Identifying temporal patterns in patient disease trajectories using dynamic time warping: A population-based study

Group based trajectory modeling identifies distinct patterns of sympathetic hyperactivity following traumatic brain injury

Background Paroxysmal Sympathetic Hyperactivity (PSH) occurs with high prevalence among critically ill Traumatic Brain Injury (TBI) patients and is associated with worse outcomes. The PSH-Assessment Measure (PSH-AM) consists of a Clinical Features Scale (CFS) and a Diagnosis Likelihood Tool (DLT), intended to quantify the severity of sympathetically-mediated symptoms and likelihood that they are due to PSH, respectively, on a daily basis. Here, we aim to identify and explore the value of dynamic trends in the evolution of sympathetic hyperactivity following acute TBI using elements of the PSH-AM. Methods We performed an observational cohort study of 221 acute critically ill TBI patients for whom daily PSH-AM scores were calculated over the first 14 days of hospitalization. A principled group-based trajectory modeling approach using unsupervised K-means clustering was used to identify distinct patterns of CFS evolution within the cohort. We also evaluated the relationships between trajectory group membership and PSH diagnosis, as well as PSH DLT score, hospital discharge GCS, ICU and hospital length of stay, duration of mechanical ventilation, and mortality. Baseline clinical and demographic features predictive of trajectory group membership were analyzed using univariate screening and multivariate multinomial logistic regression. Results We identified four distinct trajectory groups. Trajectory group membership was significantly associated with clinical outcomes including PSH diagnosis and DLT score, ICU length of stay, and duration of mechanical ventilation. Baseline features independently predictive of trajectory group membership included age and post-resuscitation motor GCS. Conclusions This study adds to the sparse research characterizing the heterogeneous temporal trends of sympathetic nervous system activation during the acute phase following TBI. This may open avenues for early identification of at-risk patients to receive tailored interventions to limit secondary brain injury associated with autonomic dysfunction and thereby improve TBI patient outcomes.

Disease Trajectories from Healthcare Data: Methodologies, Key Results, and Future Perspectives

Disease trajectories, defined as sequential, directional disease associations, have become an intense research field driven by the availability of electronic population-wide healthcare data and sufficient computational power. Here, we provide an overview of disease trajectory studies with a focus on European work, including ontologies used as well as computational methodologies for the construction of disease trajectories. We also discuss different applications of disease trajectories from descriptive risk identification to disease progression, patient stratification, and personalized predictions using machine learning. We describe challenges and opportunities in the area that eventually will benefit from initiatives such as the European Health Data Space, which, with time, will make it possible to analyze data from cohorts comprising hundreds of millions of patients.

Unraveling progression subtypes in people with Huntington's disease

Background

Huntington's disease (HD) is a progressive neurodegenerative disease caused by a CAG trinucleotide expansion in the huntingtin gene. The length of the CAG repeat is inversely correlated with disease onset. HD is characterized by hyperkinetic movement disorder, psychiatric symptoms, and cognitive deficits, which greatly impact patient's quality of life. Despite this clear genetic course, high variability of HD patients' symptoms can be observed. Current clinical diagnosis of HD solely relies on the presence of motor signs, disregarding the other important aspects of the disease. By incorporating a broader approach that encompasses motor as well as non-motor aspects of HD, predictive, preventive, and personalized (3P) medicine can enhance diagnostic accuracy and improve patient care.

Methods

Multisymptom disease trajectories of HD patients collected from the Enroll-HD study were first aligned on a common disease timescale to account for heterogeneity in disease symptom onset and diagnosis. Following this, the aligned disease trajectories were clustered using the previously published Variational Deep Embedding with Recurrence (VaDER) algorithm and resulting progression subtypes were clinically characterized. Lastly, an AI/ML model was learned to predict the progression subtype from only first visit data or with data from additional follow-up visits.

Results

Results demonstrate two distinct subtypes, one large cluster (n = 7122) showing a relative stable disease progression and a second, smaller cluster (n = 411) showing a dramatically more progressive disease trajectory. Clinical characterization of the two subtypes correlates with CAG repeat length, as well as several neurobehavioral, psychiatric, and cognitive scores. In fact, cognitive impairment was found to be the major difference between the two subtypes. Additionally, a prognostic model shows the ability to predict HD subtypes from patients' first visit only.

Conclusion

In summary, this study aims towards the paradigm shift from reactive to preventive and personalized medicine by showing that non-motor symptoms are of vital importance for predicting and categorizing each patients' disease progression pattern, as cognitive decline is oftentimes more reflective of HD progression than its motor aspects. Considering these aspects while counseling and therapy definition will personalize each individuals' treatment. The ability to provide patients with an objective assessment of their disease progression and thus a perspective for their life with HD is the key to improving their quality of life. By conducting additional analysis on biological data from both subtypes, it is possible to gain a deeper understanding of these subtypes and uncover the underlying biological factors of the disease. This greatly aligns with the goal of shifting towards 3P medicine.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-024-00368-2.

Decoding Immuno-Competence: A Novel Analysis of Complete Blood Cell Count Data in COVID-19 Outcomes

BACKGROUND

While 'immuno-competence' is a well-known term, it lacks an operational definition. To address this omission, this study explored whether the temporal and structured data of the complete blood cell count (CBC) can rapidly estimate immuno-competence. To this end, one or more ratios that included data on all monocytes, lymphocytes and neutrophils were investigated.

MATERIALS AND METHODS

Longitudinal CBC data collected from 101 COVID-19 patients (291 observations) were analyzed. Dynamics were estimated with several approaches, which included non-structured (the classic CBC format) and structured data. Structured data were assessed as complex ratios that capture multicellular interactions among leukocytes. In comparing survivors with non-survivors, the hypothesis that immuno-competence may exhibit feedback-like (oscillatory or cyclic) responses was tested.

RESULTS

While non-structured data did not distinguish survivors from non-survivors, structured data revealed immunological and statistical differences between outcomes: while survivors exhibited oscillatory data patterns, non-survivors did not. In survivors, many variables (including IL-6, hemoglobin and several complex indicators) showed values above or below the levels observed on day 1 of the hospitalization period, displaying L-shaped data distributions (positive kurtosis). In contrast, non-survivors did not exhibit kurtosis. Three immunologically defined data subsets included only survivors. Because information was based on visual patterns generated in real time, this method can, potentially, provide information rapidly.

DISCUSSION

The hypothesis that immuno-competence expresses feedback-like loops when immunological data are structured was not rejected. This function seemed to be impaired in immuno-suppressed individuals. While this method rapidly informs, it is only a guide that, to be confirmed, requires additional tests. Despite this limitation, the fact that three protective (survival-associated) immunological data subsets were observed since day 1 supports many clinical decisions, including the early and personalized prognosis and identification of targets that immunomodulatory therapies could pursue. Because it extracts more information from the same data, structured data may replace the century-old format of the CBC.

Exploring long-term breast cancer survivors' care trajectories using dynamic time warping-based unsupervised clustering

OBJECTIVES

Long-term breast cancer survivors (BCS) constitute a complex group of patients, whose number is estimated to continue rising, such that, a dedicated long-term clinical follow-up is necessary.

MATERIALS AND METHODS

A dynamic time warping-based unsupervised clustering methodology is presented in this article for the identification of temporal patterns in the care trajectories of 6214 female BCS of a large longitudinal retrospective cohort of Spain. The extracted care-transition patterns are graphically represented using directed network diagrams with aggregated patient and time information. A control group consisting of 12 412 females without breast cancer is also used for comparison.

RESULTS

The use of radiology and hospital admission are explored as patterns of special interest. In the generated networks, a more intense and complex use of certain healthcare services (eg, radiology, outpatient care, hospital admission) is shown and quantified for the BCS. Higher mortality rates and numbers of comorbidities are observed in various transitions and compared with non-breast cancer. It is also demonstrated how a wealth of patient and time information can be revealed from individual service transitions.

