Summarizing videos into a target language: Methodology, architectures and evaluation

International audienceThe aim of the work is to report the results of the Chist-Era project AMIS (Access Multilingual Information opinionS). The purpose of AMIS is to answer the following question: How to make the information in a foreign language accessible for everyone? This issue is not limited to translate a source video into a target language video since the objective is to provide only the main idea of an Arabic video in English. This objective necessitates developing research in several areas that are not, all arrived at a maturity state: Video summarization, Speech recognition, Machine translation, Audio summarization and Speech segmentation. In this article we present several possible architectures to achieve our objective, yet we focus on only one of them. The scientific locks are be presented, and we explain how to deal with them. One of the big challenges of this work is to conceive a way to evaluate objectively a system composed of several components knowing that each of them has its limits and can propagate errors through the first component. Also, a subjective evaluation procedure is proposed in which several annotators have been mobilized to test the quality of the achieved summaries

Intent Based Utterance Segmentation for Multi IntentNLU

University of Minnesota M.S. thesis. August 2019. Major: Computer Science. Advisors: Joseph Konstan, Serguei Pakhomov. 1 computer file (PDF); vii, 36 pages.Natural Language Understanding(NLU) is a process of converting the user utterance to a dialog-act after identifying domain, intent and slots from the utterance. User utterances can either contain a single intent or could express multiple intents. Building an NLU module for multi-intent utterances is a huge challenge as traditional state-of-the-art NLU modules do not differentiate between single and multi intent utterances thereby converting them to a single semantic frame which results in reduced performance. In this paper, we introduce a intent based utterance segmenter to split user utterances if each segmented clause corresponds to a different intent. Our experiments evaluate the performance of the utterance segmenter not only on the utterances from movie-ticket booking domain and restaurant reservation domain used for training but also on a new taxi ordering domain. We show that the total number of utterances that are parsed by a utterance segmenter enabled NLU surpass the utterances parsed by traditional NLU

Machine Learning for Biomedical Literature Triage

This paper presents a machine learning system for supporting the first task of the biological literature manual curation process, called triage. We compare the performance of various classification models, by experimenting with dataset sampling factors and a set of features, as well as three different machine learning algorithms (Naive Bayes, Support Vector Machine and Logistic Model Trees). The results show that the most fitting model to handle the imbalanced datasets of the triage classification task is obtained by using domain relevant features, an under-sampling technique, and the Logistic Model Trees algorithm

Comparison of the Predictive Performance and Interpretability of Random Forest and Linear Models on Benchmark Datasets

The ability to interpret the predictions made by quantitative structure activity relationships (QSARs) offers a number of advantages. Whilst QSARs built using non-linear modelling approaches, such as the popular Random Forest algorithm, might sometimes be more predictive than those built using linear modelling approaches, their predictions have been perceived as difficult to interpret. However, a growing number of approaches have been proposed for interpreting non-linear QSAR models in general and Random Forest in particular. In the current work, we compare the performance of Random Forest to two widely used linear modelling approaches: linear Support Vector Machines (SVM), or Support Vector Regression (SVR), and Partial Least Squares (PLS). We compare their performance in terms of their predictivity as well as the chemical interpretability of the predictions, using novel scoring schemes for assessing Heat Map images of substructural contributions. We critically assess different approaches to interpreting Random Forest models as well as for obtaining predictions from the forest. We assess the models on a large number of widely employed, public domain benchmark datasets corresponding to regression and binary classification problems of relevance to hit identification and toxicology. We conclude that Random Forest typically yields comparable or possibly better predictive performance than the linear modelling approaches and that its predictions may also be interpreted in a chemically and biologically meaningful way. In contrast to earlier work looking at interpreting non-linear QSAR models, we directly compare two methodologically distinct approaches for interpreting Random Forest models. The approaches for interpreting Random Forest assessed in our article were implemented using Open Source programs, which we have made available to the community. These programs are the rfFC package [https://r-forge.r-project.org/R/?group_id=1725] for the R Statistical Programming Language, along with a Python program HeatMapWrapper [https://doi.org/10.5281/zenodo.495163] for Heat Map generation

