Towards realizing the vision of precision medicine: AI based prediction of clinical drug response

Enhancing clinical trial outcome prediction with artificial intelligence: a systematic review

Clinical trials are pivotal in drug development yet fraught with uncertainties and resource-intensive demands. The application of AI models to forecast trial outcomes could mitigate failures and expedite the drug discovery process. This review discusses AI methodologies that impact clinical trial outcomes, focusing on clinical text embedding, trial multimodal learning, and prediction techniques, while addressing practical challenges and opportunities.

Deep representation learning for clustering longitudinal survival data from electronic health records

Precision medicine requires accurate identification of clinically relevant patient subgroups. Electronic health records provide major opportunities for leveraging machine learning approaches to uncover novel patient subgroups. However, many existing approaches fail to adequately capture complex interactions between diagnosis trajectories and disease-relevant risk events, leading to subgroups that can still display great heterogeneity in event risk and underlying molecular mechanisms. To address this challenge, we implemented VaDeSC-EHR, a transformer-based variational autoencoder for clustering longitudinal survival data as extracted from electronic health records. We show that VaDeSC-EHR outperforms baseline methods on both synthetic and real-world benchmark datasets with known ground-truth cluster labels. In an application to Crohn's disease, VaDeSC-EHR successfully identifies four distinct subgroups with divergent diagnosis trajectories and risk profiles, revealing clinically and genetically relevant factors in Crohn's disease. Our results show that VaDeSC-EHR can be a powerful tool for discovering novel patient subgroups in the development of precision medicine approaches.

AI and Neurology

BACKGROUND

Artificial Intelligence is influencing medicine on all levels. Neurology, one of the most complex and progressive medical disciplines, is no exception. No longer limited to neuroimaging, where data-driven approaches were initiated, machine and deep learning methodologies are taking neurologic diagnostics, prognostication, predictions, decision making and even therapy to very promising potentials.

MAIN BODY

In this review, the basic principles of different types of Artificial Intelligence and the options to apply them to neurology are summarized. Examples of noteworthy studies on such applications are presented from the fields of acute and intensive care neurology, stroke, epilepsy, and movement disorders. Finally, these potentials are matched with risks and challenges jeopardizing ethics, safety and equality, that need to be heeded by neurologists welcoming Artificial Intelligence to their field of expertise.

CONCLUSION

Artificial intelligence is and will be changing neurology. Studies need to be taken to the prospective level and algorithms undergo federated learning to reach generalizability. Neurologists need to master not only the benefits but also the risks in safety, ethics and equity of such data-driven form of medicine.

Factors associated with placebo response rate in randomized controlled trials of antiseizure medications for focal epilepsy

OBJECTIVE

Randomized controlled trials (RCTs) are necessary to evaluate the efficacy of novel treatments for epilepsy. However, there have been concerning increases in the placebo responder rate over time. To understand these trends, we evaluated features associated with increased placebo responder rate.

METHODS

Using individual-level data from 20 focal-onset seizure trials provided by seven pharmaceutical companies, we evaluated associations with change in seizure frequency in participants randomized to placebo. We used multivariable logistic regression to evaluate participant and study factors associated with differing rates of 50% reduction in seizure frequency during blinded placebo treatment, as compared to pre-randomization baseline seizure frequency. In addition, we focused on the association of placebo responder rate with pre-randomization baseline seizure frequency and country of recruitment.

RESULTS

In the pooled analysis of 1674 participants randomized to placebo, a higher 50% responder rate (50RR) was associated with a shorter duration of epilepsy (p = .006), lower baseline seizure rate (p = .002), fewer concomitant antiseizure medications (p = .004), absence of adverse events (p < .001), more trial arms (p = .006), and geographic region (p < .001). Mixture modeling indicated a significantly higher 50RR in Bulgaria, Croatia, India, and Canada (42% in the higher group vs 22% in the lower group comprising all 40 other countries, p < 10-15). In addition, there was a significantly higher 50RR in participants with a baseline seizure frequency of six or fewer seizures per 28 days (29% vs 21%, p = .00018).

SIGNIFICANCE

These results can assist future RCTs in estimating the expected placebo responder rate, which may lead to more reliable power estimates. Higher placebo responder rate was associated with markers of less-refractory epilepsy. There were concerning significant differences in placebo responder rate by country and geographic region as well as an elevated placebo responder rate in participants with baseline seizure frequency close to the minimum eligibility criteria.

How accurate are machine learning models in predicting anti-seizure medication responses: A systematic review

IMPORTANCE

Current epilepsy management protocols often depend on anti-seizure medication (ASM) trials and assessment of clinical response. This may delay the initiation of the ASM regimen that might optimally balance efficacy and tolerability for individual patients. Machine learning (ML) can offer a promising tool for efficiently predicting ASM response.

OBJECTIVE

The objective of this review is to synthesize the available information about the effectiveness and limitations of ML models in predicting and classifying the response of patients with epilepsy to ASMs, and to assess the impact of various data inputs on prediction performance.

EVIDENCE REVIEW

We conducted a comprehensive search of studies utilizing ML models for ASM response prediction using PubMed and Scopus up until November 2024.

FINDINGS

The review included 37 studies. Various data types, including clinical information, brain MRI, EEG, and genetic data, are useful in predicting responses to ASMs. Tree-based ML algorithms and Support Vector Machines are the most used models. Reported results vary widely, with certain models achieving near-perfect accuracy and others performing similar to random classifiers. The review also highlights the limitations of this research field, especially concerning the quality and quantity of data.

CONCLUSIONS AND RELEVANCE

The findings indicate that while ML models show great promise in predicting ASM responses in epilepsy, further research is required to refine these models for practical clinical application. The review underscores both the potential of ML in advancing precision medicine in epilepsy management and the need for continued research to improve prediction accuracy.

Prediction of Pharmacoresistance in Drug-Naïve Temporal Lobe Epilepsy Using Ictal EEGs Based on Convolutional Neural Network

Approximately 30%-40% of epilepsy patients do not respond well to adequate anti-seizure medications (ASMs), a condition known as pharmacoresistant epilepsy. The management of pharmacoresistant epilepsy remains an intractable issue in the clinic. Its early prediction is important for prevention and diagnosis. However, it still lacks effective predictors and approaches. Here, a classical model of pharmacoresistant temporal lobe epilepsy (TLE) was established to screen pharmacoresistant and pharmaco-responsive individuals by applying phenytoin to amygdaloid-kindled rats. Ictal electroencephalograms (EEGs) recorded before phenytoin treatment were analyzed. Based on ictal EEGs from pharmacoresistant and pharmaco-responsive rats, a convolutional neural network predictive model was constructed to predict pharmacoresistance, and achieved 78% prediction accuracy. We further found the ictal EEGs from pharmacoresistant rats have a lower gamma-band power, which was verified in seizure EEGs from pharmacoresistant TLE patients. Prospectively, therapies targeting the subiculum in those predicted as "pharmacoresistant" individual rats significantly reduced the subsequent occurrence of pharmacoresistance. These results demonstrate a new methodology to predict whether TLE individuals become resistant to ASMs in a classic pharmacoresistant TLE model. This may be of translational importance for the precise management of pharmacoresistant TLE.

