c-Cbl expression as a novel predictive marker of survival in patients with metastatic colorectal cancer.

e15090 Background: Aberrant hyperactive Wnt/ß-catenin signaling is critical in colorectal cancer (CRC) tumorigenesis. Casitas B-lineage Lymphoma (c-Cbl) is a negative regulator of Wnt signaling, and functions as a tumor suppressor. The objective of this study was to evaluate c-Cbl expression as a predictive marker of survival in patients with metastatic CRC (mCRC). Methods: Patients with mCRC treated at Boston University Medical Center between 2004 and 2014 were analyzed. c-Cbl and nuclear ß-catenin expression was quantified in explanted biopsies using a customized color-based image segmentation pipeline. Quantification was normalized to the total tumor area in an image, and deemed ‘low’ or ‘high’ according to the mean normalized values of the cohort. A supervised machine-learning model based on bootstrap aggregating was constructed with c-Cbl expression as the input feature and 3-year survival as output. Results: Of the 72 subjects with mCRC, 52.78% had high and 47.22% had low c-Cbl expression. Patients with high c-Cbl had significantly better median overall survival than those with low c-Cbl expression (3.7 years vs. 1.8 years; p = 0.0026), and experienced superior 3-year survival (47.37% vs 20.59%; p = 0.017). Intriguingly, nuclear ß-catenin expression did not correlate with survival. No significant differences were detected between high and low c-Cbl groups in baseline characteristics (demographics, comorbidities), tumor-related parameters (primary tumor location, number of metastasis, molecular features) or therapy received (surgery, chemotherapy regimen). A 5-fold cross-validated machine-learning model associated with 3-year survival demonstrated an area under the curve of 0.729, supporting c-Cbl expression as a predictor of mCRC survival. Conclusions: Our results show that c-Cbl expression is associated with and predicts mCRC survival. Demonstration of these findings despite the small cohort size underscores the power of quantitative histology and machine-learning application. While further work is needed to validate c-Cbl as a novel biomarker of mCRC survival, this study supports c-Cbl as a regulator of Wnt/ß-catenin signaling and a suppressor of other oncogenes in CRC tumorigenesis.

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An Autoencoder and Machine Learning Model to Predict Suicidal Ideation with Brain Structural Imaging

Journal of Clinical Medicine ◽

10.3390/jcm9030658 ◽

2020 ◽

Vol 9 (3) ◽

pp. 658 ◽

Cited By ~ 1

Author(s):

Jun-Cheng Weng ◽

Tung-Yeh Lin ◽

Yuan-Hsiung Tsai ◽

Man Teng Cheok ◽

Yi-Peng Eve Chang ◽

...

Keyword(s):

Machine Learning ◽

Suicidal Ideation ◽

Learning Algorithm ◽

Area Under The Curve ◽

Learning Model ◽

Supervised Machine Learning ◽

Gradient Boosting ◽

Machine Learning Model ◽

Extreme Gradient Boosting ◽

Depressive Patients

It is estimated that at least one million people die by suicide every year, showing the importance of suicide prevention and detection. In this study, an autoencoder and machine learning model was employed to predict people with suicidal ideation based on their structural brain imaging. The subjects in our generalized q-sampling imaging (GQI) dataset consisted of three groups: 41 depressive patients with suicidal ideation (SI), 54 depressive patients without suicidal thoughts (NS), and 58 healthy controls (HC). In the GQI dataset, indices of generalized fractional anisotropy (GFA), isotropic values of the orientation distribution function (ISO), and normalized quantitative anisotropy (NQA) were separately trained in different machine learning models. A convolutional neural network (CNN)-based autoencoder model, the supervised machine learning algorithm extreme gradient boosting (XGB), and logistic regression (LR) were used to discriminate SI subjects from NS and HC subjects. After five-fold cross validation, separate data were tested to obtain the accuracy, sensitivity, specificity, and area under the curve of each result. Our results showed that the best pattern of structure across multiple brain locations can classify suicidal ideates from NS and HC with a prediction accuracy of 85%, a specificity of 100% and a sensitivity of 75%. The algorithms developed here might provide an objective tool to help identify suicidal ideation risk among depressed patients alongside clinical assessment.

