Abstract

Papillary Renal Cell Carcinoma (PRCC) is a heterogeneous disease with variations in disease progression and clinical outcomes. The advent of next generation sequencing techniques (NGS) has generated data from patients that can be analysed to develop a predictive model. In this study, we have adopted a machine learning approach to identify biomarkers and build classifiers to discriminate between early and late stages of PRCC from gene expression profiles. A machine learning pipeline incorporating different feature selection algorithms and classification models is developed to analyse RNA sequencing dataset (RNASeq). Further, to get a reliable feature set, we extracted features from different partitions of the training dataset and aggregated them into feature sets for classification. We evaluated the performance of different algorithms on the basis of 10-fold cross validation and independent test dataset. 10-fold cross validation was also performed on a microarray dataset of PRCC. A random forest based feature selection (varSelRF) yielded minimum number of features (104) and a best performance with area under Precision Recall curve (PR-AUC) of 0.804, MCC (Matthews Correlation Coefficient) of 0.711 and accuracy of 88% with Shrunken Centroid classifier on a test dataset. We identified 80 genes that are consistently altered between stages by different feature selection lgorithms. The extracted features are related to cellular components - centromere, kinetochore and spindle, and biological process mitotic cell cycle. These observations reveal potential mechanisms for an increase in chromosome instability in the late stage of PRCC. Our study demonstrates that the gene expression profiles can be used to classify stages of PRCC.

Abstract

Brain connectivity analysis has provided crucial insights to pinpoint the differences between autistic and typically developing (TD) children during development. The aim of this study is to investigate the functional connectomics of autism spectrum disorder (ASD) versus TD and underpin the effects of development, disease, and their interactions on the observed atypical brain connectivity patterns. Resting-state functional magnetic resonance imaging (rs-fMRI) from the Autism Brain Imaging Data Exchange (ABIDE) data set, which is stratified into two cohorts: children (9–12 years) and adolescents (13–16 years), is used for the analysis. Differences in various graph theoretical network measures are calculated between ASD and TD in each group. Furthermore, two-factor analysis of variance test is used to study the effect of age, disease, and their interaction on the network measures and the network edges. Furthermore, the differences in connection strength between TD and ASD subjects are assessed using network-based statistics. The results showed that ASD exhibits increased functional integration at the expense of decreased functional segregation. In ASD adolescents, there is a significant decrease in odularity suggesting a less robust modular organization, and an increase in participation coefficient suggesting more random integration and widely distributed connection edges. Furthermore, there is significant hypoconnectivity observed in the adolescent group especially in the default mode network, while the children group shows both hyper- and hypoconnectivity. This study lends support to a model of global atypical connections and further identifies functional networks and areas that are independently affected by age, disease, and their interaction.

Abstract

In this study, we investigated the effects of variable Response-to-Stimulus interval (RSI) on sequence learning using both empirical and computational methods. In the empirical study, the serial reaction time task (SRT) was conducted which was followed by free generation and recognition tasks. Results showed that learning becomes explicit with increase in RSI despite its varying temporal nature. We constructed a computational model based on modified Elman network architecture to obtain a functional account of the empirical findings. The model illustrates how explicit learning could emerge due to a longer temporal window between stimuli which could potentially give insights into the mechanisms of sequence learning in variable RSI conditions.

Abstract

Bug reporting is a major part of software maintenance and due to its inherently asynchronous nature, duplicate bug reporting has become fairly common. Detecting duplicate bug reports is an important task in order to avoid the assignment of a same bug to different developers. Earlier approaches have improved duplicate bug report detection by using the notions of word embeddings, topic models and other machine learning approaches. In this poster, we attempt to combine Latent Dirichlet Allocation (LDA) and word embeddings to leverage the strengths of both approaches for this task. As a first step towards this idea, we present initial analysis and an approach which is able to outperform both word embeddings and LDA for this task. We validate our hypothesis on a real world dataset of Firefox project and show that there is potential in combining both LDA and word embeddings for duplicate bug report detection.