A stratified treatment algorithm in psychiatry: a program on stratified pharmacogenomics in severe mental illness (Psych-STRATA): concept, objectives and methodologies of a multidisciplinary project funded by Horizon Europe

Schizophrenia (SCZ), bipolar (BD) and major depression disorder (MDD) are severe psychiatric disorders that are challenging to treat, often leading to treatment resistance (TR). It is crucial to develop effective methods to identify and treat patients at risk of TR at an early stage in a personalized manner, considering their biological basis, their clinical and psychosocial characteristics. Effective translation of theoretical knowledge into clinical practice is essential for achieving this goal. The Psych-STRATA consortium addresses this research gap through a seven-step approach. First, transdiagnostic biosignatures of SCZ, BD and MDD are identified by GWAS and multi-modal omics signatures associated with treatment outcome and TR (steps 1 and 2). In a next step (step 3), a randomized controlled intervention study is conducted to test the efficacy and safety of an early intensified pharmacological treatment. Following this RCT, a combined clinical and omics-based algorithm will be developed to estimate the risk for TR. This algorithm-based tool will be designed for early detection and management of TR (step 4). This algorithm will then be implemented into a framework of shared treatment decision-making with a novel mental health board (step 5). The final focus of the project is based on patient empowerment, dissemination and education (step 6) as well as the development of a software for fast, effective and individualized treatment decisions (step 7). The project has the potential to change the current trial and error treatment approach towards an evidence-based individualized treatment setting that takes TR risk into account at an early stage.

Deep learning-based patient stratification for prognostic enrichment of clinical dementia trials

Dementia probably due to Alzheimer's disease is a progressive condition that manifests in cognitive decline and impairs patients' daily life. Affected patients show great heterogeneity in their symptomatic progression, which hampers the identification of efficacious treatments in clinical trials. Using artificial intelligence approaches to enable clinical enrichment trials serves a promising avenue to identify treatments. In this work, we used a deep learning method to cluster the multivariate disease trajectories of 283 early dementia patients along cognitive and functional scores. Two distinct subgroups were identified that separated patients into 'slow' and 'fast' progressing individuals. These subgroups were externally validated and independently replicated in a dementia cohort comprising 2779 patients. We trained a machine learning model to predict the progression subgroup of a patient from cross-sectional data at their time of dementia diagnosis. The classifier achieved a prediction performance of 0.70 ± 0.01 area under the receiver operating characteristic curve in external validation. By emulating a hypothetical clinical trial conducting patient enrichment using the proposed classifier, we estimate its potential to decrease the required sample size. Furthermore, we balance the achieved enrichment of the trial cohort against the accompanied demand for increased patient screening. Our results show that enrichment trials targeting cognitive outcomes offer improved chances of trial success and are more than 13% cheaper compared with conventional clinical trials. The resources saved could be redirected to accelerate drug development and expand the search for remedies for cognitive impairment.

Machine learning models for predicting treatment response in infantile epilepsies

Epilepsy stands as one of the prevalent and significant neurological disorders, representing a critical healthcare challenge. Recently, machine learning techniques have emerged as versatile tools across various healthcare domains, encompassing diagnostics, treatment assessment, and prognosis. We compared 11 machine learning model to find the best ML model to predict drug treatment outcomes for our cohort, which we previously evaluated using classical statistical methods.

METHODS

In our study, we evaluated patients who presented to the pediatric neurology department of our university hospital with seizures at the age of 1 to 24 months and were diagnosed with epilepsy. We utilized 11 different machine learning techniques namely Decision Tree, Bagging, K-Nearest Neighbour, Linear Discriminant Analysis, Logistic Regression, Neural Networks, Deep Neural Networks, Support Vector Machine. Besides, we compared these techniques using various performance metrics to identify anti-seizure medicine response. We also utilized the chi-square feature selection methods to enhance performance in machine learning algorithms.

RESULTS

Two hundred and twenty-nine patients (110 male and 119 female) who were diagnosed between the ages of 1-24 months were included in the study. Support Vector Machine algorithm was found to be effective in drug resistant epilepsy detection, with the highest aure under curve value (0.9934) and achieving a test accuracy of 97.06 %.

CONCLUSION

This study can shed light on future studies by showing that the Support Vector Machine algorithm can effectively determine the drug resistant epilepsy. The pediatric neurologist and experts should be referred to non-medical treatment (epilepsy surgery, ketogenic diet) at the early stages and multidisciplinary approach should be provided.

New epilepsy therapies in development

Epilepsy is a common brain disorder, characterized by spontaneous recurrent seizures, with associated neuropsychiatric and cognitive comorbidities and increased mortality. Although people at risk can often be identified, interventions to prevent the development of the disorder are not available. Moreover, in at least 30% of patients, epilepsy cannot be controlled by current antiseizure medications (ASMs). As a result of considerable progress in epilepsy genetics and the development of novel disease models, drug screening technologies and innovative therapeutic modalities over the past 10 years, more than 200 novel epilepsy therapies are currently in the preclinical or clinical pipeline, including many treatments that act by new mechanisms. Assisted by diagnostic and predictive biomarkers, the treatment of epilepsy is undergoing paradigm shifts from symptom-only ASMs to disease prevention, and from broad trial-and-error treatments for seizures in general to mechanism-based treatments for specific epilepsy syndromes. In this Review, we assess recent progress in ASM development and outline future directions for the development of new therapies for the treatment and prevention of epilepsy.

Predicting efficacy of antiseizure medication treatment with machine learning algorithms in North Indian population

PURPOSE

This study aimed to develop a classifier using supervised machine learning to effectively assess the impact of clinical, demographical, and biochemical factors in accurately predicting the antiseizure medications (ASMs) treatment response in people with epilepsy (PWE).

METHODS

Data was collected from 786 PWE at the Outpatient Department of Neurology, Institute of Human Behavior and Allied Sciences (IHBAS), New Delhi, India from 2005 to 2015. Patients were followed up at the 2nd, 4th, 8th, and 12th month over the span of 1 year for the drugs being administered and their dosage, the serum drug levels, the frequency of seizure control, drug efficacy, the adverse drug reactions (ADRs), and their compliance to ASMs. Several features, including demographic details, medical history, and auxiliary examinations electroencephalogram (EEG) or Computed Tomography (CT) were chosen to discern between patients with distinct remission outcomes. Remission outcomes were categorized into 'good responder (GR)' and 'poor responder (PR)' based on the number of seizures experienced by the patients over the study duration. Our dataset was utilized to train seven classical machine learning algorithms i.e Extreme Gradient Boost (XGB), K-Nearest Neighbor (KNN), Support Vector Classifier (SVC), Decision Tree (DT), Random Forest (RF), Naïve Bayes (NB) and Logistic Regression (LR) to construct classification models.

RESULTS

Our research findings indicate that 1) among the seven algorithms examined, XGB and SVC demonstrated superior predictive performances of ASM treatment outcomes with an accuracy of 0.66 each and ROC-AUC scores of 0.67 (XGB) and 0.66 (SVC) in distinguishing between PR and GR patients. 2) The most influential factor in discerning PR to GR patients is a family history of seizures (no), education (literate) and multitherapy with Chi-square (χ2) values of 12.1539, 8.7232 and 13.620 respectively and odds ratio (OR) of 2.2671, 0.4467, and 1.9453 each. 3). Furthermore, our surrogate analysis revealed that the null hypothesis for both XGB and SVC was rejected at a 100 % confidence level, underscoring the significance of their predictive performance. These findings underscore the robustness and reliability of XGB and SVC in our predictive modelling framework.

SIGNIFICANCE

Utilizing XG Boost and SVC-based machine learning classifier, we successfully forecasted the likelihood of a patient's response to ASM treatment, categorizing them as either PR or GR, post-completion of standard epilepsy examinations. The classifier's predictions were found to be statistically significant, suggesting their potential utility in improving treatment strategies, particularly in the personalized selection of ASM regimens for individual epilepsy patients.

Prognostic enrichment for early-stage Huntington's disease: An explainable machine learning approach for clinical trial

BACKGROUND

In Huntington's disease clinical trials, recruitment and stratification approaches primarily rely on genetic load, cognitive and motor assessment scores. They focus less on in vivo brain imaging markers, which reflect neuropathology well before clinical diagnosis. Machine learning methods offer a degree of sophistication which could significantly improve prognosis and stratification by leveraging multimodal biomarkers from large datasets. Such models specifically tailored to HD gene expansion carriers could further enhance the efficacy of the stratification process.

