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How essential are unstructured clinical narratives and information fusion to clinical trial recruitment?

Feb 13, 2015
Preethi Raghavan, James L. Chen, Eric Fosler-Lussier, Albert M. Lai

Electronic health records capture patient information using structured controlled vocabularies and unstructured narrative text. While structured data typically encodes lab values, encounters and medication lists, unstructured data captures the physician's interpretation of the patient's condition, prognosis, and response to therapeutic intervention. In this paper, we demonstrate that information extraction from unstructured clinical narratives is essential to most clinical applications. We perform an empirical study to validate the argument and show that structured data alone is insufficient in resolving eligibility criteria for recruiting patients onto clinical trials for chronic lymphocytic leukemia (CLL) and prostate cancer. Unstructured data is essential to solving 59% of the CLL trial criteria and 77% of the prostate cancer trial criteria. More specifically, for resolving eligibility criteria with temporal constraints, we show the need for temporal reasoning and information integration with medical events within and across unstructured clinical narratives and structured data.

* AMIA TBI 2014, 6 pages 

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Modelling the Lexicon in Unsupervised Part of Speech Induction

Feb 26, 2014
Greg Dubbin, Phil Blunsom

Automatically inducing the syntactic part-of-speech categories for words in text is a fundamental task in Computational Linguistics. While the performance of unsupervised tagging models has been slowly improving, current state-of-the-art systems make the obviously incorrect assumption that all tokens of a given word type must share a single part-of-speech tag. This one-tag-per-type heuristic counters the tendency of Hidden Markov Model based taggers to over generate tags for a given word type. However, it is clearly incompatible with basic syntactic theory. In this paper we extend a state-of-the-art Pitman-Yor Hidden Markov Model tagger with an explicit model of the lexicon. In doing so we are able to incorporate a soft bias towards inducing few tags per type. We develop a particle filter for drawing samples from the posterior of our model and present empirical results that show that our model is competitive with and faster than the state-of-the-art without making any unrealistic restrictions.

* To be presented at the 14th Conference of the European Chapter of the Association for Computational Linguistics 

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Japanese-Spanish Thesaurus Construction Using English as a Pivot

Mar 06, 2013
Jessica Ramírez, Masayuki Asahara, Yuji Matsumoto

We present the results of research with the goal of automatically creating a multilingual thesaurus based on the freely available resources of Wikipedia and WordNet. Our goal is to increase resources for natural language processing tasks such as machine translation targeting the Japanese-Spanish language pair. Given the scarcity of resources, we use existing English resources as a pivot for creating a trilingual Japanese-Spanish-English thesaurus. Our approach consists of extracting the translation tuples from Wikipedia, disambiguating them by mapping them to WordNet word senses. We present results comparing two methods of disambiguation, the first using VSM on Wikipedia article texts and WordNet definitions, and the second using categorical information extracted from Wikipedia, We find that mixing the two methods produces favorable results. Using the proposed method, we have constructed a multilingual Spanish-Japanese-English thesaurus consisting of 25,375 entries. The same method can be applied to any pair of languages that are linked to English in Wikipedia.

* In Proceeding of The Third International Joint Conference on Natural Language Processing (IJCNLP-08), Hyderabad, India. pages 473-480, 2008 

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Marginalized Denoising Autoencoders for Domain Adaptation

Jun 18, 2012
Minmin Chen, Zhixiang Xu, Kilian Weinberger, Fei Sha

Stacked denoising autoencoders (SDAs) have been successfully used to learn new representations for domain adaptation. Recently, they have attained record accuracy on standard benchmark tasks of sentiment analysis across different text domains. SDAs learn robust data representations by reconstruction, recovering original features from data that are artificially corrupted with noise. In this paper, we propose marginalized SDA (mSDA) that addresses two crucial limitations of SDAs: high computational cost and lack of scalability to high-dimensional features. In contrast to SDAs, our approach of mSDA marginalizes noise and thus does not require stochastic gradient descent or other optimization algorithms to learn parameters ? in fact, they are computed in closed-form. Consequently, mSDA, which can be implemented in only 20 lines of MATLAB^{TM}, significantly speeds up SDAs by two orders of magnitude. Furthermore, the representations learnt by mSDA are as effective as the traditional SDAs, attaining almost identical accuracies in benchmark tasks.