DISCUSSION

The presented methodology permits the identification and descriptive visualization of temporal patterns of the usage of healthcare services by the BCS, that otherwise would remain hidden in the trajectories.

CONCLUSION

The results could provide the basis for better understanding the BCS' circulation through the health system, with a view to more efficiently predicting their forthcoming needs and thus designing more effective personalized survivorship care plans.

Unraveling cradle-to-grave disease trajectories from multilayer comorbidity networks

We aim to comprehensively identify typical life-spanning trajectories and critical events that impact patients' hospital utilization and mortality. We use a unique dataset containing 44 million records of almost all inpatient stays from 2003 to 2014 in Austria to investigate disease trajectories. We develop a new, multilayer disease network approach to quantitatively analyze how cooccurrences of two or more diagnoses form and evolve over the life course of patients. Nodes represent diagnoses in age groups of ten years; each age group makes up a layer of the comorbidity multilayer network. Inter-layer links encode a significant correlation between diagnoses (p < 0.001, relative risk > 1.5), while intra-layers links encode correlations between diagnoses across different age groups. We use an unsupervised clustering algorithm for detecting typical disease trajectories as overlapping clusters in the multilayer comorbidity network. We identify critical events in a patient's career as points where initially overlapping trajectories start to diverge towards different states. We identified 1260 distinct disease trajectories (618 for females, 642 for males) that on average contain 9 (IQR 2-6) different diagnoses that cover over up to 70 years (mean 23 years). We found 70 pairs of diverging trajectories that share some diagnoses at younger ages but develop into markedly different groups of diagnoses at older ages. The disease trajectory framework can help us to identify critical events as specific combinations of risk factors that put patients at high risk for different diagnoses decades later. Our findings enable a data-driven integration of personalized life-course perspectives into clinical decision-making.

Comparing Location Data From Smartphone and Dedicated Global Positioning System Devices: Implications for Epidemiologic Research

In this study, we compared location data from a dedicated Global Positioning System (GPS) device with location data from smartphones. Data from the Interventions, Equity, and Action in Cities Team (INTERACT) Study, a study examining the impact of urban-form changes on health in 4 Canadian cities (Victoria, Vancouver, Saskatoon, and Montreal), were used. A total of 337 participants contributed data collected for about 6 months from the Ethica Data smartphone application (Ethica Data Inc., Toronto, Ontario, Canada) and the SenseDoc dedicated GPS (MobySens Technologies Inc., Montreal, Quebec, Canada) during the period 2017-2019. Participants recorded an average total of 14,781 Ethica locations (standard deviation, 19,353) and 197,167 SenseDoc locations (standard deviation, 111,868). Dynamic time warping and cross-correlation were used to examine the spatial and temporal similarity of GPS points. Four activity-space measures derived from the smartphone app and the dedicated GPS device were compared. Analysis showed that cross-correlations were above 0.8 at the 125-m resolution for the survey and day levels and increased as cell size increased. At the day or survey level, there were only small differences between the activity-space measures. Based on our findings, we recommend dedicated GPS devices for studies where the exposure and the outcome are both measured at high frequency and when the analysis will not be aggregate. When the exposure and outcome are measured or will be aggregated to the day level, the dedicated GPS device and the smartphone app provide similar results.

Dementia risk analysis using temporal event modeling on a large real-world dataset

The objective of the study is to identify healthcare events leading to a diagnosis of dementia from a large real-world dataset. This study uses a data-driven approach to identify temporally ordered pairs and trajectories of healthcare codes in the electronic health record (EHR). This allows for discovery of novel temporal risk factors leading to an outcome of interest that may otherwise be unobvious. We identified several known (Down syndrome RR = 116.1, thiamine deficiency RR = 76.1, and Parkinson's disease RR = 41.1) and unknown (Brief psychotic disorder RR = 68.6, Toxic effect of metals RR = 40.4, and Schizoaffective disorders RR = 40.0) factors for a specific dementia diagnosis. The associations with the greatest risk for any dementia diagnosis were found to be primarily related to mental health (Brief psychotic disorder RR = 266.5, Dissociative and conversion disorders RR = 169.8), or neurologic conditions or procedures (Dystonia RR = 121.9, Lumbar Puncture RR = 119.0). Trajectory and clustering analysis identified factors related to cerebrovascular disorders, as well as diagnoses which increase the risk of toxic imbalances. The results of this study have the ability to provide valuable insights into potential patient progression towards dementia and improve recognition of patients at risk for developing dementia.

Time warping between main epidemic time series in epidemiological surveillance

The most common reported epidemic time series in epidemiological surveillance are the daily or weekly incidence of new cases, the hospital admission count, the ICU admission count, and the death toll, which played such a prominent role in the struggle to monitor the Covid-19 pandemic. We show that pairs of such curves are related to each other by a generalized renewal equation depending on a smooth time varying delay and a smooth ratio generalizing the reproduction number. Such a functional relation is also explored for pairs of simultaneous curves measuring the same indicator in two neighboring countries. Given two such simultaneous time series, we develop, based on a signal processing approach, an efficient numerical method for computing their time varying delay and ratio curves, and we verify that its results are consistent. Indeed, they experimentally verify symmetry and transitivity requirements and we also show, using realistic simulated data, that the method faithfully recovers time delays and ratios. We discuss several real examples where the method seems to display interpretable time delays and ratios. The proposed method generalizes and unifies many recent related attempts to take advantage of the plurality of these health data across regions or countries and time, providing a better understanding of the relationship between them. An implementation of the method is publicly available at the EpiInvert CRAN package.

A software package for efficient patient trajectory analysis applied to analyzing bladder cancer development

We present the Patient Trajectory Analysis Library (PTRA), a software package for explorative analysis of patient development. PTRA provides the tools for extracting statistically relevant trajectories from the medical event histories of a patient population. These trajectories can additionally be clustered for visual inspection and identifying key events in patient progression. The algorithms of PTRA are based on a statistical method developed previously by Jensen et al, but we contribute several modifications and extensions to enable the implementation of a practical tool. This includes a new clustering strategy, filter mechanisms for controlling analysis to specific cohorts and for controlling trajectory output, a parallel implementation that executes on a single server rather than a high-performance computing (HPC) cluster, etc. PTRA is furthermore open source and the code is organized as a framework so researchers can reuse it to analyze new data sets. We illustrate our tool by discussing trajectories extracted from the TriNetX Dataworks database for analyzing bladder cancer development. We show this experiment uncovers medically sound trajectories for bladder cancer.

Using Markov chains and temporal alignment to identify clinical patterns in Dementia

In the healthcare sector, resorting to big data and advanced analytics is a great advantage when dealing with complex groups of patients in terms of comorbidities, representing a significant step towards personalized targeting. In this work, we focus on understanding key features and clinical pathways of patients with multimorbidity suffering from Dementia. This disease can result from many heterogeneous factors, potentially becoming more prevalent as the population ages. We present a set of methods that allow us to identify medical appointment patterns within a cohort of 1924 patients followed from January 2007 to August 2021 in Hospital da Luz (Lisbon), and to stratify patients into subgroups that exhibit similar patterns of interaction. With Markov Chains, we are able to identify the most prevailing medical appointments attended by Dementia patients, as well as recurring transitions between these. To perform patient stratification, we applied AliClu, a temporal sequence alignment algorithm for clustering longitudinal clinical data, which allowed us to successfully identify patient subgroups with similar medical appointment activity. A feature analysis per cluster obtained allows the identification of distinct patterns and characteristics. This pipeline provides a tool to identify prevailing clinical pathways of medical appointments within the dataset, as well as the most common transitions between medical specialities within Dementia patients. This methodology, alongside demographic and clinical data, has the potential to provide early signalling of the most likely clinical pathways and serve as a support tool for health providers in deciding the best course of treatment, considering a patient as a whole.