OBJECTIVES

To improve stratification of Huntington's disease individuals for clinical trials.

METHODS

We used data from 451 gene positive individuals with Huntington's disease (both premanifest and diagnosed) from previously published cohorts (PREDICT, TRACK, TrackON, and IMAGE). We applied whole-brain parcellation to longitudinal brain scans and measured the rate of lateral ventricular enlargement, over 3 years, which was used as the target variable for our prognostic random forest regression models. The models were trained on various combinations of features at baseline, including genetic load, cognitive and motor assessment score biomarkers, as well as brain imaging-derived features. Furthermore, a simplified stratification model was developed to classify individuals into two homogenous groups (low risk and high risk) based on their anticipated rate of ventricular enlargement.

RESULTS

The predictive accuracy of the prognostic models substantially improved by integrating brain imaging features alongside genetic load, cognitive and motor biomarkers: a 24 % reduction in the cross-validated mean absolute error, yielding an error of 530 mm3/year. The stratification model had a cross-validated accuracy of 81 % in differentiating between moderate and fast progressors (precision = 83 %, recall = 80 %).

CONCLUSIONS

This study validated the effectiveness of machine learning in differentiating between low- and high-risk individuals based on the rate of ventricular enlargement. The models were exclusively trained using features from HD individuals, which offers a more disease-specific, simplified, and accurate approach for prognostic enrichment compared to relying on features extracted from healthy control groups, as done in previous studies. The proposed method has the potential to enhance clinical utility by: i) enabling more targeted recruitment of individuals for clinical trials, ii) improving post-hoc evaluation of individuals, and iii) ultimately leading to better outcomes for individuals through personalized treatment selection.

Tailoring epilepsy treatment: personalized micro-physiological systems illuminate individual drug responses

Introduction

Approximately 50 million people worldwide have epilepsy, with many not achieving seizure freedom. Organ-on-chip technology, which mimics organ-level physiology, could revolutionize drug development for epilepsy by replacing animal models in preclinical studies. The authors' goal is to determine if customized micro-physiological systems can lead to tailored drug treatments for epileptic patients.

Materials and methods

A comprehensive literature search was conducted utilizing various databases, including PubMed, Ebscohost, Medline, and the National Library of Medicine, using a predetermined search strategy. The authors focused on articles that addressed the role of personalized micro-physiological systems in individual drug responses and articles that discussed different types of epilepsy, diagnosis, and current treatment options. Additionally, articles that explored the components and design considerations of micro-physiological systems were reviewed to identify challenges and opportunities in drug development for challenging epilepsy cases.

Results

The micro-physiological system offers a more accurate and cost-effective alternative to traditional models for assessing drug effects, toxicities, and disease mechanisms. Nevertheless, designing patient-specific models presents critical considerations, including the integration of analytical biosensors and patient-derived cells, while addressing regulatory, material, and biological complexities. Material selection, standardization, integration of vascular systems, cost efficiency, real-time monitoring, and ethical considerations are also crucial to the successful use of this technology in drug development.

Conclusion

The future of organ-on-chip technology holds great promise, with the potential to integrate artificial intelligence and machine learning for personalized treatment of epileptic patients.

Assisting the implementation of screening for type 1 diabetes by using artificial intelligence on publicly available data

The type 1 diabetes community is coalescing around the benefits and advantages of early screening for disease risk. To be accepted by healthcare providers, regulatory authorities and payers, screening programmes need to show that the testing variables allow accurate risk prediction and that individualised risk-informed monitoring plans are established, as well as operational feasibility, cost-effectiveness and acceptance at population level. Artificial intelligence (AI) has the potential to contribute to solving these issues, starting with the identification and stratification of at-risk individuals. ASSET (AI for Sustainable Prevention of Autoimmunity in the Society; www.asset.healthcare ) is a public/private consortium that was established to contribute to research around screening for type 1 diabetes and particularly to how AI can drive the implementation of a precision medicine approach to disease prevention. ASSET will additionally focus on issues pertaining to operational implementation of screening. The authors of this article, researchers and clinicians active in the field of type 1 diabetes, met in an open forum to independently debate key issues around screening for type 1 diabetes and to advise ASSET. The potential use of AI in the analysis of longitudinal data from observational cohort studies to inform the design of improved, more individualised screening programmes was also discussed. A key issue was whether AI would allow the research community and industry to capitalise on large publicly available data repositories to design screening programmes that allow the early detection of individuals at high risk and enable clinical evaluation of preventive therapies. Overall, AI has the potential to revolutionise type 1 diabetes screening, in particular to help identify individuals who are at increased risk of disease and aid in the design of appropriate follow-up plans. We hope that this initiative will stimulate further research on this very timely topic.

Artificial Intelligence: Fundamentals and Breakthrough Applications in Epilepsy

Artificial intelligence, machine learning, and deep learning are increasingly being used in all medical fields including for epilepsy research and clinical care. Already there have been resultant cutting-edge applications in both the clinical and research arenas of epileptology. Because there is a need to disseminate knowledge about these approaches, how to use them, their advantages, and their potential limitations, the goal of the 2023 Merritt-Putnam Symposium and of this synopsis review of that symposium has been to present the background and state of the art and then to draw conclusions on current and future applications of these approaches through the following: (1) Initially provide an explanation of the fundamental principles of artificial intelligence, machine learning, and deep learning. These are presented in the first section of this review by Dr Wesley Kerr. (2) Provide insights into their cutting-edge applications in screening for medications in neural organoids, in general, and for epilepsy in particular. These are presented by Dr Sandra Acosta. (3) Provide insights into how artificial intelligence approaches can predict clinical response to medication treatments. These are presented by Dr Patrick Kwan. (4) Finally, provide insights into the expanding applications to the detection and analysis of EEG signals in intensive care, epilepsy monitoring unit, and intracranial monitoring situations, as presented below by Dr Gregory Worrell. The expectation is that, in the coming decade and beyond, the increasing use of the above approaches will transform epilepsy research and care and supplement, but not replace, the diligent work of epilepsy clinicians and researchers.

Artificial intelligence applied in cardiovascular disease: a bibliometric and visual analysis

Background

With the rapid development of technology, artificial intelligence (AI) has been widely used in the diagnosis and prognosis prediction of a variety of diseases, including cardiovascular disease. Facts have proved that AI has broad application prospects in rapid and accurate diagnosis.

Objective

This study mainly summarizes the research on the application of AI in the field of cardiovascular disease through bibliometric analysis and explores possible future research hotpots.

Methods

The articles and reviews regarding application of AI in cardiovascular disease between 2000 and 2023 were selected from Web of Science Core Collection on 30 December 2023. Microsoft Excel 2019 was applied to analyze the targeted variables. VOSviewer (version 1.6.16), Citespace (version 6.2.R2), and a widely used online bibliometric platform were used to conduct co-authorship, co-citation, and co-occurrence analysis of countries, institutions, authors, references, and keywords in this field.

Results

A total of 4,611 articles were selected in this study. AI-related research on cardiovascular disease increased exponentially in recent years, of which the USA was the most productive country with 1,360 publications, and had close cooperation with many countries. The most productive institutions and researchers were the Cedar sinai medical center and Acharya, Ur. However, the cooperation among most institutions or researchers was not close even if the high research outputs. Circulation is the journal with the largest number of publications in this field. The most important keywords are "classification", "diagnosis", and "risk". Meanwhile, the current research hotpots were "late gadolinium enhancement" and "carotid ultrasound".

Conclusions

AI has broad application prospects in cardiovascular disease, and a growing number of scholars are devoted to AI-related research on cardiovascular disease. Cardiovascular imaging techniques and the selection of appropriate algorithms represent the most extensively studied areas, and a considerable boost in these areas is predicted in the coming years.

