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Automated Coding of Under-Studied Medical Concept Domains: Linking Physical Activity Reports to the International Classification of Functioning, Disability, and Health

Nov 27, 2020
Denis Newman-Griffis, Eric Fosler-Lussier

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

* 30 pages (21 text + 9 references); 9 figures, 2 tables 

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What is Wrong with Topic Modeling? (and How to Fix it Using Search-based Software Engineering)

Feb 20, 2018
Amritanshu Agrawal, Wei Fu, Tim Menzies

Context: Topic modeling finds human-readable structures in unstructured textual data. A widely used topic modeler is Latent Dirichlet allocation. When run on different datasets, LDA suffers from "order effects" i.e. different topics are generated if the order of training data is shuffled. Such order effects introduce a systematic error for any study. This error can relate to misleading results;specifically, inaccurate topic descriptions and a reduction in the efficacy of text mining classification results. Objective: To provide a method in which distributions generated by LDA are more stable and can be used for further analysis. Method: We use LDADE, a search-based software engineering tool that tunes LDA's parameters using DE (Differential Evolution). LDADE is evaluated on data from a programmer information exchange site (Stackoverflow), title and abstract text of thousands ofSoftware Engineering (SE) papers, and software defect reports from NASA. Results were collected across different implementations of LDA (Python+Scikit-Learn, Scala+Spark); across different platforms (Linux, Macintosh) and for different kinds of LDAs (VEM,or using Gibbs sampling). Results were scored via topic stability and text mining classification accuracy. Results: In all treatments: (i) standard LDA exhibits very large topic instability; (ii) LDADE's tunings dramatically reduce cluster instability; (iii) LDADE also leads to improved performances for supervised as well as unsupervised learning. Conclusion: Due to topic instability, using standard LDA with its "off-the-shelf" settings should now be depreciated. Also, in future, we should require SE papers that use LDA to test and (if needed) mitigate LDA topic instability. Finally, LDADE is a candidate technology for effectively and efficiently reducing that instability.

* Information and Software Technology Journal, 2018 
* 15 pages + 2 page references. Accepted to IST 

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CGEMs: A Metric Model for Automatic Code Generation using GPT-3

Aug 23, 2021
Aishwarya Narasimhan, Krishna Prasad Agara Venkatesha Rao, Veena M B

Today, AI technology is showing its strengths in almost every industry and walks of life. From text generation, text summarization, chatbots, NLP is being used widely. One such paradigm is automatic code generation. An AI could be generating anything; hence the output space is unconstrained. A self-driving car is driven for 100 million miles to validate its safety, but tests cannot be written to monitor and cover an unconstrained space. One of the solutions to validate AI-generated content is to constrain the problem and convert it from abstract to realistic, and this can be accomplished by either validating the unconstrained algorithm using theoretical proofs or by using Monte-Carlo simulation methods. In this case, we use the latter approach to test/validate a statistically significant number of samples. This hypothesis of validating the AI-generated code is the main motive of this work and to know if AI-generated code is reliable, a metric model CGEMs is proposed. This is an extremely challenging task as programs can have different logic with different naming conventions, but the metrics must capture the structure and logic of the program. This is similar to the importance grammar carries in AI-based text generation, Q&A, translations, etc. The various metrics that are garnered in this work to support the evaluation of generated code are as follows: Compilation, NL description to logic conversion, number of edits needed, some of the commonly used static-code metrics and NLP metrics. These metrics are applied to 80 codes generated using OpenAI's GPT-3. Post which a Neural network is designed for binary classification (acceptable/not acceptable quality of the generated code). The inputs to this network are the values of the features obtained from the metrics. The model achieves a classification accuracy of 76.92% and an F1 score of 55.56%. XAI is augmented for model interpretability.

