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Medical professionals review clinical narratives to assign medical codes for billing and care management. This manual process is inefficient and error-prone as it involves a nuanced one-to-many mapping. Recent works on automated ICD coding learn mappings between low-dimensional representations of the reports and the codes. While they propose novel neural networks for encoding varied types of information about the codes, it is unclear as to what information in the medical codes is helpful for performance improvement and why. Here, we compare different ways to represent, or embed,
the codes based on their textual, structural and statistical characteristics, using a single deep learning baseline model in quantitative evaluations on discharge reports from the MIMIC-III intensive care unit database. We also qualitatively analyse the nature of the cases that benefit most from the code embeddings and demonstrate that code embeddings are important for predicting ambiguous and oblique codes..

IJCNLP-AACL 2021

Analyzing Code Embeddings for Coding Clinical Narratives

code embeddings

medical ai

icd classification

**Welcome to ACL-IJCNLP 2021!**

The great event is jointly organized by the Association for Computational Linguistics (ACL) and Asian Federation of Natural Language Processing (AFNLP). 

As in previous years, the program of the conference includes a poster session, tutorials, workshops and demonstrations in addition to the main conference.


We were able to keep the registration fees similar to those charged for the virtual ACL 2020. The one fee allows attendance at the main conference and any/all tutorials and workshops. These fees would be $125 Regular Early and $175 Regular Late; $50 Student Early and $75 Student Late. Early registration closes at midnight July 11, 2021 (Eastern Daylight Time).

**Reminder:** It is ACL’s policy that at least one author of each accepted paper (including ACL Finding papers) must register for the conference.

**Reminder2:** Underline site will open closer to the event. If you already registered you will receive access detail

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The great event is jointly organized by the Association for Computational Linguistics (ACL) and Asian Federation of Natural Language Processing (AFNLP).

technical paper

Wet laboratory protocols (WLPs) are critical for conveying reproducible procedures in biological research. They are composed of instructions written in natural language describing the step-wise processing of materials by specific actions. This process flow description for reagents and materials synthesis in WLPs can be captured by material state transfer graphs (MSTGs), which encode global temporal and causal relationships between actions. Here, we propose methods to automatically generate a MSTG for a given protocol by extracting all action relationships across multiple sentences. We also note that previous corpora and methods focused primarily on local intra-sentence relationships between actions and entities and did not address two critical issues: (i) resolution of implicit arguments and (ii) establishing long-range dependencies across sentences. We propose a new model that incrementally learns latent structures and is better suited to resolving inter-sentence relations and implicit arguments. This model draws upon a new corpus WLP-MSTG which was created by extending annotations in the WLP corpora for inter-sentence relations and implicit arguments. Our model achieves an F1 score of 54.53% for temporal and causal relations in protocols from our corpus, which is a significant improvement over previous models - DyGIE++:28.17%; spERT:27.81%. We make our annotated WLP-MSTG corpus available to the research community.

Learning Latent Structures for Cross Action Phrase Relations in Wet Lab Protocols

To translate large volumes of text in a globally connected world, more and more translators are integrating machine translation (MT) and post-editing (PE) into their translation workflows to generate publishable quality translations. While this process has been shown to save time and reduce errors, the task of translation is changing from mostly text production from scratch to fixing errors within useful but partly incorrect MT output. This is affecting the interface design of translation tools, where better support for text editing tasks is required. Here, we present the first study that investigates the usefulness of mid-air hand gestures in combination with the keyboard (GK) for text editing in PE of MT. Guided by a gesture elicitation study with 14 freelance translators, we develop a prototype supporting mid-air hand gestures for cursor placement, text selection, deletion, and reordering. These gestures combined with the keyboard facilitate all editing types required for PE. An evaluation of the prototype shows that the average editing duration of GK is only slightly slower than the standard mouse and keyboard (MK), even though participants are very familiar with the latter, and relative novices to the former. Furthermore, the qualitative analysis shows positive attitudes towards hand gestures for PE, especially when manipulating single words.