Role of machine learning in the management of epilepsy: a systematic review protocol

INTRODUCTION

Machine learning is a rapidly expanding field and is already incorporated into many aspects of medicine including diagnostics, prognostication and clinical decision-support tools. Epilepsy is a common and disabling neurological disorder, however, management remains challenging in many cases, despite expanding therapeutic options. We present a systematic review protocol to explore the role of machine learning in the management of epilepsy.

METHODS AND ANALYSIS

This protocol has been drafted with reference to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) for Protocols. A literature search will be conducted in databases including MEDLINE, Embase, Scopus and Web of Science. A PRISMA flow chart will be constructed to summarise the study workflow. As the scope of this review is the clinical application of machine learning, the selection of papers will be focused on studies directly related to clinical decision-making in management of epilepsy, specifically the prediction of response to antiseizure medications, development of drug-resistant epilepsy, and epilepsy surgery and neuromodulation outcomes. Data will be extracted following the CHecklist for critical Appraisal and data extraction for systematic Reviews of prediction Modelling Studies checklist. Prediction model Risk Of Bias ASsessment Tool will be used for the quality assessment of the included studies. Syntheses of quantitative data will be presented in narrative format.

ETHICS AND DISSEMINATION

As this study is a systematic review which does not involve patients or animals, ethics approval is not required. The results of the systematic review will be submitted to peer-review journals for publication and presented in academic conferences.

PROSPERO REGISTRATION NUMBER

CRD42023442156.

Multi-omics approaches to studying gastrointestinal microbiome in the context of precision medicine and machine learning

The human gastrointestinal (gut) microbiome plays a critical role in maintaining host health and has been increasingly recognized as an important factor in precision medicine. High-throughput sequencing technologies have revolutionized -omics data generation, facilitating the characterization of the human gut microbiome with exceptional resolution. The analysis of various -omics data, including metatranscriptomics, metagenomics, glycomics, and metabolomics, holds potential for personalized therapies by revealing information about functional genes, microbial composition, glycans, and metabolites. This multi-omics approach has not only provided insights into the role of the gut microbiome in various diseases but has also facilitated the identification of microbial biomarkers for diagnosis, prognosis, and treatment. Machine learning algorithms have emerged as powerful tools for extracting meaningful insights from complex datasets, and more recently have been applied to metagenomics data via efficiently identifying microbial signatures, predicting disease states, and determining potential therapeutic targets. Despite these rapid advancements, several challenges remain, such as key knowledge gaps, algorithm selection, and bioinformatics software parametrization. In this mini-review, our primary focus is metagenomics, while recognizing that other -omics can enhance our understanding of the functional diversity of organisms and how they interact with the host. We aim to explore the current intersection of multi-omics, precision medicine, and machine learning in advancing our understanding of the gut microbiome. A multidisciplinary approach holds promise for improving patient outcomes in the era of precision medicine, as we unravel the intricate interactions between the microbiome and human health.

High-accuracy prediction of colorectal cancer chemotherapy efficacy using machine learning applied to gene expression data

Introduction: FOLFOX and FOLFIRI chemotherapy are considered standard first-line treatment options for colorectal cancer (CRC). However, the criteria for selecting the appropriate treatments have not been thoroughly analyzed. Methods: A newly developed machine learning model was applied on several gene expression data from the public repository GEO database to identify molecular signatures predictive of efficacy of 5-FU based combination chemotherapy (FOLFOX and FOLFIRI) in patients with CRC. The model was trained using 5-fold cross validation and multiple feature selection methods including LASSO and VarSelRF methods. Random Forest and support vector machine classifiers were applied to evaluate the performance of the models. Results and Discussion: For the CRC GEO dataset samples from patients who received either FOLFOX or FOLFIRI, validation and test sets were >90% correctly classified (accuracy), with specificity and sensitivity ranging between 85%-95%. In the datasets used from the GEO database, 28.6% of patients who failed the treatment therapy they received are predicted to benefit from the alternative treatment. Analysis of the gene signature suggests the mechanistic difference between colorectal cancers that respond and those that do not respond to FOLFOX and FOLFIRI. Application of this machine learning approach could lead to improvements in treatment outcomes for patients with CRC and other cancers after additional appropriate clinical validation.

Harnessing artificial intelligence to improve clinical trial design

Zhang et al. discuss how artificial intelligence (AI) can be used to optimize clinical trial design and potentially boost the success rate of clinical trials. AI has unparalleled potential to leverage real-world data and unlock valuable insights for innovative trial design.

Machine Learning and Artificial Intelligence Applications to Epilepsy: a Review for the Practicing Epileptologist

PURPOSE OF REVIEW

Machine Learning (ML) and Artificial Intelligence (AI) are data-driven techniques to translate raw data into applicable and interpretable insights that can assist in clinical decision making. Some of these tools have extremely promising initial results, earning both great excitement and creating hype. This non-technical article reviews recent developments in ML/AI in epilepsy to assist the current practicing epileptologist in understanding both the benefits and limitations of integrating ML/AI tools into their clinical practice.

RECENT FINDINGS

ML/AI tools have been developed to assist clinicians in almost every clinical decision including (1) predicting future epilepsy in people at risk, (2) detecting and monitoring for seizures, (3) differentiating epilepsy from mimics, (4) using data to improve neuroanatomic localization and lateralization, and (5) tracking and predicting response to medical and surgical treatments. We also discuss practical, ethical, and equity considerations in the development and application of ML/AI tools including chatbots based on Large Language Models (e.g., ChatGPT). ML/AI tools will change how clinical medicine is practiced, but, with rare exceptions, the transferability to other centers, effectiveness, and safety of these approaches have not yet been established rigorously. In the future, ML/AI will not replace epileptologists, but epileptologists with ML/AI will replace epileptologists without ML/AI.

Revisiting the concept of drug-resistant epilepsy: A TASK1 report of the ILAE/AES Joint Translational Task Force

Despite progress in the development of anti-seizure medications (ASMs), one third of people with epilepsy have drug-resistant epilepsy (DRE). The working definition of DRE, proposed by the International League Against Epilepsy (ILAE) in 2010, helped identify individuals who might benefit from presurgical evaluation early on. As the incidence of DRE remains high, the TASK1 workgroup on DRE of the ILAE/American Epilepsy Society (AES) Joint Translational Task Force discussed the heterogeneity and complexity of its presentation and mechanisms, the confounders in drawing mechanistic insights when testing treatment responses, and barriers in modeling DRE across the lifespan and translating across species. We propose that it is necessary to revisit the current definition of DRE, in order to transform the preclinical and clinical research of mechanisms and biomarkers, to identify novel, effective, precise, pharmacologic treatments, allowing for earlier recognition of drug resistance and individualized therapies.

Personalized antiseizure medication therapy in critically ill adult patients

Precision medicine has the potential to have a significant impact on both drug development and patient care. It is crucial to not only provide prompt effective antiseizure treatment for critically ill patients after seizures start but also have a proactive mindset and concentrate on epileptogenesis and the underlying cause of the seizures or seizure disorders. Critical illness presents different treatment issues compared with the ambulatory population, which makes it challenging to choose the best antiseizure medications and to administer them at the right time and at the right dose. Since there is a paucity of information available on antiseizure medication dosing in critically ill patients, therapeutic drug monitoring is a useful tool for defining each patient's personal therapeutic range and assisting clinicians in decision-making. Use of pharmacogenomic information relating to pharmacokinetics, hepatic metabolism, and seizure etiology may improve safety and efficacy by individualizing therapy. Studies evaluating the clinical implementation of pharmacogenomic information at the point-of-care and identification of biomarkers are also needed. These studies may make it possible to avoid adverse drug reactions, maximize drug efficacy, reduce drug-drug interactions, and optimize medications for each individual patient. This review will discuss the available literature and provide future insights on precision medicine use with antiseizure therapy in critically ill adult patients.

