A 3-Approximation Algorithm for the Multiple Spliced Alignment Problem and Its Application to the Gene Prediction Task

Existing research suggests that adults and older children experience a tradeoff where instruction and feedback help them solve a problem efficiently, but lead them to ignore currently irrelevant information that might be useful in the future. It is unclear whether young children experience the same tradeoff. Eighty-seven children (ages five- to eight-years) and 42 adults participated in supervised feature prediction tasks either with or without an instructional hint. Follow-up tasks assessed learning of feature correlations and feature frequencies. Younger children tended to learn frequencies of both relevant and irrelevant features without instruction, but not the diagnostic feature correlation needed for the prediction task. With instruction, younger children did learn the diagnostic feature correlation, but then failed to learn the frequencies of irrelevant features. Instruction helped older children learn the correlation without limiting attention to frequencies. Adults learned the diagnostic correlation even without instruction, but with instruction no longer learned about irrelevant frequencies. These results indicate that young children do show some costs of learning with instruction characteristic of older children and adults. However, they also receive some of the benefits. The current study illustrates just what those tradeoffs might be, and how they might change over development.

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Spliced alignment and its application in Arabidopsis thaliana

10.31274/rtd-180816-4702 ◽

2003 ◽

Author(s):

Wei Zhu

Keyword(s):

Arabidopsis Thaliana ◽

Spliced Alignment

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An Improved Sequential Polygonal Approximation Algorithm on Skeleton Curves

ACTA AUTOMATICA SINICA ◽

10.3724/sp.j.1004.2008.01467 ◽

2009 ◽

Vol 34 (12) ◽

pp. 1467-1474

Author(s):

Zhe LV ◽

Fu-Li WANG ◽

Yu-Qing CHANG ◽

Yang LIU

Keyword(s):

Approximation Algorithm ◽

Polygonal Approximation

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Cloning, expression and target gene prediction of let-7 in Paralichthys olivaceus metamorphosis

Journal of Fishery Sciences of China ◽

10.3724/sp.j.1118.2011.01211 ◽

2013 ◽

Vol 18 (6) ◽

pp. 1211-1218

Author(s):

Zhiyi SHI ◽

Minglin WU ◽

Yuanshuai FU

Keyword(s):

Target Gene ◽

Gene Prediction ◽

Paralichthys Olivaceus

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3132 Machine Learning for Prediction of Pathologic Pneumatosis Intestinalis Using CT Scans

Journal of Clinical and Translational Science ◽

10.1017/cts.2019.142 ◽

2019 ◽

Vol 3 (s1) ◽

pp. 60-61

Author(s):

Kadie Clancy ◽

Esmaeel Dadashzadeh ◽

Christof Kaltenmeier ◽

JB Moses ◽

Shandong Wu

Keyword(s):

