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Topic Modeling for Classification of Clinical Reports

Jun 19, 2017
Efsun Sarioglu Kayi, Kabir Yadav, James M. Chamberlain, Hyeong-Ah Choi

Electronic health records (EHRs) contain important clinical information about patients. Efficient and effective use of this information could supplement or even replace manual chart review as a means of studying and improving the quality and safety of healthcare delivery. However, some of these clinical data are in the form of free text and require pre-processing before use in automated systems. A common free text data source is radiology reports, typically dictated by radiologists to explain their interpretations. We sought to demonstrate machine learning classification of computed tomography (CT) imaging reports into binary outcomes, i.e. positive and negative for fracture, using regular text classification and classifiers based on topic modeling. Topic modeling provides interpretable themes (topic distributions) in reports, a representation that is more compact than the commonly used bag-of-words representation and can be processed faster than raw text in subsequent automated processes. We demonstrate new classifiers based on this topic modeling representation of the reports. Aggregate topic classifier (ATC) and confidence-based topic classifier (CTC) use a single topic that is determined from the training dataset based on different measures to classify the reports on the test dataset. Alternatively, similarity-based topic classifier (STC) measures the similarity between the reports' topic distributions to determine the predicted class. Our proposed topic modeling-based classifier systems are shown to be competitive with existing text classification techniques and provides an efficient and interpretable representation.

* 18 pages 

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Detector-Free Weakly Supervised Grounding by Separation

Apr 20, 2021
Assaf Arbelle, Sivan Doveh, Amit Alfassy, Joseph Shtok, Guy Lev, Eli Schwartz, Hilde Kuehne, Hila Barak Levi, Prasanna Sattigeri, Rameswar Panda, Chun-Fu Chen, Alex Bronstein, Kate Saenko, Shimon Ullman, Raja Giryes, Rogerio Feris, Leonid Karlinsky

Nowadays, there is an abundance of data involving images and surrounding free-form text weakly corresponding to those images. Weakly Supervised phrase-Grounding (WSG) deals with the task of using this data to learn to localize (or to ground) arbitrary text phrases in images without any additional annotations. However, most recent SotA methods for WSG assume the existence of a pre-trained object detector, relying on it to produce the ROIs for localization. In this work, we focus on the task of Detector-Free WSG (DF-WSG) to solve WSG without relying on a pre-trained detector. We directly learn everything from the images and associated free-form text pairs, thus potentially gaining an advantage on the categories unsupported by the detector. The key idea behind our proposed Grounding by Separation (GbS) method is synthesizing `text to image-regions' associations by random alpha-blending of arbitrary image pairs and using the corresponding texts of the pair as conditions to recover the alpha map from the blended image via a segmentation network. At test time, this allows using the query phrase as a condition for a non-blended query image, thus interpreting the test image as a composition of a region corresponding to the phrase and the complement region. Using this approach we demonstrate a significant accuracy improvement, of up to $8.5\%$ over previous DF-WSG SotA, for a range of benchmarks including Flickr30K, Visual Genome, and ReferIt, as well as a significant complementary improvement (above $7\%$) over the detector-based approaches for WSG.


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VL-NMS: Breaking Proposal Bottlenecks in Two-Stage Visual-Language Matching

May 12, 2021
Wenbo Ma, Long Chen, Hanwang Zhang, Jian Shao, Yueting Zhuang, Jun Xiao

The prevailing framework for matching multimodal inputs is based on a two-stage process: 1) detecting proposals with an object detector and 2) matching text queries with proposals. Existing two-stage solutions mostly focus on the matching step. In this paper, we argue that these methods overlook an obvious \emph{mismatch} between the roles of proposals in the two stages: they generate proposals solely based on the detection confidence (i.e., query-agnostic), hoping that the proposals contain all instances mentioned in the text query (i.e., query-aware). Due to this mismatch, chances are that proposals relevant to the text query are suppressed during the filtering process, which in turn bounds the matching performance. To this end, we propose VL-NMS, which is the first method to yield query-aware proposals at the first stage. VL-NMS regards all mentioned instances as critical objects, and introduces a lightweight module to predict a score for aligning each proposal with a critical object. These scores can guide the NMS operation to filter out proposals irrelevant to the text query, increasing the recall of critical objects, resulting in a significantly improved matching performance. Since VL-NMS is agnostic to the matching step, it can be easily integrated into any state-of-the-art two-stage matching methods. We validate the effectiveness of VL-NMS on two multimodal matching tasks, namely referring expression grounding and image-text matching. Extensive ablation studies on several baselines and benchmarks consistently demonstrate the superiority of VL-NMS.