Abstract

Encoding models of functional magnetic resonance imaging (fMRI) data attempt to learn a forward mapping that relates stimuli to the corresponding brain activation. Computational tractability usually forces current encoding as well as decoding solutions to typically consider only a small subset of voxels from the actual 3D volume of activation. Further, while brain decoding has received wider attention, there have been only a few attempts at constructing encoding solutions in the extant neuroimaging literature. In this paper, we present a deep autoencoder consisting of convolutional neural networks in tandem with long short-term memory (CNNLSTM) model. The model is trained on fMRI slice sequences and predicts the entire brain volume rather than a small subset of voxels from the information in stimuli (text and image). We argue that the resulting solution avoids the problem of devising encoding models based on a rule-based selection of informative voxels and the concomitant issue of wide spatial variability of such voxels across participants. The perturbation experiments indicate that the proposed deep encoder indeed learns to predict brain activations with high spatial accuracy. On the challenging universal decoder imaging datasets (Pereira et al., 2018), our model yielded encouraging results.

Abstract

Social media platforms like twitter and facebook have be-come two of the largest mediums used by people to express their views to-wards different topics. Generation of such large user data has made NLP tasks like sentiment analysis and opinion mining much more important. Using sarcasm in texts on social media has become a popular trend lately. Using sarcasm reverses the meaning and polarity of what is implied by the text which poses challenge for many NLP tasks. The task of sarcasm detection in text is gaining more and more importance for both commer-cial and security services. We present the first English-Hindi code-mixed dataset of tweets marked for presence of sarcasm and irony where each token is also annotated with a language tag. We present a baseline su-pervised classification system developed using the same dataset which achieves an average F-score of 78.4 after using random forest classifier and performing 10-fold cross validation.

Abstract

Social media has become one of the main channels for peo-ple to communicate and share their views with the society. We can often detect from these views whether the person is in favor, against or neu-tral towards a given topic. These opinions from social media are very useful for various companies. We present a new dataset that consists of 3545 English-Hindi code-mixed tweets with opinion towards Demoneti-sation that was implemented in India in 2016 which was followed by a large countrywide debate. We present a baseline supervised classification system for stance detection developed using the same dataset that uses various machine learning techniques to achieve an accuracy of 58.7% on 10-fold cross validation.

Abstract

Hate speech detection in social media texts is an important Natural language Processing task, which has several crucial applications like sentiment analysis, investigating cyberbullying and examining socio-political controversies. While relevant research has been done independently on code-mixed social media texts and hate speech detection, our work is the first attempt in detecting hate speech in Hindi-English code-mixed social media text. In this paper, we analyze the problem of hate speech detection in code-mixed texts and present a Hindi-English code-mixed dataset consisting of tweets posted online on Twitter. The tweets are annotated with the language at word level and the class they belong to (Hate Speech or Normal Speech). We also propose a supervised classification system for detecting hate speech in the text using various character level, word level, and lexicon based features.

Abstract

Machine learning approaches in sentiment analysis principally rely on the abundance of resources. To limit this dependence, we propose a novel method called Siamese Network Architecture for Sentiment Analysis (SNASA) to learn representations of resource-poor languages by jointly training them with resource-rich languages using a siamese network. SNASA model consists of twin Bi-directional Long Short-Term Memory Recurrent Neural Networks (Bi-LSTM RNN) with shared parameters joined by a contrastive loss function, based on a similarity metric. The model learns the sentence representations of resource-poor and resource-rich language in a common sentiment space by using a similarity metric based on their individual sentiments. The model, hence, projects sentences with similar sentiment closer to each other and the sentences with different sentiment farther from each other. Experiments on large-scale datasets of resource-rich languages-English and Spanish and resource-poor languages-Hindi and Telugu reveal that SNASA outperforms the state-of-the-art sentiment analysis approaches based on distributional semantics, semantic rules, lexicon lists and deep neural network representations without shared parameters.

Abstract

Previous research shows that performance is better when a high pitch is responded with up or right responses and a low pitch is responded with down or left responses, called the spatial-pitch association of response codes (SPARC) effect. Despite the intuitive coupling of perception-action, studies investigating the SPARC effect have, however, used feedback to manipulate the stimulus-response mapping. Feedback contradicts the purpose of intuitive stimulus-response mapping by enabling short-term learning. This study primarily investigates the role of feedback on SPARC effect. We believe that feedback can facilitate incongruent mapping and can, therefore, reduce the cost between incongruent and congruent mapping resulting in a diminished SPARC effect. Our results, however, show that feedback has no influence on the SPARC effect indicating that long-term associations can not be overcome by short-term learning due to robust perception-action coupling. Further, unlike previous studies, we observed a strong horizontal SPARC effect in nonmusicians as well.