* 11 pages, 6 figures, 2 tables 

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A Discriminative Semantic Ranker for Question Retrieval

Jul 18, 2021
Yinqiong Cai, Yixing Fan, Jiafeng Guo, Ruqing Zhang, Yanyan Lan, Xueqi Cheng

Similar question retrieval is a core task in community-based question answering (CQA) services. To balance the effectiveness and efficiency, the question retrieval system is typically implemented as multi-stage rankers: The first-stage ranker aims to recall potentially relevant questions from a large repository, and the latter stages attempt to re-rank the retrieved results. Most existing works on question retrieval mainly focused on the re-ranking stages, leaving the first-stage ranker to some traditional term-based methods. However, term-based methods often suffer from the vocabulary mismatch problem, especially on short texts, which may block the re-rankers from relevant questions at the very beginning. An alternative is to employ embedding-based methods for the first-stage ranker, which compress texts into dense vectors to enhance the semantic matching. However, these methods often lose the discriminative power as term-based methods, thus introduce noise during retrieval and hurt the recall performance. In this work, we aim to tackle the dilemma of the first-stage ranker, and propose a discriminative semantic ranker, namely DenseTrans, for high-recall retrieval. Specifically, DenseTrans is a densely connected Transformer, which learns semantic embeddings for texts based on Transformer layers. Meanwhile, DenseTrans promotes low-level features through dense connections to keep the discriminative power of the learned representations. DenseTrans is inspired by DenseNet in computer vision (CV), but poses a new way to use the dense connectivity which is totally different from its original design purpose. Experimental results over two question retrieval benchmark datasets show that our model can obtain significant gain on recall against strong term-based methods as well as state-of-the-art embedding-based methods.

* ICTIR'21 

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Visual-Texual Emotion Analysis with Deep Coupled Video and Danmu Neural Networks

Nov 19, 2018
Chenchen Li, Jialin Wang, Hongwei Wang, Miao Zhao, Wenjie Li, Xiaotie Deng

User emotion analysis toward videos is to automatically recognize the general emotional status of viewers from the multimedia content embedded in the online video stream. Existing works fall in two categories: 1) visual-based methods, which focus on visual content and extract a specific set of features of videos. However, it is generally hard to learn a mapping function from low-level video pixels to high-level emotion space due to great intra-class variance. 2) textual-based methods, which focus on the investigation of user-generated comments associated with videos. The learned word representations by traditional linguistic approaches typically lack emotion information and the global comments usually reflect viewers' high-level understandings rather than instantaneous emotions. To address these limitations, in this paper, we propose to jointly utilize video content and user-generated texts simultaneously for emotion analysis. In particular, we introduce exploiting a new type of user-generated texts, i.e., "danmu", which are real-time comments floating on the video and contain rich information to convey viewers' emotional opinions. To enhance the emotion discriminativeness of words in textual feature extraction, we propose Emotional Word Embedding (EWE) to learn text representations by jointly considering their semantics and emotions. Afterwards, we propose a novel visual-textual emotion analysis model with Deep Coupled Video and Danmu Neural networks (DCVDN), in which visual and textual features are synchronously extracted and fused to form a comprehensive representation by deep-canonically-correlated-autoencoder-based multi-view learning. Through extensive experiments on a self-crawled real-world video-danmu dataset, we prove that DCVDN significantly outperforms the state-of-the-art baselines.

* Draft, 25 pages 

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Pre-Trained Language Transformers are Universal Image Classifiers

Jan 25, 2022
Rahul Goel, Modar Sulaiman, Kimia Noorbakhsh, Mahdi Sharifi, Rajesh Sharma, Pooyan Jamshidi, Kallol Roy