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Assessment of urban flood susceptibility using semi-supervised machine learning model

The Science of The Total Environment ◽

10.1016/j.scitotenv.2018.12.217 ◽

2019 ◽

Vol 659 ◽

pp. 940-949 ◽

Cited By ~ 31

Author(s):

Gang Zhao ◽

Bo Pang ◽

Zongxue Xu ◽

Dingzhi Peng ◽

Liyang Xu

Keyword(s):

Machine Learning ◽

Learning Model ◽

Supervised Machine Learning ◽

Urban Flood ◽

Flood Susceptibility ◽

Machine Learning Model

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MEWS++: Enhancing the Prediction of Clinical Deterioration in Admitted Patients through a Machine Learning Model

Journal of Clinical Medicine ◽

10.3390/jcm9020343 ◽

2020 ◽

Vol 9 (2) ◽

pp. 343 ◽

Cited By ~ 4

Author(s):

Arash Kia ◽

Prem Timsina ◽

Himanshu N. Joshi ◽

Eyal Klang ◽

Rohit R. Gupta ◽

...

Keyword(s):

Machine Learning ◽

At Risk ◽

Area Under The Curve ◽

Learning Model ◽

Clinical Deterioration ◽

Early Warning Score ◽

Support Vector ◽

Adult Age ◽

Machine Learning Model ◽

Patients At Risk

Early detection of patients at risk for clinical deterioration is crucial for timely intervention. Traditional detection systems rely on a limited set of variables and are unable to predict the time of decline. We describe a machine learning model called MEWS++ that enables the identification of patients at risk of escalation of care or death six hours prior to the event. A retrospective single-center cohort study was conducted from July 2011 to July 2017 of adult (age > 18) inpatients excluding psychiatric, parturient, and hospice patients. Three machine learning models were trained and tested: random forest (RF), linear support vector machine, and logistic regression. We compared the models’ performance to the traditional Modified Early Warning Score (MEWS) using sensitivity, specificity, and Area Under the Curve for Receiver Operating Characteristic (AUC-ROC) and Precision-Recall curves (AUC-PR). The primary outcome was escalation of care from a floor bed to an intensive care or step-down unit, or death, within 6 h. A total of 96,645 patients with 157,984 hospital encounters and 244,343 bed movements were included. Overall rate of escalation or death was 3.4%. The RF model had the best performance with sensitivity 81.6%, specificity 75.5%, AUC-ROC of 0.85, and AUC-PR of 0.37. Compared to traditional MEWS, sensitivity increased 37%, specificity increased 11%, and AUC-ROC increased 14%. This study found that using machine learning and readily available clinical data, clinical deterioration or death can be predicted 6 h prior to the event. The model we developed can warn of patient deterioration hours before the event, thus helping make timely clinical decisions.

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Machine Learning Prediction for Complete Response to Hypomethylating Agents with or without Additional Agents in Patients with Newly Diagnosed Myelodysplastic Syndrome

Blood ◽

10.1182/blood-2019-130155 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 1720-1720

Author(s):

Koji Sasaki ◽

Guillermo Montalban Bravo ◽

Rashmi Kanagal-Shamanna ◽

Elias Jabbour ◽

Farhad Ravandi ◽

...

Keyword(s):

