Physical Sciences and Mathematics Commons^™

Discerning Novel Splice Junctions Derived From Rna-Seq Alignment: A Deep Learning Approach, Yi Zhang, Xinan Liu, James N. Macleod, Jinze Liu

Computer Science Faculty Publications

Background: Exon splicing is a regulated cellular process in the transcription of protein-coding genes. Technological advancements and cost reductions in RNA sequencing have made quantitative and qualitative assessments of the transcriptome both possible and widely available. RNA-seq provides unprecedented resolution to identify gene structures and resolve the diversity of splicing variants. However, currently available ab initio aligners are vulnerable to spurious alignments due to random sequence matches and sample-reference genome discordance. As a consequence, a significant set of false positive exon junction predictions would be introduced, which will further confuse downstream analyses of splice variant discovery and abundance estimation.

Results: …

Making A Good Thing Better: Enhancing Password/Pin-Based User Authentication With Smartwatch, Bing Chang, Yingjiu Li, Qiongxiao Wang, Wen-Tao Zhu, Robert H. Deng

Research Collection School Of Computing and Information Systems

Wearing smartwatches becomes increasingly popular in people’s lives. This paper shows that a smartwatch can help its bearer authenticate to a login system effectively and securely even if the bearer’s password has already been revealed. This idea is motivated by our observation that a sensor-rich smartwatch is capable of tracking the wrist motions of its bearer typing a password or PIN, which can be used as an authentication factor. The major challenge in this research is that a sophisticated attacker may imitate a user’s typing behavior as shown in previous research on keystroke dynamics based user authentication. We address this …

Transfer Learning With Deep Recurrent Neural Networks For Remaining Useful Life Estimation, Ansi Zhang, Shaobo Li, Yuxin Cui, Zhonghao Liu, Guanci Yang, Jianjun Hu

Faculty Publications

Prognostics, such as remaining useful life (RUL) prediction, is a crucial task in condition-based maintenance. A major challenge in data-driven prognostics is the difficulty of obtaining a sufficient number of samples of failure progression. However, for traditional machine learning methods and deep neural networks, enough training data is a prerequisite to train good prediction models. In this work, we proposed a transfer learning algorithm based on Bi-directional Long Short-Term Memory (BLSTM) recurrent neural networks for RUL estimation, in which the models can be first trained on different but related datasets and then fine-tuned by the target dataset. Extensive experimental results …

Transfer Learning With Deep Recurrent Neural Networks For Remaining Useful Life Estimation, Ansi Zhang, Honglei Wang, Shaobo Li, Yuxin Cui, Guanci Yang, Jianjun Hu

Faculty Publications

Prognostics, such as remaining useful life (RUL) prediction, is a crucial task in condition-based maintenance. A major challenge in data-driven prognostics is the difficulty of obtaining a sufficient number of samples of failure progression. However, for traditional machine learning methods and deep neural networks, enough training data is a prerequisite to train good prediction models. In this work, we proposed a transfer learning algorithm based on Bi-directional Long Short-Term Memory (BLSTM) recurrent neural networks for RUL estimation, in which the models can be first trained on different but related datasets and then fine-tuned by the target dataset. Extensive experimental results …

Learning Generalized Video Memory For Automatic Video Captioning, Poo-Hee Chang, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

Recent video captioning methods have made great progress by deep learning approaches with convolutional neural networks (CNN) and recurrent neural networks (RNN). While there are techniques that use memory networks for sentence decoding, few work has leveraged on the memory component to learn and generalize the temporal structure in video. In this paper, we propose a new method, namely Generalized Video Memory (GVM), utilizing a memory model for enhancing video description generation. Based on a class of self-organizing neural networks, GVM’s model is able to learn new video features incrementally. The learned generalized memory is further exploited to decode the …

Improving Knowledge Tracing Model By Integrating Problem Difficulty, Sein Minn, Feida Zhu, Michel C. Desmarais