Facial images disclose many hidden personal traits such as age, gender, race, health, emotion, and psychology. Understanding these traits will help to classify the people in different attributes. In this paper, we have presented a novel method for classifying images using a pretrained transformer model. We apply the pretrained transformer for the binary classification of facial images in criminal and non-criminal classes. The pretrained transformer of GPT-2 is trained to generate text and then fine-tuned to classify facial images. During the finetuning process with images, most of the layers of GT-2 are frozen during backpropagation and the model is frozen pretrained transformer (FPT). The FPT acts as a universal image classifier, and this paper shows the application of FPT on facial images. We also use our FPT on encrypted images for classification. Our FPT shows high accuracy on both raw facial images and encrypted images. We hypothesize the meta-learning capacity FPT gained because of its large size and trained on a large size with theory and experiments. The GPT-2 trained to generate a single word token at a time, through the autoregressive process, forced to heavy-tail distribution. Then the FPT uses the heavy-tail property as its meta-learning capacity for classifying images. Our work shows one way to avoid bias during the machine classification of images.The FPT encodes worldly knowledge because of the pretraining of one text, which it uses during the classification. The statistical error of classification is reduced because of the added context gained from the text.Our paper shows the ethical dimension of using encrypted data for classification.Criminal images are sensitive to share across the boundary but encrypted largely evades ethical concern.FPT showing good classification accuracy on encrypted images shows promise for further research on privacy-preserving machine learning.

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Deep multi-modal networks for book genre classification based on its cover

Nov 15, 2020
Chandra Kundu, Lukun Zheng

Book covers are usually the very first impression to its readers and they often convey important information about the content of the book. Book genre classification based on its cover would be utterly beneficial to many modern retrieval systems, considering that the complete digitization of books is an extremely expensive task. At the same time, it is also an extremely challenging task due to the following reasons: First, there exists a wide variety of book genres, many of which are not concretely defined. Second, book covers, as graphic designs, vary in many different ways such as colors, styles, textual information, etc, even for books of the same genre. Third, book cover designs may vary due to many external factors such as country, culture, target reader populations, etc. With the growing competitiveness in the book industry, the book cover designers and typographers push the cover designs to its limit in the hope of attracting sales. The cover-based book classification systems become a particularly exciting research topic in recent years. In this paper, we propose a multi-modal deep learning framework to solve this problem. The contribution of this paper is four-fold. First, our method adds an extra modality by extracting texts automatically from the book covers. Second, image-based and text-based, state-of-the-art models are evaluated thoroughly for the task of book cover classification. Third, we develop an efficient and salable multi-modal framework based on the images and texts shown on the covers only. Fourth, a thorough analysis of the experimental results is given and future works to improve the performance is suggested. The results show that the multi-modal framework significantly outperforms the current state-of-the-art image-based models. However, more efforts and resources are needed for this classification task in order to reach a satisfactory level.

* 23 pages, 8 figures 

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An Improved Cutting Plane Method for Convex Optimization, Convex-Concave Games and its Applications

Apr 08, 2020
Haotian Jiang, Yin Tat Lee, Zhao Song, Sam Chiu-wai Wong

Given a separation oracle for a convex set $K \subset \mathbb{R}^n$ that is contained in a box of radius $R$, the goal is to either compute a point in $K$ or prove that $K$ does not contain a ball of radius $\epsilon$. We propose a new cutting plane algorithm that uses an optimal $O(n \log (\kappa))$ evaluations of the oracle and an additional $O(n^2)$ time per evaluation, where $\kappa = nR/\epsilon$. $\bullet$ This improves upon Vaidya's $O( \text{SO} \cdot n \log (\kappa) + n^{\omega+1} \log (\kappa))$ time algorithm [Vaidya, FOCS 1989a] in terms of polynomial dependence on $n$, where $\omega < 2.373$ is the exponent of matrix multiplication and $\text{SO}$ is the time for oracle evaluation. $\bullet$ This improves upon Lee-Sidford-Wong's $O( \text{SO} \cdot n \log (\kappa) + n^3 \log^{O(1)} (\kappa))$ time algorithm [Lee, Sidford and Wong, FOCS 2015] in terms of dependence on $\kappa$. For many important applications in economics, $\kappa = \Omega(\exp(n))$ and this leads to a significant difference between $\log(\kappa)$ and $\mathrm{poly}(\log (\kappa))$. We also provide evidence that the $n^2$ time per evaluation cannot be improved and thus our running time is optimal. A bottleneck of previous cutting plane methods is to compute leverage scores, a measure of the relative importance of past constraints. Our result is achieved by a novel multi-layered data structure for leverage score maintenance, which is a sophisticated combination of diverse techniques such as random projection, batched low-rank update, inverse maintenance, polynomial interpolation, and fast rectangular matrix multiplication. Interestingly, our method requires a combination of different fast rectangular matrix multiplication algorithms.