Defining the distance between diseases using SNOMED CT embeddings

Characterizing disease relationships is essential to biomedical research to understand disease etiology and improve clinical decision-making. Measurements of distance between disease pairs enable valuable research tasks, such as subgrouping patients and identifying common time courses of disease onset. Distance metrics developed in prior work focused on smaller, targeted disease sets. Distance metrics covering all diseases have not yet been defined, which limits the applications to a broader disease spectrum. Our current study defines disease distances for all disease pairs within the International Classification of Diseases, version 10 (ICD-10), the diagnostic classification system universally used in electronic health records. Our proposed distance is computed based on a biomedical ontology, SNOMED CT (Systemized Nomenclature of Medicine, Clinical Terms), which can also be viewed as a structured knowledge graph. We compared the knowledge graph-based metric to three other distance metrics based on the hierarchical structure of ICD, clinical comorbidity, and genetic correlation, to evaluate how each may capture similar or unique aspects of disease relationships. We show that our knowledge graph-based distance metric captures known phenotypic, clinical, and molecular characteristics at a finer granularity than the other three. With the continued growth of using electronic health records data for research, we believe that our distance metric will play an important role in subgrouping patients for precision health, and enabling individualized disease prevention and treatments.

12-year evolution of multimorbidity patterns among older adults based on Hidden Markov Models

BACKGROUND

The evolution of multimorbidity patterns during aging is still an under-researched area. We lack evidence concerning the time spent by older adults within one same multimorbidity pattern, and their transitional probability across different patterns when further chronic diseases arise. The aim of this study is to fill this gap by exploring multimorbidity patterns across decades of age in older adults, and longitudinal dynamics among these patterns.

METHODS

Longitudinal study based on the Swedish National study on Aging and Care in Kungsholmen (SNAC-K) on adults ≥60 years (N=3,363). Hidden Markov Models were applied to model the temporal evolution of both multimorbidity patterns and individuals' transitions over a 12-year follow-up.

FINDINGS

Within the study population (mean age 76.1 years, 66.6% female), 87.2% had ≥2 chronic conditions at baseline. Four longitudinal multimorbidity patterns were identified for each decade. Individuals in all decades showed the shortest permanence time in an Unspecific pattern lacking any overrepresented diseases (range: 4.6-10.9 years), but the pattern with the longest permanence time varied by age. Sexagenarians remained longest in the Psychiatric-endocrine and sensorial pattern (15.4 years); septuagenarians in the Neuro-vascular and skin-sensorial pattern (11.0 years); and octogenarians and beyond in the Neuro-sensorial pattern (8.9 years). Transition probabilities varied across decades, sexagenarians showing the highest levels of stability.

INTERPRETATION

Our findings highlight the dynamism and heterogeneity underlying multimorbidity by quantifying the varying permanence times and transition probabilities across patterns in different decades. With increasing age, older adults experience decreasing stability and progressively shorter permanence time within one same multimorbidity pattern.

Data-driven comorbidity analysis of 100 common disorders reveals patient subgroups with differing mortality risks and laboratory correlates

The populational heterogeneity of a disease, in part due to comorbidity, poses several complexities. Individual comorbidity profiles, on the other hand, contain useful information to refine phenotyping, prognostication, and risk assessment, and they provide clues to underlying biology. Nevertheless, the spectrum and the implications of the diagnosis profiles remain largely uncharted. Here we mapped comorbidity patterns in 100 common diseases using 4-year retrospective data from 526,779 patients and developed an online tool to visualize the results. Our analysis exposed disease-specific patient subgroups with distinctive diagnosis patterns, survival functions, and laboratory correlates. Computational modeling and real-world data shed light on the structure, variation, and relevance of populational comorbidity patterns, paving the way for improved diagnostics, risk assessment, and individualization of care. Variation in outcomes and biological correlates of a disease emphasizes the importance of evaluating the generalizability of current treatment strategies, as well as considering the limitations that selective inclusion criteria pose on clinical trials.

Data-driven identification of heart failure disease states and progression pathways using electronic health records

Heart failure (HF) is a leading cause of morbidity, healthcare costs, and mortality. Guideline based segmentation of HF into distinct subtypes is coarse and unlikely to reflect the heterogeneity of etiologies and disease trajectories of patients. While analyses of electronic health records show promise in expanding our understanding of complex syndromes like HF in an evidence-driven way, limitations in data quality have presented challenges for large-scale EHR-based insight generation and decision-making. We present a hypothesis-free approach to generating real-world characteristics and progression patterns of HF. Patient disease state snapshots are extracted from the complaints mentioned in unstructured clinical notes. Typical disease states are generated by clustering and characterized in terms of their distinguishing features, temporal relationships, and risk of important clinical events. Our analysis generates a comprehensive "disease phenome" of real-world patients computed from large, noisy, secondary-use EHR datasets created in a routine clinical setting.

Data structuring may prevent ambiguity and improve personalized medical prognosis

Topics expected to influence personalized medicine (PM), where medical decisions, practices, and treatments are tailored to the individual patient, are reviewed. Lack of discrimination due to different biological conditions that express similar values of numerical variables (ambiguity) is regarded to be a major potential barrier for PM. This material explores possible causes and sources of ambiguity and offers suggestions for mitigating the impacts of uncertainties. Three causes of ambiguity are identified: (1) delayed adoption of innovations, (2) inadequate emphases, and (3) inadequate processes used when new medical practices are developed and validated. One example of the first problem is the relative lack of medical research on "compositional data" -the type that characterizes leukocyte data. This omission results in erroneous use of data abundantly utilized in medicine, such as the blood cell differential. Emphasis on data output ‒not biomedical interpretation that facilitates the use of clinical data‒ exemplifies the second type of problems. Reliance on tools generated in other fields (but not validated within biomedical contexts) describes the last limitation. Because reductionism is associated with these problems, non-reductionist alternatives are reviewed as potential remedies. Data structuring (converting data into information) is considered a key element that may promote PM. To illustrate a process that includes data-information-knowledge and decision-making, previously published data on COVID-19 are utilized. It is suggested that ambiguity may be prevented or ameliorated. Provided that validations are grounded on biomedical knowledge, approaches that describe certain criteria - such as non-overlapping data intervals of patients that experience different outcomes, immunologically interpretable data, and distinct graphic patterns - can inform, at personalized bases, earlier and/or with fewer observations.

The Use of a Network Analysis to Identify Associations and Temporal Patterns Among Non-communicable Diseases in Japan Based on a Large Medical Claims Database

BACKGROUND

Reducing the considerable non-communicable disease (NCD) burden in the aging Japanese population depends on better understanding of the comorbid and temporal relationships between different NCDs.

OBJECTIVE

We aimed to identify associations between NCDs and temporal patterns of NCDs in Japan using data from a large medical claims database.

METHODS

The study used three-digit International Classification of Diseases, Tenth Revision codes for NCDs for employees and their dependents included in the MinaCare database, which covers the period since 2010. Associations between pairs of NCDs were assessed by calculating risk ratios. The calculated risk ratios were used to create a network of closely associated NCDs (risk ratio > 15, statistically significant) and to assess temporal patterns of NCD diagnoses (risk ratio ≥ 5). The Infomap algorithm was used to identify clusters of diseases for different sex and age strata.

RESULTS

The analysis included 4,200,254 individuals (age < 65 years: 98%). Many of the temporal associations and patterns of the diseases of interest identified in this study were previously known. Regarding the diseases of interest, these associations can be classified as comorbidities, early manifestations initially diagnosed as something else, diseases attributable to or that cause the disease of interest, or caused by pharmacological treatment. International Classification of Diseases, Tenth Revision chapters that were most associated with other chapters included L Diseases of the skin and subcutaneous tissue. In the age-stratified and gender-stratified networks, clusters with the highest numbers of International Classification of Diseases, Tenth Revision codes included I Diseases of the circulatory system and F Mental and behavioral disorders.

