CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction.
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ABSTRACT:
SUBMITTER: Galan S
PROVIDER: S-EPMC7610641 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:OBJECTIVES:Systematic reviews and meta-analyses are labor-intensive and time-consuming. Automated extraction of quantitative data from primary studies can accelerate this process. ClinicalTrials.gov, launched in 2000, is the world's largest trial repository of results data from clinical trials; it has been used as a source instead of journal articles. We have developed a Web application called EXACT (EXtracting Accurate efficacy and safety information from ClinicalTrials.gov) that allows users without advanced programming skills to automatically extract data from ClinicalTrials.gov in analysis-ready format. We have also used the automatically extracted data to examine the reproducibility of meta-analyses in three published systematic reviews. STUDY DESIGN AND SETTING:We developed a Python-based software application (EXACT) that automatically extracts data required for meta-analysis from the ClinicalTrials.gov database in a spreadsheet format. We confirmed the accuracy of the extracted data and then used those data to repeat meta-analyses in three published systematic reviews. To ensure that we used the same statistical methods and outcomes as the published systematic reviews, we repeated the meta-analyses using data manually extracted from the relevant journal articles. For the outcomes whose results we were able to reproduce using those journal article data, we examined the usability of ClinicalTrials.gov data. RESULTS:EXACT extracted data at ClincalTrials.gov with 100% accuracy, and it required 60% less time than the usual practice of manually extracting data from journal articles. We found that 87% of the data elements extracted using EXACT matched those extracted manually from the journal articles. We were able to reproduce 24 of 28 outcomes using the journal article data. Of these 24 outcomes, we were able to reproduce 83.3% of the published estimates using data at ClinicalTrials.gov. CONCLUSION:EXACT (http://bio-nlp.org/EXACT) automatically and accurately extracted data elements from ClinicalTrials.gov and thus reduced time in data extraction. The ClinicalTrials.gov data reproduced most meta-analysis results in our study, but this conclusion needs further validation.
| S-EPMC6887103 | biostudies-literature
Project description:Enhanced accuracy and high-throughput capability in capturing genetic activities lead ChIP-sequencing technology to be applied prevalently in diverse study for tackling DNA-protein interaction problems. Till now, such questions as deciding suitable ChIP-seq arguments and comparing sample quality still haunt biologists. We propose the methods for answering such questions as deciding optimal argument pairs in global alignment of ChIP sequencing data; then we employ a modern signal processing approach to extract inherent genomic features from the global alignments of transcriptional binding activities; together with pairwise comparison from intra- and inter-sample perspectives; thus we can further determine alignment quality and decide the optimal candidate for multi-source heterogeneous high-throughput sequences. The work provides a practical approach to quantitatively compare the alignment quality for heterogeneous sequencing data, especially in determining the efficiency of transcriptional binding from replicate samples, thus it helps to exploit the potentiality of ChIP-seq for deep comprehension of inherent biological meanings from the high-throughput genomic sequences.
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Project description:Background and Objective: The emergence of the nonnutritive suck (NNS) pattern in preterm infants reflects the integrity of the brain and is used by clinicians in the neonatal intensive care unit (NICU) to assess feeding readiness and oromotor development. A critical need exists for an integrated software platform that provides NNS signal preprocessing, adaptive waveform discrimination, feature detection, and batch processing of big data sets across multiple NICU sites. Thus, the goal was to develop and describe a cross-platform graphical user interface (GUI) and terminal application known as NeoNNS for single and batch file time series and frequency-domain analyses of NNS compression pressure waveforms using analysis parameters derived from previous research on NNS dynamics. Methods. NeoNNS was implemented with Python and the Tkinter GUI package. The NNS signal-processing pipeline included a low-pass filter, asymmetric regression baseline correction, NNS peak detection, and NNS burst classification. Data visualizations and parametric analyses included time- and frequency-domain view, NNS spatiotemporal index view, and feature cluster analysis to model oral feeding readiness. Results. 568 suck assessment files sampled from 30 extremely preterm infants were processed in the batch mode (<50 minutes) to generate time- and frequency-domain analyses of infant NNS pressure waveform data. NNS cycle discrimination and NNS burst classification yield quantification of NNS waveform features as a function of postmenstrual age. Hierarchical cluster analysis (based on the Tsfresh python package and NeoNNS) revealed the capability to label NNS records for feeding readiness. Conclusions. NeoNNS provides a versatile software platform to rapidly quantify the dynamics of NNS development in time and frequency domains at cribside over repeated sessions for an individual baby or among large numbers of preterm infants at multiple hospital sites to support big data analytics. The hierarchical cluster feature analysis facilitates modeling of feeding readiness based on quantitative features of the NNS compression pressure waveform.