Physicians' Perspectives on AI in Clinical Decision Support Systems: Interview Study of the CURATE.AI Personalized Dose Optimization Platform

BACKGROUND

Physicians play a key role in integrating new clinical technology into care practices through user feedback and growth propositions to developers of the technology. As physicians are stakeholders involved through the technology iteration process, understanding their roles as users can provide nuanced insights into the workings of these technologies that are being explored. Therefore, understanding physicians' perceptions can be critical toward clinical validation, implementation, and downstream adoption. Given the increasing prevalence of clinical decision support systems (CDSSs), there remains a need to gain an in-depth understanding of physicians' perceptions and expectations toward their downstream implementation. This paper explores physicians' perceptions of integrating CURATE.AI, a novel artificial intelligence (AI)-based and clinical stage personalized dosing CDSSs, into clinical practice.

OBJECTIVE

This study aims to understand physicians' perspectives of integrating CURATE.AI for clinical work and to gather insights on considerations of the implementation of AI-based CDSS tools.

METHODS

A total of 12 participants completed semistructured interviews examining their knowledge, experience, attitudes, risks, and future course of the personalized combination therapy dosing platform, CURATE.AI. Interviews were audio recorded, transcribed verbatim, and coded manually. The data were thematically analyzed.

RESULTS

Overall, 3 broad themes and 9 subthemes were identified through thematic analysis. The themes covered considerations that physicians perceived as significant across various stages of new technology development, including trial, clinical implementation, and mass adoption.

CONCLUSIONS

The study laid out the various ways physicians interpreted an AI-based personalized dosing CDSS, CURATE.AI, for their clinical practice. The research pointed out that physicians' expectations during the different stages of technology exploration can be nuanced and layered with expectations of implementation that are relevant for technology developers and researchers.

The evolution of antiseizure medication therapy selection in adults: Is artificial intelligence -assisted antiseizure medication selection ready for prime time?

Antiseizure medications (ASMs) are the mainstay of symptomatic epilepsy treatment. The primary goal of pharmacotherapy with ASMs in epilepsy is to achieve complete seizure remission while minimizing therapy-related adverse events. Over the years, more ASMs have been introduced, with approximately 30 now in everyday use. With such a wide variety, much guidance is needed in choosing ASMs for initial therapy, subsequent replacement monotherapy, or adjunctive therapy. The specific ASMs are typically tailored by the patient's related factors, including epilepsy syndrome, age, sex, comorbidities, and ASM characteristics, including the spectrum of efficacy, pharmacokinetic properties, safety, and tolerability. Weighing these key clinical variables requires experience and expertise that may be limited. Furthermore, with this approach, patients may endure multiple trials of ineffective treatments before the most appropriate ASM is found. A more reliable way to predict response to different ASMs is needed so that the most effective and tolerated ASM can be selected. Soon, alternative approaches, such as deep machine learning (ML), could aid the individualized selection of the first and subsequent ASMs. The recognition of epilepsy as a network disorder and the integration of personalized epilepsy networks in future ML platforms can also facilitate the prediction of ASM response. Augmenting the conventional approach with artificial intelligence (AI) opens the door to personalized pharmacotherapy in epilepsy. However, more work is needed before these models are ready for primetime clinical practice.

Circadian biology to advance therapeutics for mood disorders

Mood disorders account for a significant global disease burden, and pharmacological innovation is needed as existing medications are suboptimal. A wide range of evidence implicates circadian and sleep dysfunction in the pathogenesis of mood disorders, and there is growing interest in these chronobiological pathways as a focus for treatment innovation. We review contemporary evidence in three promising areas in circadian-clock-based therapeutics in mood disorders: targeting the circadian system informed by mechanistic molecular advances; time-tailoring of medications; and personalizing treatment using circadian parameters. We also consider the limitations and challenges in accelerating the development of new circadian-informed pharmacotherapies for mood disorders.

Increasing challenges to trial recruitment and conduct over time

OBJECTIVE

This study was undertaken to evaluate how the challenges in the recruitment and retention of participants in clinical trials for focal onset epilepsy have changed over time.

METHODS

In this systematic analysis of randomized clinical trials of adjunct antiseizure medications for medication-resistant focal onset epilepsy, we evaluated how the numbers of participants, sites, and countries have changed since the first such trial in 1990. We also evaluated the proportion of participants who completed each trial phase and their reasons for early trial exit. We analyzed these trends using mixed effects generalized linear models accounting for the influence of the number of trial sites and trial-specific variability.

RESULTS

The number of participants per site has steadily decreased over decades, with recent trials recruiting fewer than five participants per site (reduction by .16 participants/site/year, p < .0001). Fewer participants also progressed from recruitment to randomization over time (odds ratio = .94/year, p = .014). Concurrently, there has been an increase in the placebo response over time (increase in median percent reduction of .4%/year, p = .02; odds ratio of increase in 50% responder rate of 1.03/year, p = .02), which was not directly associated with the number of sites per trial (p > .20).

SIGNIFICANCE

This historical analysis highlights the increasing challenges with participant recruitment and retention, as well as increasing placebo response. It serves as a call to action to change clinical trial design to address these challenges.

O’Brien T, Perucca P, Ge Z, Anderson A. Applications for Deep Learning in Epilepsy Genetic Research

Epilepsy is a group of brain disorders characterised by an enduring predisposition to generate unprovoked seizures. Fuelled by advances in sequencing technologies and computational approaches, more than 900 genes have now been implicated in epilepsy. The development and optimisation of tools and methods for analysing the vast quantity of genomic data is a rapidly evolving area of research. Deep learning (DL) is a subset of machine learning (ML) that brings opportunity for novel investigative strategies that can be harnessed to gain new insights into the genomic risk of people with epilepsy. DL is being harnessed to address limitations in accuracy of long-read sequencing technologies, which improve on short-read methods. Tools that predict the functional consequence of genetic variation can represent breaking ground in addressing critical knowledge gaps, while methods that integrate independent but complimentary data enhance the predictive power of genetic data. We provide an overview of these DL tools and discuss how they may be applied to the analysis of genetic data for epilepsy research.

Drug resistance in epilepsy

Drug resistance is estimated to affect about a third of individuals with epilepsy, but its prevalence differs in relation to the epilepsy syndrome, the cause of epilepsy, and other factors such as age of seizure onset and presence of associated neurological deficits. Although drug-resistant epilepsy is not synonymous with unresponsiveness to any drug treatment, the probability of achieving seizure freedom on a newly tried medication decreases with increasing number of previously failed treatments. After two appropriately used antiseizure medications have failed to control seizures, individuals should be referred whenever possible to a comprehensive epilepsy centre for diagnostic re-evaluation and targeted management. The feasibility of epilepsy surgery and other treatments, including those targeting the cause of epilepsy, should be considered early after diagnosis. Substantial evidence indicates that a delay in identifying an effective treatment can adversely affect ultimate outcome and carry an increased risk of cognitive disability, other comorbidities, and premature mortality. Research on mechanisms of drug resistance and novel therapeutics is progressing rapidly, and potentially improved treatments, including those targeting disease modification, are on the horizon.

Multi-omics Integration and Epilepsy: Towards a Better Understanding of Biological Mechanisms

The epilepsies are a group of complex neurological disorders characterised by recurrent seizures. Approximately 30% of patients fail to respond to anti-seizure medications, despite the recent introduction of many new drugs. The molecular processes underlying epilepsy development are not well understood and this knowledge gap impedes efforts to identify effective targets and develop novel therapies against epilepsy. Omics studies allow a comprehensive characterisation of a class of molecules. Omics-based biomarkers have led to clinically validated diagnostic and prognostic tests for personalised oncology, and more recently for non-cancer diseases. We believe that, in epilepsy, the full potential of multi-omics research is yet to be realised and we envisage that this review will serve as a guide to researchers planning to undertake omics-based mechanistic studies.