Texture Analysis Platform for Imaging Biomarker Research

abstract: The rate of progress in improving survival of patients with solid tumors is slow due to late stage diagnosis and poor tumor characterization processes that fail to effectively reflect the nature of tumor before treatment or the subsequent change in its dynamics because of treatment. Further advancement of targeted therapies relies on advancements in biomarker research. In the context of solid tumors, bio-specimen samples such as biopsies serve as the main source of biomarkers used in the treatment and monitoring of cancer, even though biopsy samples are susceptible to sampling error and more importantly, are local and offer a narrow temporal scope. Because of its established role in cancer care and its non-invasive nature imaging offers the potential to complement the findings of cancer biology. Over the past decade, a compelling body of literature has emerged suggesting a more pivotal role for imaging in the diagnosis, prognosis, and monitoring of diseases. These advances have facilitated the rise of an emerging practice known as Radiomics: the extraction and analysis of large numbers of quantitative features from medical images to improve disease characterization and prediction of outcome. It has been suggested that radiomics can contribute to biomarker discovery by detecting imaging traits that are complementary or interchangeable with other markers. This thesis seeks further advancement of imaging biomarker discovery. This research unfolds over two aims: I) developing a comprehensive methodological pipeline for converting diagnostic imaging data into mineable sources of information, and II) investigating the utility of imaging data in clinical diagnostic applications. Four validation studies were conducted using the radiomics pipeline developed in aim I. These studies had the following goals: (1 distinguishing between benign and malignant head and neck lesions (2) differentiating benign and malignant breast cancers, (3) predicting the status of Human Papillomavirus in head and neck cancers, and (4) predicting neuropsychological performances as they relate to Alzheimer’s disease progression. The long-term objective of this thesis is to improve patient outcome and survival by facilitating incorporation of routine care imaging data into decision making processes.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

A Supervised Learning Approach for Imbalanced Text Classification of Biomedical Literature Triage

This thesis presents the development of a machine learning system, called mycoSORT , for supporting the first step of the biological literature manual curation process, called triage. The manual triage of documents is very demanding, as researchers usually face the time-consuming and error- prone task of screening a large amount of data to identify relevant information. After querying scientific databases for keywords related to a specific subject, researchers generally find a long list of retrieved results, that has to be carefully analysed to identify only a few documents that show a potential of being relevant to the topic. Such an analysis represents a severe bottleneck in the knowledge discovery and decision-making processes in scientific research. Hence, biocurators could greatly benefit from an automatic support when performing the triage task. In order to support the triage of scientific documents, we have used a corpus of document instances manually labeled by biocurators as “selected” or “rejected”, with regards to their potential to indicate relevant information about fungal enzymes. This document collection is characterized by being large, since many results are retrieved and analysed to finally identify potential candidate documents; and also highly imbalanced, concerning the distribution of instances per relevance: the great majority of documents are labeled as rejected, while only a very small portion are labeled as selected. Using this dataset, we studied the design of a classification model to identify the most discriminative features to automate the triage of scientific literature and to tackle the imbalance between the two classes of documents. To identify the most suitable model, we performed a study of 324 classification models, which demonstrated the results of using 9 different data undersampling factors, 4 sets of features, and the evaluation of 2 feature selection methods as well as 3 machine learning algorithms. Our results demonstrated that the use of an undersampling technique is effective to handle imbalanced datasets and also help manage large document collections. We also found that the combination of undersampling and feature selection using Odds Ratio can improve the performance of our classification model. Finally, our results demonstrated that the best fitting model to support the triage of scientific documents is composed by domain relevant features, filtered by Odds Ratio scores, the use of dataset undersampling and the Logistic Model Trees algorithm