* ICML2012 

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Mostly-Unsupervised Statistical Segmentation of Japanese Kanji Sequences

May 10, 2002
Rie Kubota Ando, Lillian Lee

Given the lack of word delimiters in written Japanese, word segmentation is generally considered a crucial first step in processing Japanese texts. Typical Japanese segmentation algorithms rely either on a lexicon and syntactic analysis or on pre-segmented data; but these are labor-intensive, and the lexico-syntactic techniques are vulnerable to the unknown word problem. In contrast, we introduce a novel, more robust statistical method utilizing unsegmented training data. Despite its simplicity, the algorithm yields performance on long kanji sequences comparable to and sometimes surpassing that of state-of-the-art morphological analyzers over a variety of error metrics. The algorithm also outperforms another mostly-unsupervised statistical algorithm previously proposed for Chinese. Additionally, we present a two-level annotation scheme for Japanese to incorporate multiple segmentation granularities, and introduce two novel evaluation metrics, both based on the notion of a compatible bracket, that can account for multiple granularities simultaneously.

* Natural Language Engineering 9 (2), pp. 127--149, 2003 
* 22 pages. To appear in Natural Language Engineering 

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Prompt Tuning for Discriminative Pre-trained Language Models

May 23, 2022
Yuan Yao, Bowen Dong, Ao Zhang, Zhengyan Zhang, Ruobing Xie, Zhiyuan Liu, Leyu Lin, Maosong Sun, Jianyong Wang

Recent works have shown promising results of prompt tuning in stimulating pre-trained language models (PLMs) for natural language processing (NLP) tasks. However, to the best of our knowledge, existing works focus on prompt-tuning generative PLMs that are pre-trained to generate target tokens, such as BERT. It is still unknown whether and how discriminative PLMs, e.g., ELECTRA, can be effectively prompt-tuned. In this work, we present DPT, the first prompt tuning framework for discriminative PLMs, which reformulates NLP tasks into a discriminative language modeling problem. Comprehensive experiments on text classification and question answering show that, compared with vanilla fine-tuning, DPT achieves significantly higher performance, and also prevents the unstable problem in tuning large PLMs in both full-set and low-resource settings. The source code and experiment details of this paper can be obtained from https://github.com/thunlp/DPT.

* Accepted by Findings of ACL 2022 

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Why GANs are overkill for NLP

May 19, 2022
David Alvarez-Melis, Vikas Garg, Adam Tauman Kalai

This work offers a novel theoretical perspective on why, despite numerous attempts, adversarial approaches to generative modeling (e.g., GANs) have not been as popular for certain generation tasks, particularly sequential tasks such as Natural Language Generation, as they have in others, such as Computer Vision. In particular, on sequential data such as text, maximum-likelihood approaches are significantly more utilized than GANs. We show that, while it may seem that maximizing likelihood is inherently different than minimizing distinguishability, this distinction is largely artificial and only holds for limited models. We argue that minimizing KL-divergence (i.e., maximizing likelihood) is a more efficient approach to effectively minimizing the same distinguishability criteria that adversarial models seek to optimize. Reductions show that minimizing distinguishability can be seen as simply boosting likelihood for certain families of models including n-gram models and neural networks with a softmax output layer. To achieve a full polynomial-time reduction, a novel next-token distinguishability model is considered.


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The Limits of Word Level Differential Privacy

May 02, 2022
Justus Mattern, Benjamin Weggenmann, Florian Kerschbaum

As the issues of privacy and trust are receiving increasing attention within the research community, various attempts have been made to anonymize textual data. A significant subset of these approaches incorporate differentially private mechanisms to perturb word embeddings, thus replacing individual words in a sentence. While these methods represent very important contributions, have various advantages over other techniques and do show anonymization capabilities, they have several shortcomings. In this paper, we investigate these weaknesses and demonstrate significant mathematical constraints diminishing the theoretical privacy guarantee as well as major practical shortcomings with regard to the protection against deanonymization attacks, the preservation of content of the original sentences as well as the quality of the language output. Finally, we propose a new method for text anonymization based on transformer based language models fine-tuned for paraphrasing that circumvents most of the identified weaknesses and also offers a formal privacy guarantee. We evaluate the performance of our method via thorough experimentation and demonstrate superior performance over the discussed mechanisms.


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LaMemo: Language Modeling with Look-Ahead Memory

Apr 26, 2022
Haozhe Ji, Rongsheng Zhang, Zhenyu Yang, Zhipeng Hu, Minlie Huang

Although Transformers with fully connected self-attentions are powerful to model long-term dependencies, they are struggling to scale to long texts with thousands of words in language modeling. One of the solutions is to equip the model with a recurrence memory. However, existing approaches directly reuse hidden states from the previous segment that encodes contexts in a uni-directional way. As a result, this prohibits the memory to dynamically interact with the current context that provides up-to-date information for token prediction. To remedy this issue, we propose Look-Ahead Memory (LaMemo) that enhances the recurrence memory by incrementally attending to the right-side tokens, and interpolating with the old memory states to maintain long-term information in the history. LaMemo embraces bi-directional attention and segment recurrence with an additional computation overhead only linearly proportional to the memory length. Experiments on widely used language modeling benchmarks demonstrate its superiority over the baselines equipped with different types of memory.

* Accepted by NAACL 2022 

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