Pathophysiology of drug-resistant canine epilepsy

Drug resistance continues to be a major clinical problem in the therapeutic management of canine epilepsies with substantial implications for quality of life and survival times. Experimental and clinical data from human medicine provided evidence for relevant contributions of intrinsic severity of the disease as well as alterations in pharmacokinetics and -dynamics to failure to respond to antiseizure medications. In addition, several modulatory factors have been identified that can be associated with the level of therapeutic responses. Among others, the list of potential modulatory factors comprises genetic and epigenetic factors, inflammatory mediators, and metabolites. Regarding data from dogs, there are obvious gaps in knowledge when it comes to our understanding of the clinical patterns and the mechanisms of drug-resistant canine epilepsy. So far, seizure density and the occurrence of cluster seizures have been linked with a poor response to antiseizure medications. Moreover, evidence exists that the genetic background and alterations in epigenetic mechanisms might influence the efficacy of antiseizure medications in dogs with epilepsy. Further molecular, cellular, and network alterations that may affect intrinsic severity, pharmacokinetics, and -dynamics have been reported. However, the association with drug responsiveness has not yet been studied in detail. In summary, there is an urgent need to strengthen clinical and experimental research efforts exploring the mechanisms of resistance as well as their association with different etiologies, epilepsy types, and clinical courses.

Neurophysiology, Neuropsychology, and Epilepsy, in 2022: Hills We Have Climbed and Hills Ahead. Neurophysiology in epilepsy

Since the discovery of the human electroencephalogram (EEG), neurophysiology techniques have become indispensable tools in our armamentarium to localize epileptic seizures. New signal analysis techniques and the prospects of artificial intelligence and big data will offer unprecedented opportunities to further advance the field in the near future, ultimately resulting in improved quality of life for many patients with drug-resistant epilepsy. This article summarizes selected presentations from Day 1 of the two-day symposium "Neurophysiology, Neuropsychology, Epilepsy, 2022: Hills We Have Climbed and the Hills Ahead". Day 1 was dedicated to highlighting and honoring the work of Dr. Jean Gotman, a pioneer in EEG, intracranial EEG, simultaneous EEG/ functional magnetic resonance imaging, and signal analysis of epilepsy. The program focused on two main research directions of Dr. Gotman, and was dedicated to "High-frequency oscillations, a new biomarker of epilepsy" and "Probing the epileptic focus from inside and outside". All talks were presented by colleagues and former trainees of Dr. Gotman. The extended summaries provide an overview of historical and current work in the neurophysiology of epilepsy with emphasis on novel EEG biomarkers of epilepsy and source imaging and concluded with an outlook on the future of epilepsy research, and what is needed to bring the field to the next level.

Should substitution monotherapy or combination therapy be used after failure of the first antiseizure medication? Observations from a 30-year cohort study

OBJECTIVES

To assess the temporal trends in the use of second antiseizure (ASM) regimens and compare the efficacy of substitution monotherapy and combination therapy after failure of initial monotherapy in people with epilepsy.

METHODS

This was a longitudinal observational cohort study conducted at the Epilepsy Unit of the Western Infirmary in Glasgow, Scotland. We included patients who were newly treated for epilepsy with ASMs between July 1982, and October 2012. All patients were followed up for a minimum of 2 years. Seizure freedom was defined as no seizure for at least 1 year on unchanged medication at the last follow up.

RESULTS

During the study period, 498 patients were treated with a second ASM regimen after failure of the initial ASM monotherapy, of whom 346 (69%) were prescribed combination therapy and 152 (31%) were given substitution monotherapy. The proportion of patients receiving second regimen as combination therapy increased during the study period from 46% in first epoch (1985-1994) to 78% in the last (2005-2015) (RR = 1.66, 95% CI: 1.17-2.36, corrected-p = .010). Overall, 21% (104/498) of the patients achieved seizure freedom on the second ASM regimen, which was less than half of the seizure-free rate on the initial ASM monotherapy (45%, p < .001). Patients who received substitution monotherapy had similar seizure-free rate compared with those who received combination therapy (RR = 1.17, 95% CI: 0.81-1.69, p = .41). Individual ASMs used, either alone or in combination, had similar efficacy. However, the subgroup analysis was limited by small sample sizes.

SIGNIFICANCE

The choice of second regimen used based on clinical judgment was not associated with treatment outcome in patients whose initial monotherapy failed due to poor seizure control. Alternative approaches such as machine learning should be explored to aid individualized selection of the second ASM regimen.

DSCNN-LSTMs: A Lightweight and Efficient Model for Epilepsy Recognition

Epilepsy is the second most common disease of the nervous system. Because of its high disability rate and the long course of the disease, it is a worldwide medical problem and social public health problem. Therefore, the timely detection and treatment of epilepsy are very important. Currently, medical professionals use their own diagnostic experience to identify seizures by visual inspection of the electroencephalogram (EEG). Not only does it require a lot of time and effort, but the process is also very cumbersome. Machine learning-based methods have recently been proposed for epilepsy detection, which can help clinicians make rapid and correct diagnoses. However, these methods often require extracting the features of EEG signals before using the data. In addition, the selection of features often requires domain knowledge, and feature types also have a significant impact on the performance of the classifier. In this paper, a one-dimensional depthwise separable convolutional neural network and long short-term memory networks (1D DSCNN-LSTMs) model is proposed to identify epileptic seizures by autonomously extracting the features of raw EEG. On the UCI dataset, the performance of the proposed 1D DSCNN-LSTMs model is verified by cross-validation and time complexity comparison. Compared with other previous models, the experimental results show that the highest recognition rates of binary and quintuple classification are 99.57% and 81.30%, respectively. It can be concluded that the 1D DSCNN-LSTMs model proposed in this paper is an effective method to identify seizures based on EEG signals.

Genetics in parkinson's disease: From better disease understanding to machine learning based precision medicine

Parkinson's Disease (PD) is a neurodegenerative disorder with highly heterogeneous phenotypes. Accordingly, it has been challenging to robustly identify genetic factors associated with disease risk, prognosis and therapy response via genome-wide association studies (GWAS). In this review we first provide an overview of existing statistical methods to detect associations between genetic variants and the disease phenotypes in existing PD GWAS. Secondly, we discuss the potential of machine learning approaches to better quantify disease phenotypes and to move beyond disease understanding towards a better-personalized treatment of the disease.

Development and Validation of a Deep Learning Model for Predicting Treatment Response in Patients With Newly Diagnosed Epilepsy

Importance

Selection of antiseizure medications (ASMs) for epilepsy remains largely a trial-and-error approach. Under this approach, many patients have to endure sequential trials of ineffective treatments until the "right drugs" are prescribed.

Objective

To develop and validate a deep learning model using readily available clinical information to predict treatment success with the first ASM for individual patients.

Design, Setting, and Participants

This cohort study developed and validated a prognostic model. Patients were treated between 1982 and 2020. All patients were followed up for a minimum of 1 year or until failure of the first ASM. A total of 2404 adults with epilepsy newly treated at specialist clinics in Scotland, Malaysia, Australia, and China between 1982 and 2020 were considered for inclusion, of whom 606 (25.2%) were excluded from the final cohort because of missing information in 1 or more variables.

Exposures

One of 7 antiseizure medications.

Main Outcomes and Measures

With the use of the transformer model architecture on 16 clinical factors and ASM information, this cohort study first pooled all cohorts for model training and testing. The model was trained again using the largest cohort and externally validated on the other 4 cohorts. The area under the receiver operating characteristic curve (AUROC), weighted balanced accuracy, sensitivity, and specificity of the model were all assessed for predicting treatment success based on the optimal probability cutoff. Treatment success was defined as complete seizure freedom for the first year of treatment while taking the first ASM. Performance of the transformer model was compared with other machine learning models.