Machine Learning ◽

Board Of Directors ◽

Research Funding ◽

Area Under The Curve ◽

Complete Response ◽

Learning Model ◽

Hypomethylating Agents ◽

Newly Diagnosed ◽

Advisory Committees ◽

Machine Learning Model

Background: Myelodysplastic syndrome (MDS) is a heterogeneous malignant myeloid neoplasm of hematopoietic stem cells due to cytogenetic alterations and somatic mutations in genes (DNA methylation, DNA repair, chromatin regulation, RNA splicing, transcription regulation, and signal transduction). Hypomethylating agents (HMA) are the standard of care for MDS, and 40-60% of patients achieved response to HMA. However, the prediction for response is difficult due to the nature of heterogeneity and the context of clinical conditions such as the degree of cytopenias and the dependency on transfusion. Machine learning outperforms conventional statistical models for prediction in statistical competitions. Prediction with machine learning models may predict response in patients with MDS. The aim of this study is to develop a machine learning model for the prediction of complete response (CR) to HMA with or without additional therapeutic agents in patients with newly diagnosed MDS. Methods: From November 2012 to August 2017, we analyzed 435 patients with newly diagnosed MDS who received frontline therapy as follows; azacitidine (AZA) (3-day, 5-day, or 7-day) ± vorinostat ± ipilimumab ± nivolumab; decitabine (DAC) (3-day or 5-day) ± vorinostat; 5-day guadecitabine. Clinical variables, cytogenetic abnormalities, and the presence of genetic mutations by next generation sequencing (NGS) were included for variable selection. The whole cohort was randomly divided into training/validation and test cohorts at an 8:2 ratio. The training/validation cohort was used for 4-fold cross validation. Hyperparameter optimization was performed with Stampede2, which was ranked as the 15th fastest supercomputer at Texas Advanced Computing Center in June 2018. A gradient boosting decision tree-based framework with the LightGBM Python module was used after hyperparameter tuning for the development of the machine learning model with training/validation cohorts. The performance of prediction was assessed with an independent test dataset with the area under the curve. Results: We identified 435 patients with newly diagnosed MDS who enrolled on clinical trials as follows: 33 patients, 5-day AZA; 23, 5-day AZA + vorinostat; 43, 3-day AZA; 20, 5-day AZA + ipilimumab; 19 patients, AZA + nivolumab; 7, AZA + ipilumumab + nivolumab; 114, 5-day DAC; 74, 3-day DAC; 4, DAC + vorinostat; 97, 5-day guadecitabine. In the whole cohort, the median age at diagnosis was 68 years (range, 13.0-90.3); 117 (27%) patients had a history of prior radiation or cytotoxic chemotherapy; the median white blood cell count was 2.9 (×109/L) (range, 0.5-102); median absolute neutrophil count, 1.1 (×109/L) (range, 0.0-55.1); median hemoglobin count, 9.5 (g/dL) (range, 4.7-15.4); median platelet count, 63 (×109/L) (range, 2-881); and median blasts in bone marrow, 8% (range, 0-20). Among 411 evaluable patients for the revised international prognostic scoring system, 15 (4%) had very low risk disease; 42 (10%), low risk; 68 (17%), intermediate risk; 124 (30%), high risk; and 162 (39%), very high risk. Overall, 153 patients (53%) achieved CR. Hyperparameter tuning identified the optimal hyperparameters with colsample by tree of 0.175, learning rate of 0.262, the maximal depth of 2, minimal data in leaf of 29, number of leaves of 11, alpha regularization of 0.010, lambda regularization of 2.085, and subsample of 0.639. On the test cohort with 87 patients, the machine learning model accurately predicted response in 65 patients (75%); 53 non-CR among 56 non-CR (95% accuracy); and 12 CR among 31 CR (39% accuracy). The trend of accuracy improvement by iteration (i.e., the number of decision trees) is shown in Figure 1. The area under the curve was 0.761521 in the test cohort. Conclusion: Our machine learning model with clinical, cytogenetic, and NGS data can predict CR to HMA in patients with newly diagnosed MDS. This approach can identify patients who may benefit from HMA therapy with and without additional agents for response, and can optimize the timing of allogeneic stem cell transplant. Disclosures Sasaki: Otsuka: Honoraria; Pfizer: Consultancy. Jabbour:Takeda: Consultancy, Research Funding; BMS: Consultancy, Research Funding; Adaptive: Consultancy, Research Funding; Amgen: Consultancy, Research Funding; AbbVie: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Cyclacel LTD: Research Funding. Ravandi:Cyclacel LTD: Research Funding; Selvita: Research Funding; Menarini Ricerche: Research Funding; Macrogenix: Consultancy, Research Funding; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Xencor: Consultancy, Research Funding. Kadia:Pfizer: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Research Funding; Bioline RX: Research Funding; Jazz: Membership on an entity's Board of Directors or advisory committees, Research Funding; AbbVie: Consultancy, Research Funding; BMS: Research Funding; Amgen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Genentech: Membership on an entity's Board of Directors or advisory committees; Pharmacyclics: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees. Takahashi:Symbio Pharmaceuticals: Consultancy. DiNardo:syros: Honoraria; jazz: Honoraria; agios: Consultancy, Honoraria; celgene: Consultancy, Honoraria; notable labs: Membership on an entity's Board of Directors or advisory committees; medimmune: Honoraria; abbvie: Consultancy, Honoraria; daiichi sankyo: Honoraria. Cortes:Novartis: Consultancy, Honoraria, Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding; Immunogen: Consultancy, Honoraria, Research Funding; Sun Pharma: Research Funding; Pfizer: Consultancy, Honoraria, Research Funding; Astellas Pharma: Consultancy, Honoraria, Research Funding; Jazz Pharmaceuticals: Consultancy, Research Funding; Merus: Consultancy, Honoraria, Research Funding; Forma Therapeutics: Consultancy, Honoraria, Research Funding; Daiichi Sankyo: Consultancy, Honoraria, Research Funding; BiolineRx: Consultancy; Biopath Holdings: Consultancy, Honoraria; Takeda: Consultancy, Research Funding. Kantarjian:AbbVie: Honoraria, Research Funding; Cyclacel: Research Funding; Pfizer: Honoraria, Research Funding; Astex: Research Funding; Agios: Honoraria, Research Funding; Jazz Pharma: Research Funding; Daiichi-Sankyo: Research Funding; Novartis: Research Funding; Actinium: Honoraria, Membership on an entity's Board of Directors or advisory committees; Immunogen: Research Funding; Takeda: Honoraria; BMS: Research Funding; Ariad: Research Funding; Amgen: Honoraria, Research Funding. Garcia-Manero:Amphivena: Consultancy, Research Funding; Helsinn: Research Funding; Novartis: Research Funding; AbbVie: Research Funding; Celgene: Consultancy, Research Funding; Astex: Consultancy, Research Funding; Onconova: Research Funding; H3 Biomedicine: Research Funding; Merck: Research Funding.

