clinical setting.

Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics

Molecular biomarkers are certain molecules or set of molecules that can be of help for diagnosis or prognosis of diseases or disorders. In the past decades, thanks to the advances in high-throughput technologies, a huge amount of molecular 'omics' data, e.g., transcriptomics and proteomics, have been accumulated. The availability of these omics data makes it possible to screen biomarkers for diseases or disorders. Accordingly, a number of computational approaches have been developed to identify biomarkers by exploring the omics data. In this review, we present a comprehensive survey on the recent progress of identification of molecular biomarkers with machine learning approaches. Specifically, we categorize the machine learning approaches into supervised, un-supervised and recommendation approaches, where the biomarkers including single genes, gene sets and small gene networks. In addition, we further discuss potential problems underlying bio-medical data that may pose challenges for machine learning, and provide possible directions for future biomarker identification.

Machine Learning Modeling from Omics Data as Prospective Tool for Improvement of Inflammatory Bowel Disease Diagnosis and Clinical Classifications

Research of inflammatory bowel disease (IBD) has identified numerous molecular players involved in the disease development. Even so, the understanding of IBD is incomplete, while disease treatment is still far from the precision medicine. Reliable diagnostic and prognostic biomarkers in IBD are limited which may reduce efficient therapeutic outcomes. High-throughput technologies and artificial intelligence emerged as powerful tools in search of unrevealed molecular patterns that could give important insights into IBD pathogenesis and help to address unmet clinical needs. Machine learning, a subtype of artificial intelligence, uses complex mathematical algorithms to learn from existing data in order to predict future outcomes. The scientific community has been increasingly employing machine learning for the prediction of IBD outcomes from comprehensive patient data-clinical records, genomic, transcriptomic, proteomic, metagenomic, and other IBD relevant omics data. This review aims to present fundamental principles behind machine learning modeling and its current application in IBD research with the focus on studies that explored genomic and transcriptomic data. We described different strategies used for dealing with omics data and outlined the best-performing methods. Before being translated into clinical settings, the developed machine learning models should be tested in independent prospective studies as well as randomized controlled trials.

Artificial intelligence and inflammatory bowel disease

With the development of artificial intelligence (AI) and its gradual application in the medical field, AI has brought new ideas to the medical development. The research and application of AI in inflammatory l bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD), are increasing. Selecting appropriate models and methods through machine learning can help diagnose, treat, and predict the prognosis of IBD. In recent years, AI combined with endoscopy has made an appearance in the diagnosis of IBD and achieved satisfactory results. At the same time, AI plays an important role in the process of disease prediction and treatment evaluation for patients with IBD. However, we should also be aware that there are still some problems with AI. This paper gives a brief review of the practical application value of AI in IBD.

Artificial intelligence applications in inflammatory bowel disease: Emerging technologies and future directions

Inflammatory bowel disease (IBD) is a complex and multifaceted disorder of the gastrointestinal tract that is increasing in incidence worldwide and associated with significant morbidity. The rapid accumulation of large datasets from electronic health records, high-definition multi-omics (including genomics, proteomics, transcriptomics, and metagenomics), and imaging modalities (endoscopy and endomicroscopy) have provided powerful tools to unravel novel mechanistic insights and help address unmet clinical needs in IBD. Although the application of artificial intelligence (AI) methods has facilitated the analysis, integration, and interpretation of large datasets in IBD, significant heterogeneity in AI methods, datasets, and clinical outcomes and the need for unbiased prospective validations studies are current barriers to incorporation of AI into clinical practice. The purpose of this review is to summarize the most recent advances in the application of AI and machine learning technologies in the diagnosis and risk prediction, assessment of disease severity, and prediction of clinical outcomes in patients with IBD.