Research Collection School Of Computing and Information Systems

Intelligent Tutoring Systems (ITS) are designed for providing personalized instructions to students with the needs of their skills. Assessment of student knowledge acquisition dynamically is nontrivial during her learning process with ITS. Knowledge tracing, a popular student modeling technique for student knowledge assessment in adaptive tutoring, which is used for tracing student's knowledge state and detecting student's knowledge acquisition by using decomposed individual skill or problems with a single skill per problem. Unfortunately, recent KT models fail to deal with practices of complex skill composition and variety of concepts included in a problem simultaneously. Our goal is to investigate a …

End-To-End Convolutional Neural Network Model For Gear Fault Diagnosis Based On Sound Signals, Yong Yao, Honglei Wang, Shaobo Li, Zhongnhao Liu, Gui Gui, Yabo Dan, Jianjun Hu

Faculty Publications

Currently gear fault diagnosis is mainly based on vibration signals with a few studies on acoustic signal analysis. However, vibration signal acquisition is limited by its contact measuring while traditional acoustic-based gear fault diagnosis relies heavily on prior knowledge of signal processing techniques and diagnostic expertise. In this paper, a novel deep learning-based gear fault diagnosis method is proposed based on sound signal analysis. By establishing an end-to-end convolutional neural network (CNN), the time and frequency domain signals can be fed into the model as raw signals without feature engineering. Moreover, multi-channel information from different microphones can also be fused …

Toward Audio Beehive Monitoring: Deep Learning Vs. Standard Machine Learning In Classifying Beehive Audio Samples, Vladmir Kulyukin, Sarbajit Mukherjee, Prakhar Amlathe

Computer Science Faculty and Staff Publications

Electronic beehive monitoring extracts critical information on colony behavior and phenology without invasive beehive inspections and transportation costs. As an integral component of electronic beehive monitoring, audio beehive monitoring has the potential to automate the identification of various stressors for honeybee colonies from beehive audio samples. In this investigation, we designed several convolutional neural networks and compared their performance with four standard machine learning methods (logistic regression, k-nearest neighbors, support vector machines, and random forests) in classifying audio samples from microphones deployed above landing pads of Langstroth beehives. On a dataset of 10,260 audio samples where the training and testing …

Product Innovation Design Based On Deep Learning And Kansei Engineering, Huafeng Quan, Shaobo Li, Jianjun Hu

Faculty Publications

Creative product design is becoming critical to the success of many enterprises. However, the conventional product innovation process is hindered by two major challenges: the difficulty to capture users’ preferences and the lack of intuitive approaches to visually inspire the designer, which is especially true in fashion design and form design of many other types of products. In this paper, we propose to combine Kansei engineering and the deep learning for product innovation (KENPI) framework, which can transfer color, pattern, etc. of a style image in real time to a product’s shape automatically. To capture user preferences, we combine Kansei …

A Distributed Semi-Supervised Platform For Dnase-Seq Data Analytics Using Deep Generative Convolutional Networks, Shayan Shams, Richard Platania, Joohyun Kim, Jian Zhang, Kisung Lee, Seungwon Yang, Seung Jong Park

Computer Science Faculty Research & Creative Works

A deep learning approach for analyzing DNase-seq datasets is presented, which has promising potentials for unraveling biological underpinnings on transcription regulation mechanisms. Further understanding of these mechanisms can lead to important advances in life sciences in general and drug, biomarker discovery, and cancer research in particular. Motivated by recent remarkable advances in the field of deep learning, we developed a platform, Deep Semi-Supervised DNase-seq Analytics (DSSDA). Primarily empowered by deep generative Convolutional Networks (ConvNets), the most notable aspect is the capability of semi-supervised learning, which is highly beneficial for common biological settings often plagued with a less sufficient number of …

Deep Learning For Practical Image Recognition: Case Study On Kaggle Competitions, Xulei Yang, Zeng Zeng, Sin G. Teo, Li Wang, Vijay Chandrasekar, Steven C. H. Hoi

