Sequential Pattern Mining to Predict Medical In-Hospital Mortality from Administrative Data: Application to Acute Coronary Syndrome.
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SUBMITTER: Pinaire J
PROVIDER: S-EPMC8172301 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundCurrent readmission models use administrative data supplemented with clinical information. However, the majority of these result in poor predictive performance (area under the curve (AUC)<0.70).ObjectiveTo develop an administrative claim-based algorithm to predict 30-day readmission using standardized billing codes and basic admission characteristics available before discharge.Materials and methodsThe algorithm works by exploiting high-dimensional information in administrative claims data and automatically selecting empirical risk factors. We applied the algorithm to index admissions in two types of hospitalized patient: (1) medical patients and (2) patients with chronic pancreatitis (CP). We trained the models on 26,091 medical admissions and 3218 CP admissions from The Johns Hopkins Hospital (a tertiary research medical center) and tested them on 16,194 medical admissions and 706 CP admissions from Johns Hopkins Bayview Medical Center (a hospital that serves a more general patient population), and vice versa. Performance metrics included AUC, sensitivity, specificity, positive predictive values, negative predictive values, and F-measure.ResultsFrom a pool of up to 5665 International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM) diagnoses, 599 ICD-9-CM procedures, and 1815 Current Procedural Terminology codes observed, the algorithm learned a model consisting of 18 attributes from the medical patient cohort and five attributes from the CP cohort. Within-site and across-site validations had an AUC?0.75 for the medical patient cohort and an AUC?0.65 for the CP cohort.ConclusionsWe have created an algorithm that is widely applicable to various patient cohorts and portable across institutions. The algorithm performed similarly to state-of-the-art readmission models that require clinical data.
| S-EPMC3932470 | biostudies-literature
Project description:Sequential pattern mining (SPM) has been applied in many fields. However, traditional SPM neglects the pattern repetition in sequence. To solve this problem, gap constraint SPM was proposed and can avoid finding too many useless patterns. Nonoverlapping SPM, as a branch of gap constraint SPM, means that any two occurrences cannot use the same sequence letter in the same position as the occurrences. Nonoverlapping SPM can make a balance between efficiency and completeness. The frequent patterns discovered by existing methods normally contain redundant patterns. To reduce redundant patterns and improve the mining performance, this paper adopts the closed pattern mining strategy and proposes a complete algorithm, named Nettree for Nonoverlapping Closed Sequential Pattern (NetNCSP) based on the Nettree structure. NetNCSP is equipped with two key steps, support calculation and closeness determination. A backtracking strategy is employed to calculate the nonoverlapping support of a pattern on the corresponding Nettree, which reduces the time complexity. This paper also proposes three kinds of pruning strategies, inheriting, predicting, and determining. These pruning strategies are able to find the redundant patterns effectively since the strategies can predict the frequency and closeness of the patterns before the generation of the candidate patterns. Experimental results show that NetNCSP is not only more efficient but can also discover more closed patterns with good compressibility. Furtherly, in biological experiments NetNCSP mines the closed patterns in SARS-CoV-2 and SARS viruses. The results show that the two viruses are of similar pattern composition with different combinations.
| S-EPMC7118609 | biostudies-literature
Project description:Nonoverlapping sequential pattern mining, as a kind of repetitive sequential pattern mining with gap constraints, can find more valuable patterns. Traditional algorithms focused on finding all frequent patterns and found lots of redundant short patterns. However, it not only reduces the mining efficiency, but also increases the difficulty in obtaining the demand information. To reduce the frequent patterns and retain its expression ability, this paper focuses on the Nonoverlapping Maximal Sequential Pattern (NMSP) mining which refers to finding frequent patterns whose super-patterns are infrequent. In this paper, we propose an effective mining algorithm, Nettree for NMSP mining (NetNMSP), which has three key steps: calculating the support, generating the candidate patterns, and determining NMSPs. To efficiently calculate the support, NetNMSP employs the backtracking strategy to obtain a nonoverlapping occurrence from the leftmost leaf to its root with the leftmost parent node method in a Nettree. To reduce the candidate patterns, NetNMSP generates candidate patterns by the pattern join strategy. Furthermore, to determine NMSPs, NetNMSP adopts the screening method. Experiments on biological sequence datasets verify that not only does NetNMSP outperform the state-of-the-arts algorithms, but also NMSP mining has better compression performance than closed pattern mining. On sales datasets, we validate that our algorithm guarantees the best scalability on large scale datasets. Moreover, we mine NMSPs and frequent patterns in SARS-CoV-1, SARS-CoV-2 and MERS-CoV. The results show that the three viruses are similar in the short patterns but different in the long patterns. More importantly, NMSP mining is easier to find the differences between the virus sequences.