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Translationese and Post-editese: How comparable is comparable quality?

Linguistica Antverpiensia, New Series – Themes in Translation Studies ◽

10.52034/lanstts.v16i0.434 ◽

2018 ◽

Vol 16 ◽

Author(s):

Joke Daems ◽

Orphée De Clercq ◽

Lieve Macken

Keyword(s):

Machine Learning ◽

Learning Model ◽

Supervised Machine Learning ◽

Original Text ◽

High Quality ◽

Machine Learning Model ◽

Comparable Quality

Whereas post-edited texts have been shown to be either of comparable quality to human translations or better, one study shows that people still seem to prefer human-translated texts. The idea of texts being inherently different despite being of high quality is not new. Translated texts, for example, are also different from original texts, a phenomenon referred to as ‘Translationese’. Research into Translationese has shown that, whereas humans cannot distinguish between translated and original text, computers have been trained to detect Translationese successfully. It remains to be seen whether the same can be done for what we call Post-editese. We first establish whether humans are capable of distinguishing post-edited texts from human translations, and then establish whether it is possible to build a supervised machine-learning model that can distinguish between translated and post-edited text.

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Predicting Sentiment Polarity of Microblogs using an LSTM – CNN Deep Learning Model

International Journal of Engineering and Advanced Technology - Regular Issue ◽

10.35940/ijeat.f8933.088619 ◽

2019 ◽

Vol 8 (6) ◽

pp. 4368-4373

Keyword(s):

Neural Network ◽

Machine Learning ◽

Prediction Accuracy ◽

Short Term Memory ◽

Learning Model ◽

Supervised Machine Learning ◽

Machine Learning Model ◽

Proposed Model ◽

Network Approaches

In this paper we propose a novel supervised machine learning model to predict the polarity of sentiments expressed in microblogs. The proposed model has a stacked neural network structure consisting of Long Short Term Memory (LSTM) and Convolutional Neural Network (CNN) layers. In order to capture the long-term dependencies of sentiments in the text ordering of a microblog, the proposed model employs an LSTM layer. The encodings produced by the LSTM layer are then fed to a CNN layer, which generates localized patterns of higher accuracy. These patterns are capable of capturing both local and global long-term dependences in the text of the microblogs. It was observed that the proposed model performs better and gives improved prediction accuracy when compared to semantic, machine learning and deep neural network approaches such as SVM, CNN, LSTM, CNN-LSTM, etc. This paper utilizes the benchmark Stanford Large Movie Review dataset to show the significance of the new approach. The prediction accuracy of the proposed approach is comparable to other state-of-art approaches.

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