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Project description:This paper aims to assess the use of Inertial Measurement Unit (IMU) sensors to identify gait asymmetry by extracting automatic gait features. We design and develop an android app to collect real time synchronous IMU data from legs. The results from our method are validated using a Qualisys Motion Capture System. The data are collected from 10 young and 10 older subjects. Each performed a trial in a straight corridor comprising 15 strides of normal walking, a turn around and another 15 strides. We analyse the data for total distance, total time, total velocity, stride, step, cadence, step ratio, stance, and swing. The accuracy of detecting the stride number using the proposed method is 100% for young and 92.67% for older subjects. The accuracy of estimating travelled distance using the proposed method for young subjects is 97.73% and 98.82% for right and left legs; and for the older, is 88.71% and 89.88% for right and left legs. The average travelled distance is 37.77 (95% CI ± 3.57) meters for young subjects and is 22.50 (95% CI ± 2.34) meters for older subjects. The average travelled time for young subjects is 51.85 (95% CI ± 3.08) seconds and for older subjects is 84.02 (95% CI ± 9.98) seconds. The results show that wearable sensors can be used for identifying gait asymmetry without the requirement and expense of an elaborate laboratory setup. This can serve as a tool in diagnosing gait abnormalities in individuals and opens the possibilities for home based self-gait asymmetry assessment.
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Project description:BackgroundAutomated ICD coding on medical texts via machine learning has been a hot topic. Related studies from medical field heavily relies on conventional bag-of-words (BoW) as the feature extraction method, and do not commonly use more complicated methods, such as word2vec (W2V) and large pretrained models like BERT. This study aimed at uncovering the most effective feature extraction methods for coding models by comparing BoW, W2V and BERT variants.MethodsWe experimented with a Chinese dataset from Fuwai Hospital, which contains 6947 records and 1532 unique ICD codes, and a public Spanish dataset, which contains 1000 records and 2557 unique ICD codes. We designed coding tasks with different code frequency thresholds (denoted as [Formula: see text]), with a lower threshold indicating a more complex task. Using traditional classifiers, we compared BoW, W2V and BERT variants on accomplishing these coding tasks.ResultsWhen [Formula: see text] was equal to or greater than 140 for Fuwai dataset, and 60 for the Spanish dataset, the BERT variants with the whole network fine-tuned was the best method, leading to a Micro-F1 of 93.9% for Fuwai data when [Formula: see text], and a Micro-F1 of 85.41% for the Spanish dataset when [Formula: see text]. When [Formula: see text] fell below 140 for Fuwai dataset, and 60 for the Spanish dataset, BoW turned out to be the best, leading to a Micro-F1 of 83% for Fuwai dataset when [Formula: see text], and a Micro-F1 of 39.1% for the Spanish dataset when [Formula: see text]. Our experiments also showed that both the BERT variants and BoW possessed good interpretability, which is important for medical applications of coding models.ConclusionsThis study shed light on building promising machine learning models for automated ICD coding by revealing the most effective feature extraction methods. Concretely, our results indicated that fine-tuning the whole network of the BERT variants was the optimal method for tasks covering only frequent codes, especially codes that represented unspecified diseases, while BoW was the best for tasks involving both frequent and infrequent codes. The frequency threshold where the best-performing method varied differed between different datasets due to factors like language and codeset.
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Project description:The identification of biomarker signatures in omics molecular profiling is usually performed to predict outcomes in a precision medicine context, such as patient disease susceptibility, diagnosis, prognosis, and treatment response. To identify these signatures, we have developed a biomarker discovery tool, called BioDiscML. From a collection of samples and their associated characteristics, i.e., the biomarkers (e.g., gene expression, protein levels, clinico-pathological data), BioDiscML exploits various feature selection procedures to produce signatures associated to machine learning models that will predict efficiently a specified outcome. To this purpose, BioDiscML uses a large variety of machine learning algorithms to select the best combination of biomarkers for predicting categorical or continuous outcomes from highly unbalanced datasets. The software has been implemented to automate all machine learning steps, including data pre-processing, feature selection, model selection, and performance evaluation. BioDiscML is delivered as a stand-alone program and is available for download at https://github.com/mickaelleclercq/BioDiscML.