| S-EPMC8743106 | biostudies-literature
Project description:BackgroundThe use of knowledge models facilitates information retrieval, knowledge base development, and therefore supports new knowledge discovery that ultimately enables decision support applications. Most existing works have employed machine learning techniques to construct a knowledge base. However, they often suffer from low precision in extracting entity and relationships. In this paper, we described a data-driven sublanguage pattern mining method that can be used to create a knowledge model. We combined natural language processing (NLP) and semantic network analysis in our model generation pipeline.MethodsAs a use case of our pipeline, we utilized data from an open source imaging case repository, Radiopaedia.org , to generate a knowledge model that represents the contents of medical imaging reports. We extracted entities and relationships using the Stanford part-of-speech parser and the "Subject:Relationship:Object" syntactic data schema. The identified noun phrases were tagged with the Unified Medical Language System (UMLS) semantic types. An evaluation was done on a dataset comprised of 83 image notes from four data sources.ResultsA semantic type network was built based on the co-occurrence of 135 UMLS semantic types in 23,410 medical image reports. By regrouping the semantic types and generalizing the semantic network, we created a knowledge model that contains 14 semantic categories. Our knowledge model was able to cover 98% of the content in the evaluation corpus and revealed 97% of the relationships. Machine annotation achieved a precision of 87%, recall of 79%, and F-score of 82%.ConclusionThe results indicated that our pipeline was able to produce a comprehensive content-based knowledge model that could represent context from various sources in the same domain.
| S-EPMC6035419 | biostudies-literature
Project description:BackgroundMortality prediction models generally require clinical data or are derived from information coded at discharge, limiting adjustment for presenting severity of illness in observational studies using administrative data.ObjectivesTo develop and validate a mortality prediction model using administrative data available in the first 2 hospital days.Research designAfter dividing the dataset into derivation and validation sets, we created a hierarchical generalized linear mortality model that included patient demographics, comorbidities, medications, therapies, and diagnostic tests administered in the first 2 hospital days. We then applied the model to the validation set.SubjectsPatients aged ? 18 years admitted with pneumonia between July 2007 and June 2010 to 347 hospitals in Premier, Inc.'s Perspective database.MeasuresIn hospital mortality.ResultsThe derivation cohort included 200,870 patients and the validation cohort had 50,037. Mortality was 7.2%. In the multivariable model, 3 demographic factors, 25 comorbidities, 41 medications, 7 diagnostic tests, and 9 treatments were associated with mortality. Factors that were most strongly associated with mortality included receipt of vasopressors, non-invasive ventilation, and bicarbonate. The model had a c-statistic of 0.85 in both cohorts. In the validation cohort, deciles of predicted risk ranged from 0.3% to 34.3% with observed risk over the same deciles from 0.1% to 33.7%.ConclusionsA mortality model based on detailed administrative data available in the first 2 hospital days had good discrimination and calibration. The model compares favorably to clinically based prediction models and may be useful in observational studies when clinical data are not available.
| S-EPMC3909106 | biostudies-literature
Project description:BACKGROUND: Identifying a regulatory module (RM), a bi-set of co-regulated genes and co-regulating conditions (or samples), has been an important challenge in functional genomics and bioinformatics. Given a microarray gene-expression matrix, biclustering has been the most common method for extracting RMs. Among biclustering methods, order-preserving biclustering by a sequential pattern mining technique has native advantage over the conventional biclustering approaches since it preserves the order of genes (or conditions) according to the magnitude of the expression value. However, previous sequential pattern mining-based biclustering has several weak points in that they can easily be computationally intractable in the real-size of microarray data and sensitive to inherent noise in the expression value. RESULTS: In this paper, we propose a novel sequential pattern mining algorithm that is scalable in the size of microarray data and robust with respect to noise. When applied to the microarray data of yeast, the proposed algorithm successfully found long order-preserving patterns, which are biologically significant but cannot be found in randomly shuffled data. The resulting patterns are well enriched to known annotations and are consistent with known biological knowledge. Furthermore, RMs as well as inter-module relations were inferred from the biologically significant patterns. CONCLUSIONS: Our approach for identifying RMs could be valuable for systematically revealing the mechanism of gene regulation at a genome-wide level.
| S-EPMC3333188 | biostudies-literature
Project description:Phylogenetic tree is essential to understand evolution and it is usually constructed through multiple sequence alignment, which suffers from heavy computational burdens and requires sophisticated parameter tuning. Recently, alignment free methods based on k-mer profiles or common substrings provide alternative ways to construct phylogenetic trees. However, most of these methods ignore the global similarities between sequences or some specific valuable features, e.g., frequent patterns overall datasets. To make further improvement, we propose an alignment free algorithm based on sequential pattern mining, where each sequence is converted into a binary representation of sequential patterns among sequences. The phylogenetic tree is further constructed via clustering distance matrix which is calculated from pattern vectors. To increase accuracy for highly divergent sequences, we consider pattern weight and filtering redundancy sub-patterns. Both simulated and real data demonstrates our method outperform other alignment free methods, especially for large sequence set with low similarity.