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Zero-Shot Detection via Vision and Language Knowledge Distillation

Apr 28, 2021
Xiuye Gu, Tsung-Yi Lin, Weicheng Kuo, Yin Cui

Zero-shot image classification has made promising progress by training the aligned image and text encoders. The goal of this work is to advance zero-shot object detection, which aims to detect novel objects without bounding box nor mask annotations. We propose ViLD, a training method via Vision and Language knowledge Distillation. We distill the knowledge from a pre-trained zero-shot image classification model (e.g., CLIP) into a two-stage detector (e.g., Mask R-CNN). Our method aligns the region embeddings in the detector to the text and image embeddings inferred by the pre-trained model. We use the text embeddings as the detection classifier, obtained by feeding category names into the pre-trained text encoder. We then minimize the distance between the region embeddings and image embeddings, obtained by feeding region proposals into the pre-trained image encoder. During inference, we include text embeddings of novel categories into the detection classifier for zero-shot detection. We benchmark the performance on LVIS dataset by holding out all rare categories as novel categories. ViLD obtains 16.1 mask AP$_r$ with a Mask R-CNN (ResNet-50 FPN) for zero-shot detection, outperforming the supervised counterpart by 3.8. The model can directly transfer to other datasets, achieving 72.2 AP$_{50}$, 36.6 AP and 11.8 AP on PASCAL VOC, COCO and Objects365, respectively.


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Align and Prompt: Video-and-Language Pre-training with Entity Prompts

Dec 23, 2021
Dongxu Li, Junnan Li, Hongdong Li, Juan Carlos Niebles, Steven C. H. Hoi

Video-and-language pre-training has shown promising improvements on various downstream tasks. Most previous methods capture cross-modal interactions with a transformer-based multimodal encoder, not fully addressing the misalignment between unimodal video and text features. Besides, learning fine-grained visual-language alignment usually requires off-the-shelf object detectors to provide object information, which is bottlenecked by the detector's limited vocabulary and expensive computation cost. We propose Align and Prompt: an efficient and effective video-and-language pre-training framework with better cross-modal alignment. First, we introduce a video-text contrastive (VTC) loss to align unimodal video-text features at the instance level, which eases the modeling of cross-modal interactions. Then, we propose a new visually-grounded pre-training task, prompting entity modeling (PEM), which aims to learn fine-grained region-entity alignment. To achieve this, we first introduce an entity prompter module, which is trained with VTC to produce the similarity between a video crop and text prompts instantiated with entity names. The PEM task then asks the model to predict the entity pseudo-labels (i.e~normalized similarity scores) for randomly-selected video crops. The resulting pre-trained model achieves state-of-the-art performance on both text-video retrieval and videoQA, outperforming prior work by a substantial margin. Our code and pre-trained models are available at https://github.com/salesforce/ALPRO.


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Quantifying literature quality using complexity criteria

Jan 15, 2017
Gerardo Febres, Klaus Jaffe

We measured entropy and symbolic diversity for English and Spanish texts including literature Nobel laureates and other famous authors. Entropy, symbol diversity and symbol frequency profiles were compared for these four groups. We also built a scale sensitive to the quality of writing and evaluated its relationship with the Flesch's readability index for English and the Szigriszt's perspicuity index for Spanish. Results suggest a correlation between entropy and word diversity with quality of writing. Text genre also influences the resulting entropy and diversity of the text. Results suggest the plausibility of automated quality assessment of texts.

* Journal of Quantitative Linguistics, 2017, Vol 24, Iss 1 
* Submitted for publication. 29 pages. 8 figures, 4 tables, 4 appendixes 

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Marvin: Semantic annotation using multiple knowledge sources

Feb 02, 2016
Nikola Milosevic

People are producing more written material then anytime in the history. The increase is so high that professionals from the various fields are no more able to cope with this amount of publications. Text mining tools can offer tools to help them and one of the tools that can aid information retrieval and information extraction is semantic text annotation. In this report we present Marvin, a text annotator written in Java, which can be used as a command line tool and as a Java library. Marvin is able to annotate text using multiple sources, including WordNet, MetaMap, DBPedia and thesauri represented as SKOS.