CONCLUSIONS

Our findings reinforce established associations between NCDs and underline the importance of comprehensive NCD care.

Network-medicine framework for studying disease trajectories in U.S. veterans

A better understanding of the sequential and temporal aspects in which diseases occur in patient's lives is essential for developing improved intervention strategies that reduce burden and increase the quality of health services. Here we present a network-based framework to study disease relationships using Electronic Health Records from > 9 million patients in the United States Veterans Health Administration (VHA) system. We create the Temporal Disease Network, which maps the sequential aspects of disease co-occurrence among patients and demonstrate that network properties reflect clinical aspects of the respective diseases. We use the Temporal Disease Network to identify disease groups that reflect patterns of disease co-occurrence and the flow of patients among diagnoses. Finally, we define a strategy for the identification of trajectories that lead from one disease to another. The framework presented here has the potential to offer new insights for disease treatment and prevention in large health care systems.

Systems redox biology in health and disease

Living organisms need to be able to cope with environmental challenges and other stressors and mount adequate responses that are as varied as the spectrum of those challenges. Understanding how the multi-layered biological stress responses become integrated across and between different levels of organization within an organism can provide a different perspective on the nature and inter-relationship of complex systems in health and disease. We here compare two concepts which have been very influential in stress research: Selye's 'General Adaptation Syndrome' and Sies's 'Oxidative Stress' paradigm. We show that both can be embraced within a more general framework of 'change and response'. The 'Reactive Species Interactome' allows each of these to be considered as distinct but complementary aspects of the same system, representative of roles at different levels of organization within a functional hierarchy. The versatile chemistry of sulfur - exemplified by hydrogen sulfide, glutathione and proteinous cysteine thiols - enriched by its interactions with reactive oxygen, nitrogen and sulfur species, would seem to sit at the heart of the 'Redox Code' and underpin the ability of complex organisms to cope with stress.

Biomarkers and Disease Trajectories Influencing Women's Health: Results from the UK Biobank Cohort

Women's health is important for society. Despite the known biological and sex-related factors influencing the risk of diseases among women, the network of the full spectrum of diseases in women is underexplored. This study aimed to systematically examine the women-specific temporal pattern (trajectory) of the disease network, including the role of baseline physical examination indexes, and blood and urine biomarkers. In the UK Biobank study, 502,650 participants entered the cohort from 2006 to 2010, and were followed up until 2019 to identify disease incidence via linkage to the patient registers. For those diseases with increased risk among women, conditional logistic regression models were used to estimate odds ratios (ORs), and the binomial test of direction was further used to build disease trajectories. Among 301 diseases, 82 diseases in women had ORs > 1.2 and p < 0.00017 when compared to men, involving mainly diseases in the endocrine, skeletal and digestive systems. Diseases with the highest ORs included breast diseases, osteoporosis, hyperthyroidism, and deformity of the toes. The biomarker and disease trajectories suggested estradiol as a risk predictor for breast cancer, while a high percentage of reticulocyte, body mass index and waist circumference were associated with an increased risk of upper-limb neuropathy. In addition, the risk of cholelithiasis was increased in women diagnosed with dyspepsia and diaphragmatic hernia. In conclusion, women are at an increased risk of endocrine, skeletal and digestive diseases. The biomarker and disease trajectories in women suggested key pathways to a range of adverse outcomes downstream, which may shed light on promising targets for early detection and prevention of these diseases.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-022-00054-1.

Trajectories: a framework for detecting temporal clinical event sequences from health data standardized to the Observational Medical Outcomes Partnership (OMOP) Common Data Model

Objective

To develop a framework for identifying temporal clinical event trajectories from Observational Medical Outcomes Partnership-formatted observational healthcare data.

Materials and Methods

A 4-step framework based on significant temporal event pair detection is described and implemented as an open-source R package. It is used on a population-based Estonian dataset to first replicate a large Danish population-based study and second, to conduct a disease trajectory detection study for type 2 diabetes patients in the Estonian and Dutch databases as an example.

Results

As a proof of concept, we apply the methods in the Estonian database and provide a detailed breakdown of our findings. All Estonian population-based event pairs are shown. We compare the event pairs identified from Estonia to Danish and Dutch data and discuss the causes of the differences. The overlap in the results was only 2.4%, which highlights the need for running similar studies in different populations.

Conclusions

For the first time, there is a complete software package for detecting disease trajectories in health data.

Learning the impact of acute and chronic diseases on forecasting neonatal encephalopathy

OBJECTIVE

There is a wide range of risk factors predisposing to the onset of neonatal encephalopathy (NE), including maternal antepartum/intrapartum comorbidities or events. However, few studies have investigated the difference in the impact of acute and chronic diseases on forecasting NE, which could assist clinicians in choosing the best course of action to prevent NE or reduce its severity and complications. In this study, we aimed to engineer features based on acute and chronic diseases and assess the differences of the impact of acute and chronic diseases on NE prediction using machine learning models.

MATERIALS AND METHODS

We used ten years of electronic health records of mothers from a large academic medical center to develop three types of features: chronic disease, recurrence of an acute disease, and temporal relationships between acute diseases. Two types of NE prediction models, based on acute and chronic diseases, respectively, were trained with feature selection. We further compared the prediction performance of the models with two state-of-the-art NE forecasting models. The machine learning models ranked the three types of engineered features based on their contributions to the NE prediction.

RESULTS

The NE model trained on acute disease features showed significantly higher AUC than the model relying on chronic disease features (AUC difference: 0.161, p-value < 0.001). The NE model trained on both acute and chronic disease features achieved the highest average AUC (0.889), with a significant improvement over the best existing model (0.854) with p = 0.0129. Recurrence of "known or suspected fetal abnormality affecting management of mother (655)" was assigned the highest weights in predicting NE.

CONCLUSIONS

Machine learning models based on the three types of engineered features significantly improve NE prediction. Our results specifically suggest that acute disease-associated features play a more important role in predicting NE.

Dynamic time warp analysis of individual symptom trajectories in depressed patients treated with electroconvulsive therapy

BACKGROUND

Although electroconvulsive therapy (ECT) effectively improves severity scores of depression, its effects on its individual symptoms has scarcely been studied. We aimed to study which depressive symptom trajectories dynamically cluster together in individuals as well as groups of patients during ECT using Dynamic Time Warp (DTW) analysis.

METHODS

We analysed the standardized weekly scores on the 25-item abbreviated version of the Comprehensive Psychopathological Rating Scale (CPRS) in depressed patients before and during their first six weeks of ECT treatment. DTW analysis was used to analyse the (dis)similarity of time series of items scores at the patient level (300 'DTW distances' per patient) as well as on the group level. Hierarchical cluster, network, and Distatis analyses yielded symptom dimensions.

RESULTS

We included 133 patients, 64.7% female, with an average age of 60.4 years (SD 15.1). Individual DTW distance matrices and networks revealed marked differences in hierarchical and network clusters among patients. Based on cluster analyses of the aggregated matrices, four symptom clusters emerged. In patients who reached remission, the average DTW distance between their symptoms was significantly smaller than non-remitters, reflecting denser symptom networks in remitters than non-remitters (p=0.04).

LIMITATIONS

The assessments were done only weekly during the first six weeks of ECT treatment. The use of individual items of the abbreviated CPRS may have led to measurement error as well as floor and ceiling effects.

CONCLUSION

DTW offers an efficient new approach to analyse symptom trajectories within individuals as well as groups of patients, aiding personalized medicine of psychopathology.