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Project description:The Golgi Apparatus (GA) is a major collection and dispatch station for numerous proteins destined for secretion, plasma membranes and lysosomes. The dysfunction of GA proteins can result in neurodegenerative diseases. Therefore, accurate identification of protein subGolgi localizations may assist in drug development and understanding the mechanisms of the GA involved in various cellular processes. In this paper, a new computational method is proposed for identifying cis-Golgi proteins from trans-Golgi proteins. Based on the concept of Common Spatial Patterns (CSP), a novel feature extraction technique is developed to extract evolutionary information from protein sequences. To deal with the imbalanced benchmark dataset, the Synthetic Minority Over-sampling Technique (SMOTE) is adopted. A feature selection method called Random Forest-Recursive Feature Elimination (RF-RFE) is employed to search the optimal features from the CSP based features and g-gap dipeptide composition. Based on the optimal features, a Random Forest (RF) module is used to distinguish cis-Golgi proteins from trans-Golgi proteins. Through the jackknife cross-validation, the proposed method achieves a promising performance with a sensitivity of 0.889, a specificity of 0.880, an accuracy of 0.885, and a Matthew's Correlation Coefficient (MCC) of 0.765, which remarkably outperforms previous methods. Moreover, when tested on a common independent dataset, our method also achieves a significantly improved performance. These results highlight the promising performance of the proposed method to identify Golgi-resident protein types. Furthermore, the CSP based feature extraction method may provide guidelines for protein function predictions.
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Project description:The large p small n problem is a challenge without a de facto standard method available to it. In this study, we propose a tensor-decomposition (TD)-based unsupervised feature extraction (FE) formalism applied to multiomics datasets, in which the number of features is more than 100,000 whereas the number of samples is as small as about 100, hence constituting a typical large p small n problem. The proposed TD-based unsupervised FE outperformed other conventional supervised feature selection methods, random forest, categorical regression (also known as analysis of variance, or ANOVA), penalized linear discriminant analysis, and two unsupervised methods, multiple non-negative matrix factorization and principal component analysis (PCA) based unsupervised FE when applied to synthetic datasets and four methods other than PCA based unsupervised FE when applied to multiomics datasets. The genes selected by TD-based unsupervised FE were enriched in genes known to be related to tissues and transcription factors measured. TD-based unsupervised FE was demonstrated to be not only the superior feature selection method but also the method that can select biologically reliable genes. To our knowledge, this is the first study in which TD-based unsupervised FE has been successfully applied to the integration of this variety of multiomics measurements.
| S-EPMC7763286 | biostudies-literature
Project description:Analysis of single-cell multiomics datasets is a novel topic and is considerably challenging because such datasets contain a large number of features with numerous missing values. In this study, we implemented a recently proposed tensor-decomposition (TD)-based unsupervised feature extraction (FE) technique to address this difficult problem. The technique can successfully integrate single-cell multiomics data composed of gene expression, DNA methylation, and accessibility. Although the last two have large dimensions, as many as ten million, containing only a few percentage of nonzero values, TD-based unsupervised FE can integrate three omics datasets without filling in missing values. Together with UMAP, which is used frequently when embedding single-cell measurements into two-dimensional space, TD-based unsupervised FE can produce two-dimensional embedding coincident with classification when integrating single-cell omics datasets. Genes selected based on TD-based unsupervised FE are also significantly related to reasonable biological roles.
| S-EPMC8468466 | biostudies-literature
Project description:Single-cell chromatin accessibility sequencing (scCAS) technologies have enabled characterizing the epigenomic heterogeneity of individual cells. However, the identification of features of scCAS data that are relevant to underlying biological processes remains a significant gap. Here, we introduce a novel method Cofea, to fill this gap. Through comprehensive experiments on 5 simulated and 54 real datasets, Cofea demonstrates its superiority in capturing cellular heterogeneity and facilitating downstream analysis. Applying this method to identification of cell type-specific peaks and candidate enhancers, as well as pathway enrichment analysis and partitioned heritability analysis, we illustrate the potential of Cofea to uncover functional biological process.
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