* 9 pages, 4 figures, keywords: Semantic annotation, text normalization, semantic web, linked data, information management, text mining, information extraction, data curation 

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DOM-LM: Learning Generalizable Representations for HTML Documents

Jan 25, 2022
Xiang Deng, Prashant Shiralkar, Colin Lockard, Binxuan Huang, Huan Sun

HTML documents are an important medium for disseminating information on the Web for human consumption. An HTML document presents information in multiple text formats including unstructured text, structured key-value pairs, and tables. Effective representation of these documents is essential for machine understanding to enable a wide range of applications, such as Question Answering, Web Search, and Personalization. Existing work has either represented these documents using visual features extracted by rendering them in a browser, which is typically computationally expensive, or has simply treated them as plain text documents, thereby failing to capture useful information presented in their HTML structure. We argue that the text and HTML structure together convey important semantics of the content and therefore warrant a special treatment for their representation learning. In this paper, we introduce a novel representation learning approach for web pages, dubbed DOM-LM, which addresses the limitations of existing approaches by encoding both text and DOM tree structure with a transformer-based encoder and learning generalizable representations for HTML documents via self-supervised pre-training. We evaluate DOM-LM on a variety of webpage understanding tasks, including Attribute Extraction, Open Information Extraction, and Question Answering. Our extensive experiments show that DOM-LM consistently outperforms all baselines designed for these tasks. In particular, DOM-LM demonstrates better generalization performance both in few-shot and zero-shot settings, making it attractive for making it suitable for real-world application settings with limited labeled data.


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Exploration and Exploitation of Victorian Science in Darwin's Reading Notebooks

Feb 02, 2017
Jaimie Murdock, Colin Allen, Simon DeDeo

Search in an environment with an uncertain distribution of resources involves a trade-off between exploitation of past discoveries and further exploration. This extends to information foraging, where a knowledge-seeker shifts between reading in depth and studying new domains. To study this decision-making process, we examine the reading choices made by one of the most celebrated scientists of the modern era: Charles Darwin. From the full-text of books listed in his chronologically-organized reading journals, we generate topic models to quantify his local (text-to-text) and global (text-to-past) reading decisions using Kullback-Liebler Divergence, a cognitively-validated, information-theoretic measure of relative surprise. Rather than a pattern of surprise-minimization, corresponding to a pure exploitation strategy, Darwin's behavior shifts from early exploitation to later exploration, seeking unusually high levels of cognitive surprise relative to previous eras. These shifts, detected by an unsupervised Bayesian model, correlate with major intellectual epochs of his career as identified both by qualitative scholarship and Darwin's own self-commentary. Our methods allow us to compare his consumption of texts with their publication order. We find Darwin's consumption more exploratory than the culture's production, suggesting that underneath gradual societal changes are the explorations of individual synthesis and discovery. Our quantitative methods advance the study of cognitive search through a framework for testing interactions between individual and collective behavior and between short- and long-term consumption choices. This novel application of topic modeling to characterize individual reading complements widespread studies of collective scientific behavior.

* Cognition 159 (2017) 117-126 
* Cognition pre-print, published February 2017; 22 pages, plus 17 pages supporting information, 7 pages references 

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Settling the Sample Complexity of Model-Based Offline Reinforcement Learning

Apr 11, 2022
Gen Li, Laixi Shi, Yuxin Chen, Yuejie Chi, Yuting Wei

This paper is concerned with offline reinforcement learning (RL), which learns using pre-collected data without further exploration. Effective offline RL would be able to accommodate distribution shift and limited data coverage. However, prior algorithms or analyses either suffer from suboptimal sample complexities or incur high burn-in cost to reach sample optimality, thus posing an impediment to efficient offline RL in sample-starved applications. We demonstrate that the model-based (or "plug-in") approach achieves minimax-optimal sample complexity without burn-in cost for tabular Markov decision processes (MDPs). Concretely, consider a finite-horizon (resp. $\gamma$-discounted infinite-horizon) MDP with $S$ states and horizon $H$ (resp. effective horizon $\frac{1}{1-\gamma}$), and suppose the distribution shift of data is reflected by some single-policy clipped concentrability coefficient $C^{\star}_{\text{clipped}}$. We prove that model-based offline RL yields $\varepsilon$-accuracy with a sample complexity of \[ \begin{cases} \frac{H^{4}SC_{\text{clipped}}^{\star}}{\varepsilon^{2}} & (\text{finite-horizon MDPs}) \frac{SC_{\text{clipped}}^{\star}}{(1-\gamma)^{3}\varepsilon^{2}} & (\text{infinite-horizon MDPs}) \end{cases} \] up to log factor, which is minimax optimal for the entire $\varepsilon$-range. Our algorithms are "pessimistic" variants of value iteration with Bernstein-style penalties, and do not require sophisticated variance reduction.


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