Revealing Prognosis-Related Pathways at the Individual Level by a Comprehensive Analysis of Different Cancer Transcription Data

Identifying perturbed pathways at an individual level is important to discover the causes of cancer and develop individualized custom therapeutic strategies. Though prognostic gene lists have had success in prognosis prediction, using single genes that are related to the relevant system or specific network cannot fully reveal the process of tumorigenesis. We hypothesize that in individual samples, the disruption of transcription homeostasis can influence the occurrence, development, and metastasis of tumors and has implications for patient survival outcomes. Here, we introduced the individual-level pathway score, which can measure the correlation perturbation of the pathways in a single sample well. We applied this method to the expression data of 16 different cancer types from The Cancer Genome Atlas (TCGA) database. Our results indicate that different cancer types as well as their tumor-adjacent tissues can be clearly distinguished by the individual-level pathway score. Additionally, we found that there was strong heterogeneity among different cancer types and the percentage of perturbed pathways as well as the perturbation proportions of tumor samples in each pathway were significantly different. Finally, the prognosis-related pathways of different cancer types were obtained by survival analysis. We demonstrated that the individual-level pathway score (iPS) is capable of classifying cancer types and identifying some key prognosis-related pathways.

Big data in IBD: big progress for clinical practice

IBD is a complex multifactorial inflammatory disease of the gut driven by extrinsic and intrinsic factors, including host genetics, the immune system, environmental factors and the gut microbiome. Technological advancements such as next-generation sequencing, high-throughput omics data generation and molecular networks have catalysed IBD research. The advent of artificial intelligence, in particular, machine learning, and systems biology has opened the avenue for the efficient integration and interpretation of big datasets for discovering clinically translatable knowledge. In this narrative review, we discuss how big data integration and machine learning have been applied to translational IBD research. Approaches such as machine learning may enable patient stratification, prediction of disease progression and therapy responses for fine-tuning treatment options with positive impacts on cost, health and safety. We also outline the challenges and opportunities presented by machine learning and big data in clinical IBD research.

Computational Approaches for Unraveling the Effects of Variation in the Human Genome and Microbiome

The past two decades of analytical efforts have highlighted how much more remains to be learned about the human genome and, particularly, its complex involvement in promoting disease development and progression. While numerous computational tools exist for the assessment of the functional and pathogenic effects of genome variants, their precision is far from satisfactory, particularly for clinical use. Accumulating evidence also suggests that the human microbiome's interaction with the human genome plays a critical role in determining health and disease states. While numerous microbial taxonomic groups and molecular functions of the human microbiome have been associated with disease, the reproducibility of these findings is lacking. The human microbiome–genome interaction in healthy individuals is even less well understood. This review summarizes the available computational methods built to analyze the effect of variation in the human genome and microbiome. We address the applicability and precision of these methods across their possible uses. We also briefly discuss the exciting, necessary, and now possible integration of the two types of data to improve the understanding of pathogenicity mechanisms.

A systematic review of the applications of artificial intelligence and machine learning in autoimmune diseases

Autoimmune diseases are chronic, multifactorial conditions. Through machine learning (ML), a branch of the wider field of artificial intelligence, it is possible to extract patterns within patient data, and exploit these patterns to predict patient outcomes for improved clinical management. Here, we surveyed the use of ML methods to address clinical problems in autoimmune disease. A systematic review was conducted using MEDLINE, embase and computers and applied sciences complete databases. Relevant papers included "machine learning" or "artificial intelligence" and the autoimmune diseases search term(s) in their title, abstract or key words. Exclusion criteria: studies not written in English, no real human patient data included, publication prior to 2001, studies that were not peer reviewed, non-autoimmune disease comorbidity research and review papers. 169 (of 702) studies met the criteria for inclusion. Support vector machines and random forests were the most popular ML methods used. ML models using data on multiple sclerosis, rheumatoid arthritis and inflammatory bowel disease were most common. A small proportion of studies (7.7% or 13/169) combined different data types in the modelling process. Cross-validation, combined with a separate testing set for more robust model evaluation occurred in 8.3% of papers (14/169). The field may benefit from adopting a best practice of validation, cross-validation and independent testing of ML models. Many models achieved good predictive results in simple scenarios (e.g. classification of cases and controls). Progression to more complex predictive models may be achievable in future through integration of multiple data types.

Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification

Since similar complex diseases are much alike in clinical symptoms, patients are easily misdiagnosed and mistreated. It is crucial to accurately predict the disease status and identify markers with high sensitivity and specificity for classifying similar complex diseases. Many approaches incorporating network information have been put forward to predict outcomes, but they are not robust because of their low reproducibility. Several pathway-based methods are robust and functionally interpretable. However, few methods characterize the disease-specific states of single samples from the perspective of pathways. In this study, we propose a novel framework, Pathway Activation for Single Sample (PASS), which utilizes the pathway information in a single sample way to better recognize the differences between two similar complex diseases. PASS can mainly be divided into two parts: for each pathway, the extent of perturbation of edges and the statistic difference of genes caused by a single disease sample are quantified; then, a novel method, named as an AUCpath, is applied to evaluate the pathway activation for single samples from the perspective of genes and their interactions. We have applied PASS to two main types of inflammatory bowel disease (IBD) and widely verified the characteristics of PASS. For a new patient, PASS features can be used as the indicators or potential pathway biomarkers to precisely diagnose complex diseases, discover significant features with interpretability and explore changes in the biological mechanisms of diseases.

Pathway and network embedding methods for prioritizing psychiatric drugs

One in five Americans experience mental illness, and roughly 75% of psychiatric prescriptions do not successfully treat the patient's condition. Extensive evidence implicates genetic factors and signaling disruption in the pathophysiology of these diseases. Changes in transcription often underlie this molecular pathway dysregulation; individual patient transcriptional data can improve the efficacy of diagnosis and treatment. Recent large-scale genomic studies have uncovered shared genetic modules across multiple psychiatric disorders - providing an opportunity for an integrated multi-disease approach for diagnosis. Moreover, network-based models informed by gene expression can represent pathological biological mechanisms and suggest new genes for diagnosis and treatment. Here, we use patient gene expression data from multiple studies to classify psychiatric diseases, integrate knowledge from expert-curated databases and publicly available experimental data to create augmented disease-specific gene sets, and use these to recommend disease-relevant drugs. From Gene Expression Omnibus, we extract expression data from 145 cases of schizophrenia, 82 cases of bipolar disorder, 190 cases of major depressive disorder, and 307 shared controls. We use pathway-based approaches to predict psychiatric disease diagnosis with a random forest model (78% accuracy) and derive important features to augment available drug and disease signatures. Using protein-protein-interaction networks and embedding-based methods, we build a pipeline to prioritize treatments for psychiatric diseases that achieves a 3.4-fold improvement over a background model. Thus, we demonstrate that gene-expression-derived pathway features can diagnose psychiatric diseases and that molecular insights derived from this classification task can inform treatment prioritization for psychiatric diseases.

Big data in IBD: a look into the future

Big data methodologies, made possible with the increasing generation and availability of digital data and enhanced analytical capabilities, have produced new insights to improve outcomes in many disciplines. Application of big data in the health-care sector is in its early stages, although the potential for leveraging underutilized data to gain a better understanding of disease and improve quality of care is enormous. Owing to the intrinsic characteristics of inflammatory bowel disease (IBD) and the management dilemmas that it imposes, the implementation of big data research strategies not only can complement current research efforts but also could represent the only way to disentangle the complexity of the disease. In this Review, we explore important potential applications of big data in IBD research, including predictive models of disease course and response to therapy, characterization of disease heterogeneity, drug safety and development, precision medicine and cost-effectiveness of care. We also discuss the strengths and limitations of potential data sources that big data analytics could draw from in the field of IBD, including electronic health records, clinical trial data, e-health applications and genomic, transcriptomic, proteomic, metabolomic and microbiomic data.