Hospital healthcare flows: A longitudinal clustering approach of acute coronary syndrome in women over 45 years

Acute coronary syndrome (ACS) in women is a growing public health issue and a death leading cause. We explored whether the hospital healthcare trajectory was characterizable using a longitudinal clustering approach in women with ACS. From the 2009-2014 French nationwide hospital database, we extracted spatio-temporal patterns in ACS patient trajectories, by replacing the spatiality by their hospitalization cause. We used these patterns to characterize hospital healthcare flows in a visualization tool. We clustered these trajectories with kmlShape to identify time gap and tariff profiles. ACS hospital healthcare flows have three key categories: Angina pectoris, Myocardial Infarction or Ischemia. Elderly flows were more complex. Time gap profiles showed that readmissions were closer together as time goes by. Tariff profiles were different according to age and initial event. Our approach might be applied to monitoring other chronic diseases. Further work is needed to integrate these results into a medical decision-making tool.

Self-rated health trajectories: A dynamic time warp analysis

Self-rated health (SRH), individuals’ overall perception of their health, is a key predictor of health events. To target disease prevention efforts, it is important to understand how SRH develops over time. The goal of this short communication is to find prototypic SRH trajectories by applying dynamic time warping, a time series comparison technique initially developed for speech recognition. Revealing prototypic SRH trajectories can help direct disease prevention efforts towards trajectories that are more likely to result in adverse health events. Based on data from a Dutch representative sample of 2,154 individuals, our dynamic time warp analysis suggests that Dutch individuals do not typically show a steady growth or decline in SRH. Instead, we identified four relatively stable SRH trajectories that differed in average SRH. One of these trajectories is a path of consistent low SRH.

Multimorbid disease trajectories for people with periodontitis

AIM

Periodontitis is a multifactorial condition linked to increased risk of systemic diseases. This study aimed to identify disease trajectories of people with periodontitis using the process mining technique as a heuristic approach.

MATERIALS AND METHODS

A total of 188,863 participants from the UK Biobank cohort were included. Self-reported oral health indicators (bleeding gums, painful gums, loose teeth) were surrogates for periodontitis at baseline. Systemic disease diagnoses and dates formed the process mining event log. Relative risk (RR) of systemic diseases, disease trajectories, and Cox proportional hazard ratio models for mortality were compared to age- and sex-matched controls who did not report a history of periodontitis.

RESULTS

Participants with loose teeth had shorter median time to most systemic diseases, and crude RR was increased for several diseases including cardiovascular disease (crude RR: 1.15, 95% CI: 1.03-1.28), hypertension (crude RR: 1.14, 95% CI: 1.05-1.24), and depression (crude RR: 1.33, 95% CI: 1.09-1.61). Participants with loose teeth had increased RR for 20 disease trajectories, though these were not significant after adjustments. Participants with bleeding/painful gums had similar disease trajectories as those of matched controls.

CONCLUSIONS

Self-reported periodontitis may be associated with early and frequent multimorbidity development, though further evidence is required to confirm this hypothesis. People with periodontitis should be informed of the risks of disease progression and be targeted in prevention initiatives.

Data-driven identification of complex disease phenotypes

Disease interaction in multimorbid patients is relevant to treatment and prognosis, yet poorly understood. In the present work, we combine approaches from network science, machine learning and computational phenotyping to assess interactions between two or more diseases in a transparent way across the full diagnostic spectrum. We demonstrate that health states of hospitalized patients can be better characterized by including higher-order features capturing interactions between more than two diseases. We identify a meaningful set of higher-order diagnosis features that account for synergistic disease interactions in a population-wide (N = 9 M) medical claims dataset. We construct a generalized disease network where (higher-order) diagnosis features are linked if they predict similar diagnoses across the whole diagnostic spectrum. The fact that specific diagnoses are generally represented multiple times in the network allows for the identification of putatively different disease phenotypes that may reflect different disease aetiologies. At the example of obesity, we demonstrate the purely data-driven detection of two complex phenotypes of obesity. As indicated by a matched comparison between patients having these phenotypes, we show that these phenotypes show specific characteristics of what has been controversially discussed in the medical literature as metabolically healthy and unhealthy obesity, respectively. The findings also suggest that metabolically healthy patients show some progression towards more unhealthy obesity over time, a finding that is consistent with longitudinal studies indicating a transient nature of metabolically healthy obesity. The disease network is available for exploration at https://disease.network/.

Outcome-Oriented Deep Temporal Phenotyping of Disease Progression

Chronic diseases evolve slowly throughout a patient's lifetime creating heterogeneous progression patterns that make clinical outcomes remarkably varied across individual patients. A tool capable of identifying temporal phenotypes based on the patients different progression patterns and clinical outcomes would allow clinicians to better forecast disease progression by recognizing a group of similar past patients, and to better design treatment guidelines that are tailored to specific phenotypes. To build such a tool, we propose a deep learning approach, which we refer to as outcome-oriented deep temporal phenotyping (ODTP), to identify temporal phenotypes of disease progression considering what type of clinical outcomes will occur and when based on the longitudinal observations. More specifically, we model clinical outcomes throughout a patient's longitudinal observations via time-to-event (TTE) processes whose conditional intensity functions are estimated as non-linear functions using a recurrent neural network. Temporal phenotyping of disease progression is carried out by our novel loss function that is specifically designed to learn discrete latent representations that best characterize the underlying TTE processes. The key insight here is that learning such discrete representations groups progression patterns considering the similarity in expected clinical outcomes, and thus naturally provides outcome-oriented temporal phenotypes. We demonstrate the power of ODTP by applying it to a real-world heterogeneous cohort of 11 779 stage III breast cancer patients from the U.K. National Cancer Registration and Analysis Service. The experiments show that ODTP identifies temporal phenotypes that are strongly associated with the future clinical outcomes and achieves significant gain on the homogeneity and heterogeneity measures over existing methods. Furthermore, we are able to identify the key driving factors that lead to transitions between phenotypes which can be translated into actionable information to support better clinical decision-making.

Multimorbidity clusters among long-term breast cancer survivors in Spain: Results of the SURBCAN study

The disease management of long-term breast cancer survivors (BCS) is hampered by the scarce knowledge of multimorbidity patterns. The aim of our study was to identify multimorbidity clusters among long-term BCS and assess their impact on mortality and health services use. We conducted a retrospective study using electronic health records of 6512 BCS from Spain surviving at least 5 years. Hierarchical cluster analysis was used to identify groups of similar patients based on their chronic diagnoses, which were assessed using the Clinical Classifications Software. As a result, multimorbidity clusters were obtained, clinically defined and named according to the comorbidities with higher observed/expected prevalence ratios. Multivariable Cox and negative binomial regression models were fitted to estimate overall mortality risk and probability of contacting health services according to the clusters identified. 83.7% of BCS presented multimorbidity, essential hypertension (34.5%) and obesity and other metabolic disorders (27.4%) being the most prevalent chronic diseases at the beginning of follow-up. Five multimorbidity clusters were identified: C1-unspecific (29.9%), C2-metabolic and neurodegenerative (28.3%), C3-anxiety and fractures (9.7%), C4-musculoskeletal and cardiovascular (9.6%) and C5-thyroid disorders (5.3%). All clusters except C5-thyroid disorders were associated with higher mortality compared to BCS without comorbidities. The risk of mortality in C4 was increased by 64% (adjusted hazard ratio 1.64, 95% confidence interval 1.52-2.07). Stratified analysis showed an increased risk of death among BCS with 5 to 10 years of survival in all clusters. These results help to identify subgroups of long-term BCS with specific needs and mortality risks and to guide BCS clinical practice regarding multimorbidity.

Machine learning for modeling the progression of Alzheimer disease dementia using clinical data: a systematic literature review

OBJECTIVE

Alzheimer disease (AD) is the most common cause of dementia, a syndrome characterized by cognitive impairment severe enough to interfere with activities of daily life. We aimed to conduct a systematic literature review (SLR) of studies that applied machine learning (ML) methods to clinical data derived from electronic health records in order to model risk for progression of AD dementia.

MATERIALS AND METHODS

We searched for articles published between January 1, 2010, and May 31, 2020, in PubMed, Scopus, ScienceDirect, IEEE Explore Digital Library, Association for Computing Machinery Digital Library, and arXiv. We used predefined criteria to select relevant articles and summarized them according to key components of ML analysis such as data characteristics, computational algorithms, and research focus.