Results

The final pooled cohort included 1798 adults (54.5% female; median age, 34 years [IQR, 24-50 years]). The transformer model that was trained using the pooled cohort had an AUROC of 0.65 (95% CI, 0.63-0.67) and a weighted balanced accuracy of 0.62 (95% CI, 0.60-0.64) on the test set. The model that was trained using the largest cohort only had AUROCs ranging from 0.52 to 0.60 and a weighted balanced accuracy ranging from 0.51 to 0.62 in the external validation cohorts. Number of pretreatment seizures, presence of psychiatric disorders, electroencephalography, and brain imaging findings were the most important clinical variables for predicted outcomes in both models. The transformer model that was developed using the pooled cohort outperformed 2 of the 5 other models tested in terms of AUROC.

Conclusions and Relevance

In this cohort study, a deep learning model showed the feasibility of personalized prediction of response to ASMs based on clinical information. With improvement of performance, such as by incorporating genetic and imaging data, this model may potentially assist clinicians in selecting the right drug at the first trial.

Computerized application for epilepsy in China: Does the era of artificial intelligence comes?

Epilepsy, one of the most common neurological diseases in China, is notorious for its spontaneous, unprovoked and recurrent seizures. The etiology of epilepsy varies among individual patients, including congenital gene mutation, traumatic injury, infections, etc. This heterogeneity partly hampered the accurate diagnosis and choice of appropriate treatments. Encouragingly, great achievements have been achieved in computational science, making it become a key player in medical fields gradually and bringing new hope for rapid and accurate diagnosis as well as targeted therapies in epilepsy. Here, we historically review the advances of computerized applications in epilepsy-especially those tremendous findings achieved in China-for different purposes including seizure prediction, localization of epileptogenic zone, post-surgical prognosis, etc. Special attentions are paid to the great progress based on artificial intelligence (AI), which is more "sensitive", "smart" and "in-depth" than human capacities. At last, we give a comprehensive discussion about the disadvantages and limitations of current computerized applications for epilepsy and propose some future directions as further stepping stones to embrace "the era of AI" in epilepsy.

Deqi Sensation to Predict Acupuncture Effect on Functional Dyspepsia: A Machine Learning Study

Objectives

The aim of the study was to predict the effect of acupuncture for treating functional dyspepsia (FD) using the support vector machine (SVM) techniques based on initial deqi sensations of patients.

Methods

This retrospective study involved 90 FD patients who had received four weeks of acupuncture treatment. The support vector classification model was used to distinguish higher responders (patients with Symptom Index of Dyspepsia improvement score ≥ 2) from lower responders (patients with Symptom Index of Dyspepsia improvement score < 2). A support vector regression model was used to predict the change in the Symptom Index of Dyspepsia at the end of acupuncture treatment. Deqi sensations of patients in the first acupuncture treatment of a 20-session acupuncture intervention were defined as features and used to train models. Models were validated by 10-fold cross-validation and evaluated by accuracy, specificity, sensitivity, the area under the receive-operating curve, the coefficient of determination (R²), and the mean squared error.

Results

The two models could predict the efficacy of acupuncture successfully. These models had an accuracy of 0.84 in predicting acupuncture response, and an R² of 0.16 in the prediction of symptom improvements, respectively. The presence or absence of deqi sensation, the duration of deqi sensation, distention, and pain were finally selected as significant predicting features.

Conclusion

Based on the SVM algorithms and deqi sensation, the current study successfully predicted the acupuncture response as well as clinical symptom improvement in FD patients at the end of treatment. Our prediction models are expected to promote the clinical efficacy of acupuncture treatment for FD, reduce medical expenditures, and optimize the allocation of medical resources.

Moving the field forward: detection of epileptiform abnormalities on scalp electroencephalography using deep learning—clinical application perspectives

The application of deep learning approaches for the detection of interictal epileptiform discharges is a nascent field, with most studies published in the past 5 years. Although many recent models have been published demonstrating promising results, deficiencies in descriptions of data sets, unstandardized methods, variation in performance evaluation and lack of demonstrable generalizability have made it difficult for these algorithms to be compared and progress to clinical validity. A few recent publications have provided a detailed breakdown of data sets and relevant performance metrics to exemplify the potential of deep learning in epileptiform discharge detection. This review provides an overview of the field and equips computer and data scientists with a synopsis of EEG data sets, background and epileptiform variation, model evaluation parameters and an awareness of the performance metrics of high impact and interest to the trained clinical and neuroscientist EEG end user. The gold standard and inter-rater disagreements in defining epileptiform abnormalities remain a challenge in the field, and a hierarchical proposal for epileptiform discharge labelling options is recommended. Standardized descriptions of data sets and reporting metrics are a priority. Source code-sharing and accessibility to public EEG data sets will increase the rigour, quality and progress in the field and allow validation and real-world clinical translation.

The Neurogenetics Collection: emerging themes and future considerations for the field in Brain

Genomics has emerged over the last two decades as a fundamental approach to understanding the molecular basis of human diseases. This Collection brings together some recent articles published in Brain, selected to illustrate the impact of genomics on neurology and to highlight emerging themes in the neurogenetics space.

State-dependent effects of neural stimulation on brain function and cognition

Invasive and non-invasive brain stimulation methods are widely used in neuroscience to establish causal relationships between distinct brain regions and the sensory, cognitive and motor functions they subserve. When combined with concurrent brain imaging, such stimulation methods can reveal patterns of neuronal activity responsible for regulating simple and complex behaviours at the level of local circuits and across widespread networks. Understanding how fluctuations in physiological states and task demands might influence the effects of brain stimulation on neural activity and behaviour is at the heart of how we use these tools to understand cognition. Here we review the concept of such 'state-dependent' changes in brain activity in response to neural stimulation, and consider examples from research on altered states of consciousness (for example, sleep and anaesthesia) and from task-based manipulations of selective attention and working memory. We relate relevant findings from non-invasive methods used in humans to those obtained from direct electrical and optogenetic stimulation of neuronal ensembles in animal models. Given the widespread use of brain stimulation as a research tool in the laboratory and as a means of augmenting or restoring brain function, consideration of the influence of changing physiological and cognitive states is crucial for increasing the reliability of these interventions.

Deep Phenotyping on Chinese Electronic Health Records by Recognizing Linguistic Patterns of Phenotypic Narratives with a Sequence Motif Discovery Tool: Algorithm Development and Validation (Preprint)

Background

Phenotype information in electronic health records (EHRs) is mainly recorded in unstructured free text, which cannot be directly used for clinical research. EHR-based deep-phenotyping methods can structure phenotype information in EHRs with high fidelity, making it the focus of medical informatics. However, developing a deep-phenotyping method for non-English EHRs (ie, Chinese EHRs) is challenging. Although numerous EHR resources exist in China, fine-grained annotation data that are suitable for developing deep-phenotyping methods are limited. It is challenging to develop a deep-phenotyping method for Chinese EHRs in such a low-resource scenario.

Objective

In this study, we aimed to develop a deep-phenotyping method with good generalization ability for Chinese EHRs based on limited fine-grained annotation data.

Methods

The core of the methodology was to identify linguistic patterns of phenotype descriptions in Chinese EHRs with a sequence motif discovery tool and perform deep phenotyping of Chinese EHRs by recognizing linguistic patterns in free text. Specifically, 1000 Chinese EHRs were manually annotated based on a fine-grained information model, PhenoSSU (Semantic Structured Unit of Phenotypes). The annotation data set was randomly divided into a training set (n=700, 70%) and a testing set (n=300, 30%). The process for mining linguistic patterns was divided into three steps. First, free text in the training set was encoded as single-letter sequences (P: phenotype, A: attribute). Second, a biological sequence analysis tool—MEME (Multiple Expectation Maximums for Motif Elicitation)—was used to identify motifs in the single-letter sequences. Finally, the identified motifs were reduced to a series of regular expressions representing linguistic patterns of PhenoSSU instances in Chinese EHRs. Based on the discovered linguistic patterns, we developed a deep-phenotyping method for Chinese EHRs, including a deep learning–based method for named entity recognition and a pattern recognition–based method for attribute prediction.