| S-EPMC6410268 | biostudies-literature
Project description:ObjectiveThis study aimed to develop and validate a claims-based, machine learning algorithm to predict clinical outcomes across both medical and surgical patient populations.MethodsThis retrospective, observational cohort study, used a random 5% sample of 770,777 fee-for-service Medicare beneficiaries with an inpatient hospitalization between 2009-2011. The machine learning algorithms tested included: support vector machine, random forest, multilayer perceptron, extreme gradient boosted tree, and logistic regression. The extreme gradient boosted tree algorithm outperformed the alternatives and was the machine learning method used for the final risk model. Primary outcome was 30-day mortality. Secondary outcomes were: rehospitalization, and any of 23 adverse clinical events occurring within 30 days of the index admission date.ResultsThe machine learning algorithm performance was evaluated by both the area under the receiver operating curve (AUROC) and Brier Score. The risk model demonstrated high performance for prediction of: 30-day mortality (AUROC = 0.88; Brier Score = 0.06), and 17 of the 23 adverse events (AUROC range: 0.80-0.86; Brier Score range: 0.01-0.05). The risk model demonstrated moderate performance for prediction of: rehospitalization within 30 days (AUROC = 0.73; Brier Score: = 0.07) and six of the 23 adverse events (AUROC range: 0.74-0.79; Brier Score range: 0.01-0.02). The machine learning risk model performed comparably on a second, independent validation dataset, confirming that the risk model was not overfit.Conclusions and relevanceWe have developed and validated a robust, claims-based, machine learning risk model that is applicable to both medical and surgical patient populations and demonstrates comparable predictive accuracy to existing risk models.
| S-EPMC8174683 | biostudies-literature
Project description:Given a set of sequences comprised of time-ordered events, sequential pattern mining is useful to identify frequent subsequences from different sequences or within the same sequence. However, in sport, these techniques cannot determine the importance of particular patterns of play to good or bad outcomes, which is often of greater interest to coaches and performance analysts. In this study, we apply a recently proposed supervised sequential pattern mining algorithm called safe pattern pruning (SPP) to 490 labelled event sequences representing passages of play from one rugby team's matches in the 2018 Japan Top League season. We obtain patterns that are the most discriminative between scoring and non-scoring outcomes from both the team's and opposition teams' perspectives using SPP, and compare these with the most frequent patterns obtained with well-known unsupervised sequential pattern mining algorithms when applied to subsets of the original dataset, split on the label. From our obtained results, line breaks, successful line-outs, regained kicks in play, repeated phase-breakdown play, and failed exit plays by the opposition team were found to be the patterns that discriminated most between the team scoring and not scoring. Opposition team line breaks, errors made by the team, opposition team line-outs, and repeated phase-breakdown play by the opposition team were found to be the patterns that discriminated most between the opposition team scoring and not scoring. It was also found that, probably because of the supervised nature and pruning/safe-screening mechanisms of SPP, compared to the patterns obtained by the unsupervised methods, those obtained by SPP were more sophisticated in terms of containing a greater variety of events, and when interpreted, the SPP-obtained patterns would also be more useful for coaches and performance analysts.
| S-EPMC8460049 | biostudies-literature
Project description:BACKGROUND: Identification of protein interacting sites is an important task in computational molecular biology. As more and more protein sequences are deposited without available structural information, it is strongly desirable to predict protein binding regions by their sequences alone. This paper presents a pattern mining approach to tackle this problem. It is observed that a functional region of protein structures usually consists of several peptide segments linked with large wildcard regions. Thus, the proposed mining technology considers large irregular gaps when growing patterns, in order to find the residues that are simultaneously conserved but largely separated on the sequences. A derived pattern is called a cluster-like pattern since the discovered conserved residues are always grouped into several blocks, which each corresponds to a local conserved region on the protein sequence. RESULTS: The experiments conducted in this work demonstrate that the derived long patterns automatically discover the important residues that form one or several hot regions of protein-protein interactions. The methodology is evaluated by conducting experiments on the web server MAGIIC-PRO based on a well known benchmark containing 220 protein chains from 72 distinct complexes. Among the tested 218 proteins, there are 900 sequential blocks discovered, 4.25 blocks per protein chain on average. About 92% of the derived blocks are observed to be clustered in space with at least one of the other blocks, and about 66% of the blocks are found to be near the interface of protein-protein interactions. It is summarized that for about 83% of the tested proteins, at least two interacting blocks can be discovered by this approach. CONCLUSION: This work aims to demonstrate that the important residues associated with the interface of protein-protein interactions may be automatically discovered by sequential pattern mining. The detected regions possess high conservation and thus are considered as the computational hot regions. This information would be useful to characterizing protein sequences, predicting protein function, finding potential partners, and facilitating protein docking for drug discovery.
| S-EPMC1892096 | biostudies-literature