RESULTS

There has been a considerable rise over the past 5 years in the number of research papers using ML-based analysis for AD dementia modeling. We reviewed 64 relevant articles in our SLR. The results suggest that majority of existing research has focused on predicting progression of AD dementia using publicly available datasets containing both neuroimaging and clinical data (neurobehavioral status exam scores, patient demographics, neuroimaging data, and laboratory test values).

DISCUSSION

Identifying individuals at risk for progression of AD dementia could potentially help to personalize disease management to plan future care. Clinical data consisting of both structured data tables and clinical notes can be effectively used in ML-based approaches to model risk for AD dementia progression. Data sharing and reproducibility of results can enhance the impact, adaptation, and generalizability of this research.

A system-level analysis of patient disease trajectories based on clinical, phenotypic and molecular similarities

MOTIVATION

Incorporating the temporal dimension into multimorbidity studies has shown to be crucial for achieving a better understanding of the disease associations. Furthermore, due to the multifactorial nature of human disease, exploring disease associations from different perspectives can provide a holistic view to support the study of their aetiology.

RESULTS

In this work, a temporal systems-medicine approach is proposed for identifying time-dependent multimorbidity patterns from patient disease trajectories, by integrating data from electronic health records with genetic and phenotypic information. Specifically, the disease trajectories are clustered using an unsupervised algorithm based on dynamic time warping and three disease similarity metrics: clinical, genetic and phenotypic. An evaluation method is also presented for quantitatively assessing, in the different disease spaces, both the cluster homogeneity and the respective similarities between the associated diseases within individual trajectories. The latter can facilitate exploring the origin(s) in the identified disease patterns. The proposed integrative methodology can be applied to any longitudinal cohort and disease of interest. In this article, prostate cancer is selected as a use case of medical interest to demonstrate, for the first time, the identification of temporal disease multimorbidities in different disease spaces.

AVAILABILITY AND IMPLEMENTATION

https://gitlab.com/agiannoula/diseasetrajectories.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Predicting morbidity by local similarities in multi-scale patient trajectories

Patient Trajectories (PTs) are a method of representing the temporal evolution of patients. They can include information from different sources and be used in socio-medical or clinical domains. PTs have generally been used to generate and study the most common trajectories in, for instance, the development of a disease. On the other hand, healthcare predictive models generally rely on static snapshots of patient information. Only a few works about prediction in healthcare have been found that use PTs, and therefore benefit from their temporal dimension. All of them, however, have used PTs created from single-source information. Therefore, the use of longitudinal multi-scale data to build PTs and use them to obtain predictions about health conditions is yet to be explored. Our hypothesis is that local similarities on small chunks of PTs can identify similar patients concerning their future morbidities. The objectives of this work are (1) to develop a methodology to identify local similarities between PTs before the occurrence of morbidities to predict these on new query individuals; and (2) to validate this methodology on risk prediction of cardiovascular diseases (CVD) occurrence in patients with diabetes. We have proposed a novel formal definition of PTs based on sequences of longitudinal multi-scale data. Moreover, a dynamic programming methodology to identify local alignments on PTs for predicting future morbidities is proposed. Both the proposed methodology for PT definition and the alignment algorithm are generic to be applied on any clinical domain. We validated this solution for predicting CVD in patients with diabetes and we achieved a precision of 0.33, a recall of 0.72 and a specificity of 0.38. Therefore, the proposed solution in the diabetes use case can result of utmost utility to secondary screening.

Analysis of Health Trajectories Leading to Adverse Opioid-Related Events

Identifying patient risk factors leading to adverse opioid-related events (AOEs) may enable targeted risk-based interventions, uncover potential causal mechanisms, and enhance prognosis. In this article, we aim to discover patient diagnosis, procedure, and medication event trajectories associated with AOEs using large-scale data mining methods. The individual temporally preceding factors associated with the highest relative risk (RR) for AOEs were opioid withdrawal therapy agents, toxic encephalopathy, problems related to housing and economic circumstances, and unspecified viral hepatitis, with RR of 33.4, 26.1, 19.9, and 18.7, respectively. Patient cohorts with a socioeconomic or mental health code had a larger RR for over 75% of all identified trajectories compared to the average population. By analyzing health trajectories leading to AOEs, we discover novel, temporally-connected combinations of diagnoses and health service events that significantly increase risk of AOEs, including natural histories marked by socioeconomic and mental health diagnoses.

Decompression of Multimorbidity Along the Disease Trajectories of Diabetes Mellitus Patients

Multimorbidity, the presence of two or more diseases in a patient, is maybe the greatest health challenge for the aging populations of many high-income countries. One of the main drivers of multimorbidity is diabetes mellitus (DM) due to its large number of risk factors and complications. Yet, we currently have very limited understanding of how to quantify multimorbidity beyond a simple counting of diseases and thereby inform prevention and intervention strategies tailored to the needs of elderly DM patients. Here, we conceptualize multimorbidity as typical temporal progression patterns of multiple diseases, so-called trajectories, and develop a framework to perform a matched and sex-specific comparison between DM and non-diabetic patients. We find that these disease trajectories can be organized into a multi-level hierarchy in which DM patients progress from relatively healthy states with low mortality to high-mortality states characterized by cardiovascular diseases, chronic lower respiratory diseases, renal failure, and different combinations thereof. The same disease trajectories can be observed in non-diabetic patients, however, we find that DM patients typically progress at much higher rates along their trajectories. Comparing male and female DM patients, we find a general tendency that females progress faster toward high multimorbidity states than males, in particular along trajectories that involve obesity. Males, on the other hand, appear to progress faster in trajectories that combine heart diseases with cerebrovascular diseases. Our results show that prevention and efficient management of DM are key to achieve a compression of morbidity into higher patient ages. Multidisciplinary efforts involving clinicians as well as experts in machine learning and data visualization are needed to better understand the identified disease trajectories and thereby contribute to solving the current multimorbidity crisis in healthcare.

Noise-tolerant similarity search in temporal medical data

Temporal medical data are increasingly integrated into the development of data-driven methods to deliver better healthcare. Searching such data for patterns can improve the detection of disease cases and facilitate the design of preemptive interventions. For example, specific temporal patterns could be used to recognize low-prevalence diseases, which are often under-diagnosed. However, searching these patterns in temporal medical data is challenging, as the data are often noisy, complex, and large in scale. In this work, we propose an effective and efficient solution to search for patients who exhibit conditions that resemble the input query. In our solution, we propose a similarity notion based on the Longest Common Subsequence (LCSS), which is used to measure the similarity between the query and the patient's temporal medical data and to ensure robustness against noise in the data. Our solution adopts locality sensitive hashing techniques to address the high dimensionality of medical data, by embedding the recorded clinical events (e.g., medications and diagnosis codes) into compact signatures. To perform pattern search in large EHR datasets, we propose a filtering approach based on tandem patterns, which effectively identifies candidate matches while discarding irrelevant data. The evaluations conducted using a real-world dataset demonstrate that our solution is highly accurate while significantly accelerating the similarity search.

Latent Class Trajectory Modeling of 2-Component Disease Activity Score in 28 Joints Identifies Multiple Rheumatoid Arthritis Phenotypes of Response to Biologic Disease-Modifying Antirheumatic Drugs

OBJECTIVE

To determine whether using a reweighted disease activity score that better reflects joint synovitis, i.e., the 2-component Disease Activity Score in 28 joints (DAS28) (based on swollen joint count and C-reactive protein level), produces more clinically relevant treatment outcome trajectories compared to the standard 4-component DAS28.