Results

In total, 51 sequence motifs with statistical significance were mined from 700 Chinese EHRs in the training set and were combined into six regular expressions. It was found that these six regular expressions could be learned from a mean of 134 (SD 9.7) annotated EHRs in the training set. The deep-phenotyping algorithm for Chinese EHRs could recognize PhenoSSU instances with an overall accuracy of 0.844 on the test set. For the subtask of entity recognition, the algorithm achieved an F1 score of 0.898 with the Bidirectional Encoder Representations from Transformers–bidirectional long short-term memory and conditional random field model; for the subtask of attribute prediction, the algorithm achieved a weighted accuracy of 0.940 with the linguistic pattern–based method.

Conclusions

We developed a simple but effective strategy to perform deep phenotyping of Chinese EHRs with limited fine-grained annotation data. Our work will promote the second use of Chinese EHRs and give inspiration to other non–English-speaking countries.

EEG-Driven Prediction Model of Oxcarbazepine Treatment Outcomes in Patients With Newly-Diagnosed Focal Epilepsy

Objective: Antiseizure medicine (ASM) is the first choice for patients with epilepsy. The choice of ASM is determined by the type of epilepsy or epileptic syndrome, which may not be suitable for certain patients. This initial choice of a particular drug affects the long-term prognosis of patients, so it is critical to select the appropriate ASMs based on the individual characteristics of a patient at the early stage of the disease. The purpose of this study is to develop a personalized prediction model to predict the probability of achieving seizure control in patients with focal epilepsy, which will help in providing a more precise initial medication to patients.

Methods: Based on response to oxcarbazepine (OXC), enrolled patients were divided into two groups: seizure-free (52 patients), not seizure-free (NSF) (22 patients). We created models to predict patients' response to OXC monotherapy by combining Electroencephalogram (EEG) complexities and 15 clinical features. The prediction models were gradient boosting decision tree-Kolmogorov complexity (GBDT-KC) and gradient boosting decision tree-Lempel-Ziv complexity (GBDT-LZC). We also constructed two additional prediction models, support vector machine-Kolmogorov complexity (SVM-KC) and SVM-LZC, and these two models were compared with the GBDT models. The performance of the models was evaluated by calculating the accuracy, precision, recall, F1-score, sensitivity, specificity, and area under the curve (AUC) of these models.

Results: The mean accuracy, precision, recall, F1-score, sensitivity, specificity, AUC of GBDT-LZC model after five-fold cross-validation were 81%, 84%, 91%, 87%, 91%, 64%, 81%, respectively. The average accuracy, precision, recall, F1-score, sensitivity, specificity, AUC of GBDT-KC model with five-fold cross-validation were 82%, 84%, 92%, 88%, 83%, 92%, 83%, respectively. We used the rank of absolute weights to separately calculate the features that have the most significant impact on the classification of the two models.

Conclusion: (1) The GBDT-KC model has the potential to be used in the clinic to predict seizure-free with OXC monotherapy. (2). Electroencephalogram complexity, especially Kolmogorov complexity (KC) may be a potential biomarker in predicting the treatment efficacy of OXC in newly diagnosed patients with focal epilepsy.

Novel treatments in epilepsy guided by genetic diagnosis

In recent years, precision medicine has emerged as a new paradigm for improved and more individualized patient care. Its key objective is to provide the right treatment, to the right patient at the right time, by basing medical decisions on individual characteristics, including specific genetic biomarkers. In order to realize this objective researchers and physicians must first identify the underlying genetic cause; over the last 10 years, advances in genetics have made this possible for several monogenic epilepsies. Through next generation techniques, a precise genetic aetiology is attainable in 30-50% of genetic epilepsies beginning in the paediatric age. While committed in such search for novel genes carrying disease-causing variants, progress in the study of experimental models of epilepsy has also provided a better understanding of the mechanisms underlying the condition. Such advances are already being translated into improving care, management and treatment of some patients. Identification of a precise genetic aetiology can already direct physicians to prescribe treatments correcting specific metabolic defects, avoid antiseizure medicines that might aggravate functional consequences of the disease-causing variant or select the drugs that counteract the underlying, genetically determined, functional disturbance. Personalized, tailored treatments should not just focus on how to stop seizures but possibly prevent their onset and cure the disorder, often consisting of seizures and its comorbidities including cognitive, motor and behaviour deficiencies. This review discusses the therapeutic implications following a specific genetic diagnosis and the correlation between genetic findings, pathophysiological mechanisms and tailored seizure treatment, emphasizing the impact on current clinical practice.

New advances in pharmacoresistant epilepsy towards precise management-from prognosis to treatments

Epilepsy, one of the most severe neurological diseases, is characterized by abrupt recurrent seizures. Despite great progress in the development of antiseizure drugs (ASDs) based on diverse molecular targets, more than one third of epilepsy patients still show resistance to ASDs, a condition termed pharmacoresistant epilepsy. The management of pharmacoresistant epilepsy involves serious challenges. In the past decade, promising advances have been made in the use of interdisciplinary techniques involving biophysics, bioinformatics, biomaterials and biochemistry, which allow more precise prognosis and development of drug target for pharmacoresistant epilepsy. Notably, novel experimental tools such as viral vector gene delivery, optogenetics and chemogenetics have provided a framework for promising approaches to the precise treatment of pharmacoresistant epilepsy. In this review, historical achievements especially recent advances of the past decade in the prognosis and treatment of pharmacoresistant epilepsy from both clinical and laboratory settings are presented and summarized. We propose that the further development of novel experimental tools at cellular or molecular levels with both temporal and spatial precision are necessary to make improve the management and drug development for pharmacoresistant epilepsy in the clinical arena.

Revisiting Secondary Information Related to Pharmacogenetic Testing

Incidental or secondary findings have been a major part of the discussion of genomic medicine research and clinical applications. For pharmacogenetic (PGx) testing, secondary findings arise due to the pleiotropic effects of pharmacogenes, often related to their endogenous functions. Unlike the guidelines that have been developed for whole exome or genome sequencing applications for management of secondary findings (though slightly different from PGx testing in that these refer to detection of variants in multiple genes, some with clinical significance and actionability), no corresponding guidelines have been developed for PGx clinical laboratories. Nonetheless, patient and provider education will remain key components of any PGx testing program to minimize adverse responses related to secondary findings.

The pharmacological treatment of epilepsy: recent advances and future perspectives

The pharmacological armamentarium against epilepsy has expanded considerably over the last three decades, and currently includes over 30 different antiseizure medications. Despite this large armamentarium, about one third of people with epilepsy fail to achieve sustained seizure freedom with currently available medications. This sobering fact, however, is mitigated by evidence that clinical outcomes for many people with epilepsy have improved over the years. In particular, physicians now have unprecedented opportunities to tailor treatment choices to the characteristics of the individual, in order to maximize efficacy and tolerability. The present article discusses advances in the drug treatment of epilepsy in the last 5 years, focusing in particular on comparative effectiveness trials of second-generation drugs, the introduction of new pharmaceutical formulations for emergency use, and the results achieved with the newest medications. The article also includes a discussion of potential future developments, including those derived from advances in information technology, the development of novel precision treatments, the introduction of disease modifying agents, and the discovery of biomarkers to facilitate conduction of clinical trials as well as routine clinical management.