Mid-Air Hand Gestures for Post-Editing of Machine Translation

Geometry problem solving has attracted much attention in the NLP community recently. The task is challenging as it requires abstract problem understanding and symbolic reasoning with axiomatic knowledge. However, current datasets are either small in scale or not publicly available. Thus, we construct a new large-scale benchmark, Geometry3K, consisting of 3,002 geometry problems with dense annotation in formal language. We further propose a novel geometry solving approach with formal language and symbolic reasoning, called Interpretable Geometry Problem Solver (Inter-GPS). Inter-GPS first parses the problem text and diagram into formal language automatically via rule-based text parsing and neural object detecting, respectively. Unlike implicit learning in existing methods, Inter-GPS incorporates theorem knowledge as conditional rules and performs symbolic reasoning step by step. Also, a theorem predictor is designed to infer the theorem application sequence fed to the symbolic solver for the more efficient and reasonable searching path. Extensive experiments on the Geometry3K and GEOS datasets demonstrate that Inter-GPS achieves significant improvements over existing methods. The project with code and data is available at https://lupantech.github.io/inter-gps.

Inter-GPS: Interpretable Geometry Problem Solving with Formal Language and Symbolic Reasoning

Simultaneous speech-to-text translation is widely useful in many scenarios. The conventional cascaded approach uses a pipeline of streaming ASR followed by simultaneous MT, but suffers from error propagation and extra latency. To alleviate these issues, recent efforts attempt to directly translate the source speech into target text simultaneously, but this is much harder due to the combination of two separate tasks. We instead propose a new paradigm with the advantages of both cascaded and end-to-end approaches. The key idea is to use two separate, but synchronized, decoders on streaming ASR and direct speech-to-text translation (ST), respectively, and the intermediate results of ASR guide the decoding policy of (but is not fed as input to) ST. During training time, we use multitask learning to jointly learn these two tasks with a shared encoder. En-to-De and En-to-Es experiments on the MuST-C dataset demonstrate that our proposed technique achieves substantially better translation quality at similar levels of latency.

Direct Simultaneous Speech-to-Text Translation Assisted by Synchronized Streaming ASR

Understanding linguistics and morphology of resource-scarce code-mixed texts remains a key challenge in text processing. Although word embedding comes in handy to support downstream tasks for low-resource languages, there are plenty of scopes in improving the quality of language representation particularly for code-mixed languages. In this paper, we propose HIT, a robust representation learning method for code-mixed texts. HIT is a hierarchical transformer-based framework that captures the semantic relationship among words and hierarchically learns the sentence-level semantics using a fused attention mechanism. HIT incorporates two attention modules, a multi-headed self-attention and an outer product attention module, and computes their weighted sum to obtain the attention weights. Our evaluation of HIT on one European (Spanish) and five Indic (Hindi, Bengali, Tamil, Telugu, and Malayalam) languages across four NLP tasks on eleven datasets suggests significant performance improvement against various state-of-the-art systems. We further show the adaptability of learned representation across tasks in a transfer learning setup (with and without fine-tuning).

HIT - A Hierarchically Fused Deep Attention Network for Robust Code-mixed Language Representation

The paradigm of data programming, that uses weak supervision in the form of rules/labelling functions, and semi-supervised learning, which augments small amounts of labelled data with a large unlabelled dataset, have shown great promise in several text classification scenarios. In this work, we argue that by not using any labelled data, data programming based approaches can yield suboptimal performances, particularly in cases when the labelling functions are noisy. The first contribution of this work is an introduction of a framework, SPEAR, which is a semi-supervised data programming paradigm, which learns a joint model that effectively uses the rules/labelling functions along with semi-supervised loss functions on the feature space. Next, we also study SPEAR-SS, which additionally does subset selection on top of the joint semi-supervised data programming objective, and selects a set of examples that can be used as the labelled set. The goal of SPEAR-SS, is to ensure that the labelled data can complement the labelling functions, thereby benefiting from both data-programming as well as appropriately selected data for human labelling. We demonstrate that by effectively combining semi-supervision, data-programming and subset selection paradigms, we significantly outperform the current state-of-the-art on seven publicly available datasets.