METHODS

Latent class mixed modeling of response to biologic treatment was applied to 2,991 rheumatoid arthritis (RA) patients in whom treatment with a biologic disease-modifying antirheumatic drug was being initiated within the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate cohort, using both 4-component and 2-component DAS28 scores as outcome measures. Patient groups with similar trajectories were compared in terms of pretreatment baseline characteristics (including disability and comorbidities) and follow-up characteristics (including antidrug antibody events, adherence to treatments, and blood drug levels). We compared the trajectories obtained using the 4- and 2-component scores to determine which characteristics were better captured by each.

RESULTS

Using the 4-component DAS28, we identified 3 trajectory groups, which is consistent with previous findings. We showed that the 4-component DAS28 captures information relating to depression. Using the 2-component DAS28, 7 trajectory groups were identified; among them, distinct groups of nonresponders had a higher incidence of respiratory comorbidities and a higher proportion of antidrug antibody events. We also identified a group of patients for whom the 2-component DAS28 scores remained relatively low; this group included a high percentage of patients who were nonadherent to treatment. This highlights the utility of both the 4- and 2-component DAS28 for monitoring different components of disease activity.

CONCLUSION

Here we show that the 2-component modified DAS28 defines important biologic and clinical phenotypes associated with treatment outcome in RA and characterizes important underlying response mechanisms to biologic drugs.

Untangling the complexity of multimorbidity with machine learning

The prevalence of multimorbidity has been increasing in recent years, posing a major burden for health care delivery and service. Understanding its determinants and impact is proving to be a challenge yet it offers new opportunities for research to go beyond the study of diseases in isolation. In this paper, we review how the field of machine learning provides many tools for addressing research challenges in multimorbidity. We highlight recent advances in promising methods such as matrix factorisation, deep learning, and topological data analysis and how these can take multimorbidity research beyond cross-sectional, expert-driven or confirmatory approaches to gain a better understanding of evolving patterns of multimorbidity. We discuss the challenges and opportunities of machine learning to identify likely causal links between previously poorly understood disease associations while giving an estimate of the uncertainty on such associations. We finally summarise some of the challenges for wider clinical adoption of machine learning research tools and propose some solutions.

Identifying disease trajectories with predicate information from a knowledge graph

BACKGROUND

Knowledge graphs can represent the contents of biomedical literature and databases as subject-predicate-object triples, thereby enabling comprehensive analyses that identify e.g. relationships between diseases. Some diseases are often diagnosed in patients in specific temporal sequences, which are referred to as disease trajectories. Here, we determine whether a sequence of two diseases forms a trajectory by leveraging the predicate information from paths between (disease) proteins in a knowledge graph. Furthermore, we determine the added value of directional information of predicates for this task. To do so, we create four feature sets, based on two methods for representing indirect paths, and both with and without directional information of predicates (i.e., which protein is considered subject and which object). The added value of the directional information of predicates is quantified by comparing the classification performance of the feature sets that include or exclude it.

RESULTS

Our method achieved a maximum area under the ROC curve of 89.8% and 74.5% when evaluated with two different reference sets. Use of directional information of predicates significantly improved performance by 6.5 and 2.0 percentage points respectively.

CONCLUSIONS

Our work demonstrates that predicates between proteins can be used to identify disease trajectories. Using the directional information of predicates significantly improved performance over not using this information.

Subphenotyping depression using machine learning and electronic health records

Objective

To identify depression subphenotypes from Electronic Health Records (EHRs) using machine learning methods, and analyze their characteristics with respect to patient demographics, comorbidities, and medications.

Materials and Methods

Using EHRs from the INSIGHT Clinical Research Network (CRN) database, multiple machine learning (ML) algorithms were applied to analyze 11 275 patients with depression to discern depression subphenotypes with distinct characteristics.

Results

Using the computational approaches, we derived three depression subphenotypes: Phenotype_A (n = 2791; 31.35%) included patients who were the oldest (mean (SD) age, 72.55 (14.93) years), had the most comorbidities, and took the most medications. The most common comorbidities in this cluster of patients were hyperlipidemia, hypertension, and diabetes. Phenotype_B (mean (SD) age, 68.44 (19.09) years) was the largest cluster (n = 4687; 52.65%), and included patients suffering from moderate loss of body function. Asthma, fibromyalgia, and Chronic Pain and Fatigue (CPF) were common comorbidities in this subphenotype. Phenotype_C (n = 1452; 16.31%) included patients who were younger (mean (SD) age, 63.47 (18.81) years), had the fewest comorbidities, and took fewer medications. Anxiety and tobacco use were common comorbidities in this subphenotype.

Conclusion

Computationally deriving depression subtypes can provide meaningful insights and improve understanding of depression as a heterogeneous disorder. Further investigation is needed to assess the utility of these derived phenotypes to inform clinical trial design and interpretation in routine patient care.

Toolkit to Compute Time-Based Elixhauser Comorbidity Indices and Extension to Common Data Models

Objectives

The time-dependent study of comorbidities provides insight into disease progression and trajectory. We hypothesize that understanding longitudinal disease characteristics can lead to more timely intervention and improve clinical outcomes. As a first step, we developed an efficient and easy-to-install toolkit, the Time-based Elixhauser Comorbidity Index (TECI), which pre-calculates time-based Elixhauser comorbidities and can be extended to common data models (CDMs).

Methods

A Structured Query Language (SQL)-based toolkit, TECI, was built to pre-calculate time-specific Elixhauser comorbidity indices using data from a clinical data repository (CDR). Then it was extended to the Informatics for Integrating Biology and the Bedside (I2B2) and Observational Medical Outcomes Partnership (OMOP) CDMs.

Results

At the University of Arkansas for Medical Sciences (UAMS), the TECI toolkit was successfully installed to compute the indices from CDR data, and the scores were integrated into the I2B2 and OMOP CDMs. Comorbidity scores calculated by TECI were validated against: scores available in the 2015 quarter 1–3 Nationwide Readmissions Database (NRD) and scores calculated using the comorbidities using a previously validated algorithm on the 2015 quarter 4 NRD. Furthermore, TECI identified 18,846 UAMS patients that had changes in comorbidity scores over time (year 2013 to 2019). Comorbidities for a random sample of patients were independently reviewed, and in all cases, the results were found to be 100% accurate.

Conclusions

TECI facilitates the study of comorbidities within a time-dependent context, allowing better understanding of disease associations and trajectories, which has the potential to improve clinical outcomes.

Non-Linear Template-Based Approach for the Study of Locomotion

The automatic detection of gait events (i.e., Initial Contact (IC) and Final Contact (FC)) is crucial for the characterisation of gait from Inertial Measurements Units. In this article, we present a method for detecting steps (i.e., IC and FC) from signals of gait sequences of individuals recorded with a gyrometer. The proposed approach combines the use of a dictionary of templates and a Dynamic Time Warping (DTW) measure of fit to retrieve these templates into input signals. Several strategies for choosing and learning the adequate templates from annotated data are also described. The method is tested on thirteen healthy subjects and compared to gold standard. Depending of the template choice, the proposed algorithm achieves average errors from 0.01 to 0.03 s for the detection of IC, FC and step duration. Results demonstrate that the use of DTW allows achieving these performances with only one single template. DTW is a convenient tool to perform pattern recognition on gait gyrometer signals. This study paves the way for new step detection methods: it shows that using one single template associated with non-linear deformations may be sufficient to model the gait of healthy subjects.

High-risk multimorbidity patterns on the road to cardiovascular mortality

BACKGROUND

Multimorbidity, the co-occurrence of two or more diseases in one patient, is a frequent phenomenon. Understanding how different diseases condition each other over the lifetime of a patient could significantly contribute to personalised prevention efforts. However, most of our current knowledge on the long-term development of the health of patients (their disease trajectories) is either confined to narrow time spans or specific (sets of) diseases. Here, we aim to identify decisive events that potentially determine the future disease progression of patients.

METHODS

Health states of patients are described by algorithmically identified multimorbidity patterns (groups of included or excluded diseases) in a population-wide analysis of 9,000,000 patient histories of hospital diagnoses observed over 17 years. Over time, patients might acquire new diagnoses that change their health state; they describe a disease trajectory. We measure the age- and sex-specific risks for patients that they will acquire certain sets of diseases in the future depending on their current health state.