* STOC 2020 

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Graph Neural Networks with Continual Learning for Fake News Detection from Social Media

Jul 07, 2020
Yi Han, Shanika Karunasekera, Christopher Leckie

Although significant effort has been applied to fact-checking, the prevalence of fake news over social media, which has profound impact on justice, public trust and our society as a whole, remains a serious problem. In this work, we focus on propagation-based fake news detection, as recent studies have demonstrated that fake news and real news spread differently online. Specifically, considering the capability of graph neural networks (GNNs) in dealing with non-Euclidean data, we use GNNs to differentiate between the propagation patterns of fake and real news on social media. In particular, we concentrate on two questions: (1) Without relying on any text information, e.g., tweet content, replies and user descriptions, how accurately can GNNs identify fake news? Machine learning models are known to be vulnerable to adversarial attacks, and avoiding the dependence on text-based features can make the model less susceptible to the manipulation of advanced fake news fabricators. (2) How to deal with new, unseen data? In other words, how does a GNN trained on a given dataset perform on a new and potentially vastly different dataset? If it achieves unsatisfactory performance, how do we solve the problem without re-training the model on the entire data from scratch, which would become prohibitively expensive in practice as the data volumes grow? We study the above questions on two datasets with thousands of labelled news, and our results show that: (1) GNNs can indeed achieve comparable or superior performance without any text information to state-of-the-art methods. (2) GNNs trained on a given dataset may perform poorly on new, unseen data, and direct incremental training cannot solve the problem. In order to solve the problem, we propose a method that achieves balanced performance on both existing and new datasets, by using techniques from continual learning to train GNNs incrementally.

* 10 pages, 12 figures, 3 tables 

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TI-CNN: Convolutional Neural Networks for Fake News Detection

Jun 03, 2018
Yang Yang, Lei Zheng, Jiawei Zhang, Qingcai Cui, Zhoujun Li, Philip S. Yu

With the development of social networks, fake news for various commercial and political purposes has been appearing in large numbers and gotten widespread in the online world. With deceptive words, people can get infected by the fake news very easily and will share them without any fact-checking. For instance, during the 2016 US president election, various kinds of fake news about the candidates widely spread through both official news media and the online social networks. These fake news is usually released to either smear the opponents or support the candidate on their side. The erroneous information in the fake news is usually written to motivate the voters' irrational emotion and enthusiasm. Such kinds of fake news sometimes can bring about devastating effects, and an important goal in improving the credibility of online social networks is to identify the fake news timely. In this paper, we propose to study the fake news detection problem. Automatic fake news identification is extremely hard, since pure model based fact-checking for news is still an open problem, and few existing models can be applied to solve the problem. With a thorough investigation of a fake news data, lots of useful explicit features are identified from both the text words and images used in the fake news. Besides the explicit features, there also exist some hidden patterns in the words and images used in fake news, which can be captured with a set of latent features extracted via the multiple convolutional layers in our model. A model named as TI-CNN (Text and Image information based Convolutinal Neural Network) is proposed in this paper. By projecting the explicit and latent features into a unified feature space, TI-CNN is trained with both the text and image information simultaneously. Extensive experiments carried on the real-world fake news datasets have demonstrate the effectiveness of TI-CNN.

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