Semi-Supervised Data Programming with Subset Selection

There are concerns that the ability of language models (LMs) to generate high-quality synthetic text can be misused to launch spam, disinformation, or propaganda. Therefore, the research community is actively working on detecting whether a given text is organic or synthetic. While this is a useful first step, it is important to be able to further fingerprint the author LM to attribute its origin. Prior work on fingerprinting LMs is limited to attributing synthetic text generated by a handful (usually <10) of pre-trained LMs. However, LMs such as GPT2 are commonly fine-tuned in a myriad of ways (e.g., on a domain-specific text corpus) before being used to generate synthetic text. Thus, it is challenging to fingerprinting fine-tuned LMs because the universe of fine-tuned LMs is much larger in realistic scenarios. To address this challenge, we study the problem of large-scale fingerprinting of fine-tuned LMs in the wild. Using a real-world dataset of synthetic text generated by 108 different fine-tuned LM, we conduct comprehensive experiments to demonstrate the limitations of existing fingerprinting approaches. Our results show that fine-tuning itself is most effective in attributing the synthetic text generated by fine-tuned LMs.

Fingerprinting Fine-tuned Language Models in the Wild

Pre-trained language models have emerged as highly successful methods for learning good text representations. However, the amount of structured knowledge retained in such models, and how (if at all) it can be extracted, remains an open question. In this work, we aim at directly learning text representations that leverage structured knowledge about entities mentioned in the text. This can be particularly beneficial for downstream tasks which are knowledge-intensive. Our approach utilizes self-attention between words in the text and knowledge graph (KG) entities mentioned in the text. While existing methods require entity-linked data for pre-training, we train using a mention-span masking objective and a candidate ranking objective -- which doesn't require any entity-links and only assumes access to an alias table for retrieving candidates, enabling large-scale pre-training. We show that the proposed model learns knowledge-informed text representations that yield improvements on the downstream tasks over existing methods.

Simultaneously Self-Attending to Text and Entities forKnowledge-Informed Text Representations

Models based on the transformer architecture, such as BERT, have marked a crucial step forward in the field of Natural Language Processing. Importantly, they allow the creation of word embeddings that capture important semantic information about words in context. However, as single entities, these embeddings are difficult to interpret and the models used to create them have been described as opaque. Binder and colleagues proposed an intuitive embedding space where each dimension is based on one of 65 core semantic features. Unfortunately, the space only exists for a small data-set of 535 words, limiting its uses. Previous work (Utsumi, 2018, 2020; Turton et al., 2020) has shown that Binder features can be derived from static embeddings and successfully extrapolated to a large new vocabulary. Taking the next step, this paper demonstrates that Binder features can be derived from the BERT embedding space. This provides two things; (1) semantic feature values derived from contextualised word embeddings and (2) insights into how semantic features are represented across the different layers of the BERT model.

Deriving Contextualised Semantic Features from BERT (and Other Transformer Model) Embeddings

While vector-based language representations from pretrained language models have set a new standard for many NLP tasks, there is not yet a complete accounting of their inner workings. In particular, it is not entirely clear what aspects of sentence-level syntax are captured by these representations, nor how (if at all) they are built along the stacked layers of the network. In this paper, we aim to address such questions with a general class of interventional, input perturbation-based analyses of representations from pretrained language models. Importing from computational and cognitive neuroscience the notion of representational invariance, we perform a series of probes designed to test the sensitivity of these representations to several kinds of structure in sentences. Each probe involves swapping words in a sentence and comparing the representations from perturbed sentences against the original. We experiment with three different perturbations: (1) random permutations of n-grams of varying width, to test the scale at which a representation is sensitive to word position; (2) swapping of two spans which do or do not form a syntactic phrase, to test sensitivity to global phrase structure; and (3) swapping of two adjacent words which do or do not break apart a syntactic phrase, to test sensitivity to local phrase structure.
Results from these probes collectively suggest that Transformers build sensitivity to larger parts of the sentence along their layers, and that hierarchical phrase structure plays a role in this process. More broadly, our results also indicate that structured input perturbations widens the scope of analyses that can be performed on often-opaque deep learning systems, and can serve as a complement to existing tools (such as supervised linear probes) for interpreting complex black-box models.

Analyzing Code Embeddings for Coding Clinical Narratives

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Learning Latent Structures for Cross Action Phrase Relations in Wet Lab Protocols

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Analyzing Code Embeddings for Coding Clinical Narratives

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Next from IJCNLP-AACL 2021

Learning Latent Structures for Cross Action Phrase Relations in Wet Lab Protocols

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How effective is BERT without word ordering? Implications for language understanding and data privacy

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

COMPANY

RESOURCES

Downloads