RESULTS

In the present analysis, the population is described by a set of 132 different multimorbidity patterns. For elderly patients, we find 3 groups of multimorbidity patterns associated with low (yearly in-hospital mortality of 0.2-0.3%), medium (0.3-1%) and high in-hospital mortality (2-11%). We identify combinations of diseases that significantly increase the risk to reach the high-mortality health states in later life. For instance, in men (women) aged 50-59 diagnosed with diabetes and hypertension, the risk for moving into the high-mortality region within 1 year is increased by the factor of 1.96 ± 0.11 (2.60 ± 0.18) compared with all patients of the same age and sex, respectively, and by the factor of 2.09 ± 0.12 (3.04 ± 0.18) if additionally diagnosed with metabolic disorders.

CONCLUSIONS

Our approach can be used both to forecast future disease burdens, as well as to identify the critical events in the careers of patients which strongly determine their disease progression, therefore constituting targets for efficient prevention measures. We show that the risk for cardiovascular diseases increases significantly more in females than in males when diagnosed with diabetes, hypertension and metabolic disorders.

Evaluating global and local sequence alignment methods for comparing patient medical records

Background

Sequence alignment is a way of arranging sequences (e.g., DNA, RNA, protein, natural language, financial data, or medical events) to identify the relatedness between two or more sequences and regions of similarity. For Electronic Health Records (EHR) data, sequence alignment helps to identify patients of similar disease trajectory for more relevant and precise prognosis, diagnosis and treatment of patients.

Methods

We tested two cutting-edge global sequence alignment methods, namely dynamic time warping (DTW) and Needleman-Wunsch algorithm (NWA), together with their local modifications, DTW for Local alignment (DTWL) and Smith-Waterman algorithm (SWA), for aligning patient medical records. We also used 4 sets of synthetic patient medical records generated from a large real-world EHR database as gold standard data, to objectively evaluate these sequence alignment algorithms.

Results

For global sequence alignments, 47 out of 80 DTW alignments and 11 out of 80 NWA alignments had superior similarity scores than reference alignments while the rest 33 DTW alignments and 69 NWA alignments had the same similarity scores as reference alignments. Forty-six out of 80 DTW alignments had better similarity scores than NWA alignments with the rest 34 cases having the equal similarity scores from both algorithms. For local sequence alignments, 70 out of 80 DTWL alignments and 68 out of 80 SWA alignments had larger coverage and higher similarity scores than reference alignments while the rest DTWL alignments and SWA alignments received the same coverage and similarity scores as reference alignments. Six out of 80 DTWL alignments showed larger coverage and higher similarity scores than SWA alignments. Thirty DTWL alignments had the equal coverage but better similarity scores than SWA. DTWL and SWA received the equal coverage and similarity scores for the rest 44 cases.

Conclusions

DTW, NWA, DTWL and SWA outperformed the reference alignments. DTW (or DTWL) seems to align better than NWA (or SWA) by inserting new daily events and identifying more similarities between patient medical records. The evaluation results could provide valuable information on the strengths and weakness of these sequence alignment methods for future development of sequence alignment methods and patient similarity-based studies.

Disease trajectories and mortality among women diagnosed with breast cancer

Purpose

Breast cancer is a common disease with a relatively good prognosis. Therefore, understanding the spectrum of diseases and mortality among breast cancer patients is important, though currently incomplete. We systematically examined the incidence and mortality of all diseases following a breast cancer diagnosis, as well as the sequential association of disease occurrences (trajectories).

Methods

In this national cohort study, 57,501 breast cancer patients (2001–2011) were compared to 564,703 matched women from the general Swedish population and followed until 2012. The matching criteria included year of birth, county of residence, and socioeconomic status. Based on information from the Swedish Patient and Cause of Death Registries, hazard ratios (HR) were estimated for disease incidence and mortality. Conditional logistic regression models were used to identify disease trajectories among breast cancer patients.

Results

Among 225 diseases, 45 had HRs > 1.5 and p < 0.0002 when comparing breast cancer patients with the general population. Diseases with highest HRs included lymphedema, radiodermatitis, and neutropenia, which are side effects of surgery, radiotherapy, and chemotherapy. Other than breast cancer, the only significantly increased cause of death was other solid cancers (HR = 1.16, 95% CI = 1.08–1.24). Two main groups of disease trajectories were identified, which suggest menopausal disorders as indicators for other solid cancers, and both neutropenia and dorsalgia as diseases and symptoms preceding death due to breast cancer.

Conclusions

While an increased incidence of other diseases was found among breast cancer patients, increased mortality was only due to other solid cancers. Preventing death due to breast cancer should be a priority to prolong life in breast cancer patients, but closer surveillance of other solid cancers is also needed.

Electronic supplementary material

The online version of this article (10.1186/s13058-019-1181-5) contains supplementary material, which is available to authorized users.

Next Generation Networks: Featuring the Potential Role of Emerging Applications in Translational Oncology

Nowadays, networks are pervasively used as examples of models suitable to mathematically represent and visualize the complexity of systems associated with many diseases, including cancer. In the cancer context, the concept of network entropy has guided many studies focused on comparing equilibrium to disequilibrium (i.e., perturbed) conditions. Since these conditions reflect both structural and dynamic properties of network interaction maps, the derived topological characterizations offer precious support to conduct cancer inference. Recent innovative directions have emerged in network medicine addressing especially experimental omics approaches integrated with a variety of other data, from molecular to clinical and also electronic records, bioimaging etc. This work considers a few theoretically relevant concepts likely to impact the future of applications in personalized/precision/translational oncology. The focus goes to specific properties of networks that are still not commonly utilized or studied in the oncological domain, and they are: controllability, synchronization and symmetry. The examples here provided take inspiration from the consideration of metastatic processes, especially their progression through stages and their hallmark characteristics. Casting these processes into computational frameworks and identifying network states with specific modular configurations may be extremely useful to interpret or even understand dysregulation patterns underlying cancer, and associated events (onset, progression) and disease phenotypes.

Geometrical Information Flow Regulated by Time Lengths: An Initial Approach

The article analyzes Bernoulli's binary sequences in the representation of empirical events about water usage and continuous expenditure systems. The main purpose is to identify among variables that constitute water resources consumption at public schools, the link between consumption and expenditures oscillations. It was obtained a theoretical model of how oscillations patterns are originated and how time lengths have an important role over expenditures oscillations ergodicity and non-ergodicity.

Risk and temporal order of disease diagnosis of comorbidities in patients with COPD: a population health perspective

Introduction

Comorbidities in patients with chronic obstructive pulmonary disease (COPD) generate a major burden on healthcare. Identification of cost-effective strategies aiming at preventing and enhancing management of comorbid conditions in patients with COPD requires deeper knowledge on epidemiological patterns and on shared biological pathways explaining co-occurrence of diseases.

Methods

The study assesses the co-occurrence of several chronic conditions in patients with COPD using two different datasets: Catalan Healthcare Surveillance System (CHSS) (ES, 1.4 million registries) and Medicare (USA, 13 million registries). Temporal order of disease diagnosis was analysed in the CHSS dataset.

Results

The results demonstrate higher prevalence of most of the diseases, as comorbid conditions, in elderly (>65) patients with COPD compared with non-COPD subjects, an effect observed in both CHSS and Medicare datasets. Analysis of temporal order of disease diagnosis showed that comorbid conditions in elderly patients with COPD tend to appear after the diagnosis of the obstructive disease, rather than before it.

Conclusion

The results provide a population health perspective of the comorbidity challenge in patients with COPD, indicating the increased risk of developing comorbid conditions in these patients. The research reinforces the need for novel approaches in the prevention and management of comorbidities in patients with COPD to effectively reduce the overall burden of the disease on these patients.