Machine Learning ◽

Decision Making ◽

Pneumatosis Intestinalis ◽

Learning Models ◽

Surgical Decision ◽

Prediction Task ◽

Svm Model ◽

Surgical Decision Making ◽

Intraoperative Visualization ◽

Machine Learning Models

OBJECTIVES/SPECIFIC AIMS: This retrospective study aims to create and train machine learning models using a radiomic-based feature extraction method for two classification tasks: benign vs. pathologic PI and operation of benefit vs. operation not needed. The long-term goal of our study is to build a computerized model that incorporates both radiomic features and critical non-imaging clinical factors to improve current surgical decision-making when managing PI patients. METHODS/STUDY POPULATION: Searched radiology reports from 2010-2012 via the UPMC MARS Database for reports containing the term “pneumatosis” (subsequently accounting for negations and age restrictions). Our inclusion criteria included: patient age 18 or older, clinical data available at time of CT diagnosis, and PI visualized on manual review of imaging. Cases with intra-abdominal free air were excluded. Collected CT imaging data and an additional 149 clinical data elements per patient for a total of 75 PI cases. Data collection of an additional 225 patients is ongoing. We trained models for two clinically-relevant prediction tasks. The first (referred to as prediction task 1) classifies between benign and pathologic PI. Benign PI is defined as either lack of intraoperative visualization of transmural intestinal necrosis or successful non-operative management until discharge. Pathologic PI is defined as either intraoperative visualization of transmural PI or withdrawal of care and subsequent death during hospitalization. The distribution of data samples for prediction task 1 is 47 benign cases and 38 pathologic cases. The second (referred to as prediction task 2) classifies between whether the patient benefitted from an operation or not. “Operation of benefit” is defined as patients with PI, be it transmural or simply mucosal, who benefited from an operation. “Operation not needed” is defined as patients who were safely discharged without an operation or patients who had an operation, but nothing was found. The distribution of data samples for prediction task 2 is 37 operation not needed cases and 38 operation of benefit cases. An experienced surgical resident from UPMC manually segmented 3D PI ROIs from the CT scans (5 mm Axial cut) for each case. The most concerning ~10-15 cm segment of bowel for necrosis with a 1 cm margin was selected. A total of 7 slices per patient were segmented for consistency. For both prediction task 1 and prediction task 2, we independently completed the following procedure for testing and training: 1.) Extracted radiomic features from the 3D PI ROIs that resulted in 99 total features. 2.) Used LASSO feature selection to determine the subset of the original 99 features that are most significant for performance of the prediction task. 3.) Used leave-one-out cross-validation for testing and training to account for the small dataset size in our preliminary analysis. Implemented and trained several machine learning models (AdaBoost, SVM, and Naive Bayes). 4.) Evaluated the trained models in terms of AUC and Accuracy and determined the ideal model structure based on these performance metrics. RESULTS/ANTICIPATED RESULTS: Prediction Task 1: The top-performing model for this task was an SVM model trained using 19 features. This model had an AUC of 0.79 and an accuracy of 75%. Prediction Task 2: The top-performing model for this task was an SVM model trained using 28 features. This model had an AUC of 0.74 and an accuracy of 64%. DISCUSSION/SIGNIFICANCE OF IMPACT: To the best of our knowledge, this is the first study to use radiomic-based machine learning models for the prediction of tissue ischemia, specifically intestinal ischemia in the setting of PI. In this preliminary study, which serves as a proof of concept, the performance of our models has demonstrated the potential of machine learning based only on radiomic imaging features to have discriminative power for surgical decision-making problems. While many non-imaging-related clinical factors play a role in the gestalt of clinical decision making when PI presents, we have presented radiomic-based models that may augment this decision-making process, especially for more difficult cases when clinical features indicating acute abdomen are absent. It should be noted that prediction task 2, whether or not a patient presenting with PI would benefit from an operation, has lower performance than prediction task 1 and is also a more challenging task for physicians in real clinical environments. While our results are promising and demonstrate potential, we are currently working to increase our dataset to 300 patients to further train and assess our models. References DuBose, Joseph J., et al. “Pneumatosis Intestinalis Predictive Evaluation Study (PIPES): a multicenter epidemiologic study of the Eastern Association for the Surgery of Trauma.” Journal of Trauma and Acute Care Surgery 75.1 (2013): 15-23. Knechtle, Stuart J., Andrew M. Davidoff, and Reed P. Rice. “Pneumatosis intestinalis. Surgical management and clinical outcome.” Annals of Surgery 212.2 (1990): 160.

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The minimum zone fitting and error evaluation for the logarithmic curve based on geometry optimization approximation algorithm

Transactions of the Institute of Measurement and Control ◽

10.1177/0142331219858855 ◽

2019 ◽

Vol 41 (15) ◽

pp. 4380-4386

Author(s):

Tu Xianping ◽

Lei Xianqing ◽

Ma Wensuo ◽

Wang Xiaoyi ◽

Hu Luqing ◽

...

Keyword(s):

Approximation Algorithm ◽

Evaluation Method ◽

Geometry Optimization ◽

Reference Points ◽

Approximation Technique ◽

Error Evaluation ◽

Iterative Approximation ◽

Logarithmic Curve ◽

Normal Distance ◽

Minimum Zone

The minimum zone fitting and error evaluation for the logarithmic curve has important applications. Based on geometry optimization approximation algorithm whilst considering geometric characteristics of logarithmic curves, a new fitting and error evaluation method for the logarithmic curve is presented. To this end, two feature points, to serve as reference, are chosen either from those located on the least squares logarithmic curve or from amongst measurement points. Four auxiliary points surrounding each of the two reference points are then arranged to resemble vertices of a square. Subsequently, based on these auxiliary points, a series of auxiliary logarithmic curves (16 curves) are constructed, and the normal distance and corresponding range of values between each measurement point and all auxiliary logarithmic curves are calculated. Finally, by means of an iterative approximation technique consisting of comparing, evaluating, and changing reference points; determining new auxiliary points; and constructing corresponding auxiliary logarithmic curves, minimum zone fitting and evaluation of logarithmic curve profile errors are implemented. The example results show that the logarithmic curve can be fitted, and its profile error can be evaluated effectively and precisely using the presented method.

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