Research Collection School Of Computing and Information Systems

In past years, deep convolutional neural networks (DCNN) have achieved big successes in image classification and object detection, as demonstrated on ImageNet in academic field. However, There are some unique practical challenges remain for real-world image recognition applications, e.g., small size of the objects, imbalanced data distributions, limited labeled data samples, etc. In this work, we are making efforts to deal with these challenges through a computational framework by incorporating latest developments in deep learning. In terms of two-stage detection scheme, pseudo labeling, data augmentation, cross-validation and ensemble learning, the proposed framework aims to achieve better performances for practical image …

Towards Distributed Cyberinfrastructure For Smart Cities Using Big Data And Deep Learning Technologies, Shayan Shams, Sayan Goswami, Kisung Lee, Seungwon Yang, Seung Jong Park

Computer Science Faculty Research & Creative Works

Recent advances in big data and deep learning technologies have enabled researchers across many disciplines to gain new insight into large and complex data. For example, deep neural networks are being widely used to analyze various types of data including images, videos, texts, and time-series data. In another example, various disciplines such as sociology, social work, and criminology are analyzing crowd-sourced and online social network data using big data technologies to gain new insight from a plethora of data. Even though many different types of data are being generated and analyzed in various domains, the development of distributed city-level cyberinfrastructure …

Deep Learning For Link Prediction In Dynamic Networks Using Weak Estimators, Carter Chiu, Justin Zhan

Computer Science Faculty Research

Link prediction is the task of evaluating the probability that an edge exists in a network, and it has useful applications in many domains. Traditional approaches rely on measuring the similarity between two nodes in a static context. Recent research has focused on extending link prediction to a dynamic setting, predicting the creation and destruction of links in networks that evolve over time. Though a difficult task, the employment of deep learning techniques have shown to make notable improvements to the accuracy of predictions. To this end, we propose the novel application of weak estimators in addition to the utilization …

Deep Code Comment Generation, Xing Hu, Ge Li, Xin Xia, David Lo, Zhi Jin

Research Collection School Of Computing and Information Systems

During software maintenance, code comments help developerscomprehend programs and reduce additional time spent on readingand navigating source code. Unfortunately, these comments areoften mismatched, missing or outdated in the software projects.Developers have to infer the functionality from the source code.This paper proposes a new approach named DeepCom to automatically generate code comments for Java methods. The generatedcomments aim to help developers understand the functionalityof Java methods. DeepCom applies Natural Language Processing(NLP) techniques to learn from a large code corpus and generatescomments from learned features. We use a deep neural networkthat analyzes structural information of Java methods for bettercomments generation. We conduct …

Ai-Human Collaboration Via Eeg, Adam Noack

All College Thesis Program, 2016-2019

As AI becomes ever more competent and integrated into our lives, the issue of AI-human goal misalignment looms larger. This is partially because there is often a rift between what humans explicitly command and what they actually mean. Most contemporary AI systems cannot bridge this gap. In this study we attempted to reconcile the goals of human and machine by using EEG signals from a human to help a simulated agent complete a task.

Speech Emotion Recognition Using Convolutional Neural Networks, Somayeh Shahsavarani

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Automatic speech recognition is an active field of study in artificial intelligence and machine learning whose aim is to generate machines that communicate with people via speech. Speech is an information-rich signal that contains paralinguistic information as well as linguistic information. Emotion is one key instance of paralinguistic information that is, in part, conveyed by speech. Developing machines that understand paralinguistic information, such as emotion, facilitates the human-machine communication as it makes the communication more clear and natural. In the current study, the efficacy of convolutional neural networks in recognition of speech emotions has been investigated. Wide-band spectrograms of the …

Attributed Social Network Embedding, Lizi Liao, Xiangnan He, Hanwang Zhang, Tat-Seng Chua

Research Collection School Of Computing and Information Systems

Embedding network data into a low-dimensional vector space has shown promising performance for many real-world applications, such as node classification and entity retrieval. However, most existing methods focused only on leveraging network structure. For social networks, besides the network structure, there also exists rich information about social actors, such as user profiles of friendship networks and textual content of citation networks. These rich attribute information of social actors reveal the homophily effect, exerting huge impacts on the formation of social networks. In this paper, we explore the rich evidence source of attributes in social networks to improve network embedding. We …

Patent Keyword Extraction Algorithm Based On Distributed Representation For Patent Classification, Jie Hu, Shaobo Li, Yong Yao, Liya Yu, Guanci Yang, Jianjun Hu

Faculty Publications

Many text mining tasks such as text retrieval, text summarization, and text comparisons depend on the extraction of representative keywords from the main text. Most existing keyword extraction algorithms are based on discrete bag-of-words type of word representation of the text. In this paper, we propose a patent keyword extraction algorithm (PKEA) based on the distributed Skip-gram model for patent classification. We also develop a set of quantitative performance measures for keyword extraction evaluation based on information gain and cross-validation, based on Support Vector Machine (SVM) classification, which are valuable when human-annotated keywords are not available. We used a standard …

Continuous Restricted Boltzmann Machines, Robert W. Harrison

EBCS Articles

Restricted Boltzmann machines are a generative neural network. They summarize their input data to build a probabilistic model that can then be used to reconstruct missing data or to classify new data. Unlike discrete Boltzmann machines, where the data are mapped to the space of integers or bitstrings, continuous Boltzmann machines directly use floating point numbers and therefore represent the data with higher fidelity. The primary limitation in using Boltzmann machines for big-data problems is the efficiency of the training algorithm. This paper describes an efficient deterministic algorithm for training continuous machines.

Review Of Deep Learning Methods In Robotic Grasp Detection, Shehan Caldera, Alexander Rassau, Douglas Chai

Research outputs 2014 to 2021

For robots to attain more general-purpose utility, grasping is a necessary skill to master. Such general-purpose robots may use their perception abilities to visually identify grasps for a given object. A grasp describes how a robotic end-effector can be arranged to securely grab an object and successfully lift it without slippage. Traditionally, grasp detection requires expert human knowledge to analytically form the task-specific algorithm, but this is an arduous and time-consuming approach. During the last five years, deep learning methods have enabled significant advancements in robotic vision, natural language processing, and automated driving applications. The successful results of these methods …

Estimating Meteorological Visibility Range Under Foggy Weather Conditions: A Deep Learning Approach, Hazar Chaabani, Naoufel Werghi, Faouzi Kamoun, Bilal Taha, Fatma Outay, Ansar Ul Haque Yasar

All Works

© 2018 The Authors. Published by Elsevier Ltd. Systems capable of estimating visibility distances under foggy weather conditions are extremely useful for next-generation cooperative situational awareness and collision avoidance systems. In this paper, we present a brief review of noticeable approaches for determining visibility distance under foggy weather conditions. We then propose a novel approach based on the combination of a deep learning method for feature extraction and an SVM classifier. We present a quantitative evaluation of the proposed solution and show that our approach provides better performance results compared to an earlier approach that was based on the combination …

A Comparison Of Classical Versus Deep Learning Techniques For Abusive Content Detection On Social Media Sites, Hao Che, Susan Mckeever, Sarah Jane Delany

Conference papers

The automated detection of abusive content on social media websites faces a variety of challenges including imbalanced training sets, the identification of an appropriate feature representation and the selection of optimal classifiers. Classifiers such as support vector machines (SVM), combined with bag of words or ngram feature representation, have traditionally dominated in text classification for decades. With the recent emergence of deep learning and word embeddings, an increasing number of researchers have started to focus on deep neural networks. In this paper, our aim is to explore cutting-edge techniques in automated abusive content detection. We use two deep learning approaches: …