Ireland

Summarizing biomedical discovery from genomics data using natural languages is an essential step in biomedical research but is mostly done manually. Here, we introduce Textomics, a novel dataset of genomics data description, which contains 22,273 pairs of genomics data matrices and their summaries. Each summary is written by the researchers who generated the data and associated with a scientific paper. Based on this dataset, we study two novel tasks: generating textual summary from a genomics data matrix and vice versa. Inspired by the successful applications of k nearest neighbors in modeling genomics data, we propose a kNN-Vec2Text model to address these tasks and observe substantial improvement on our dataset. We further illustrate how Textomics can be used to advance other applications, including evaluating scientific paper embeddings and generating masked templates for scientific paper understanding. Textomics serves as the first benchmark for generating textual summaries for genomics data and we envision it will be broadly applied to other biomedical and natural language processing applications.

ACL 2022

Textomics: A Dataset for Genomics Data Summary Generation

text generation

dataset

poster

# Welcome everyone to ACL 2022!

The 60th Annual Meeting of the Association for Computational Linguistics is taking place May 22-27, 2022 as a hybrid event, in Dublin and online. We are happy to welcome all of you to this anniversary edition with an almost 50-50 in-person and virtual participation. 
The main conference program features oral presentations, in-person and virtual posters and demo sessions, a plenary session for our best paper presentations and awards, three amazing keynote events and two new initiatives of invited talks: Spotlight Talks for Young Rising Stars (STIRS) and The Next Big Idea Talks. Posters (including Findings of ACL 2022) and demos are grouped by areas for both the in-person and the virtual sessions. For the virtual component, the talks will be on Zoom and the posters and the demos will be in GatherTown. The Student Research Workshop will have an oral session and a poster session as part of Poster Session 1. The program also features eight Tutorials and 28 Workshops. 

 
We wish you a wonderful conference! 
[**The ACL 2022 Organizing Committee**](https://www.2022.aclweb.org/organisers)
 
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The Association for Computational Linguistics (ACL) is the premier international scientific and professional society for people working on computational problems involving human language, a field often referred to as either computational linguistics or natural language processing (NLP). 

The evolution of language follows the rule of gradual change. Grammar, vocabulary, and lexical semantic shifts take place over time, resulting in a diachronic linguistic gap. As such, a considerable amount of texts are written in languages of different eras, which creates obstacles for natural language processing tasks, such as word segmentation and machine translation. Although the Chinese language has a long history, previous Chinese natural language processing research has primarily focused on tasks within a specific era. Therefore, we propose a cross-era learning framework for Chinese word segmentation (CWS), CROSSWISE, which uses the Switch-memory (SM) module to incorporate era-specific linguistic knowledge. Experiments on four corpora from different eras show that the performance of each corpus significantly improves. Further analyses also demonstrate that the SM can effectively integrate the knowledge of the eras into the neural network.

That Slepen Al the Nyght with Open Ye! Cross-era Sequence Segmentation with Switch-memory

Although contextualized embeddings generated from large-scale pre-trained models perform well in many tasks, traditional static embeddings (e.g., Skip-gram, Word2Vec) still play an important role in low-resource and lightweight settings due to their low computational cost, ease of deployment, and stability. In this paper, we aim to improve word embeddings by 1) incorporating more contextual information from existing pre-trained models into the Skip-gram framework, which we call Context-to-Vec; 2) proposing a post-processing retrofitting method for static embeddings independent of training by employing priori synonym knowledge and weighted vector distribution. Through extrinsic and intrinsic tasks, our methods are well proven to outperform the baselines by a large margin.

Using Context-to-Vector with Graph Retrofitting to Improve Word Embeddings

For a natural language understanding benchmark to be useful in research, it has to consist of examples that are diverse and difficult enough to discriminate among current and near-future state-of-the-art systems. However, we do not yet know how best to select text sources to collect a variety of challenging examples. In this study, we crowdsource multiple-choice reading comprehension questions for passages taken from seven qualitatively distinct sources, analyzing what attributes of passages contribute to the difficulty and question types of the collected examples. To our surprise, we find that passage source, length, and readability measures do not significantly affect question difficulty. Through our manual annotation of seven reasoning types, we observe several trends between passage sources and reasoning types, e.g., logical reasoning is more often required in questions written for technical passages. These results suggest that when creating a new benchmark dataset, selecting a diverse set of passages can help ensure a diverse range of question types, but that passage difficulty need not be a priority.

What Makes Reading Comprehension Questions Difficult?

Automatic ICD coding is defined as assigning disease codes to electronic medical records (EMRs). Existing methods usually apply label attention with code representations to match related text snippets. Unlike these works that model the label with the code hierarchy or description, we argue that the code synonyms can provide more comprehensive knowledge based on the observation that the code expressions in EMRs vary from their descriptions in ICD. By aligning codes to concepts in UMLS, we collect synonyms of every code. Then, we propose a multiple synonyms matching network to leverage synonyms for better code representation learning, and finally help the code classification. Experiments on the MIMIC-III dataset show that our proposed method outperforms previous state-of-the-art methods.

Code Synonyms Do Matter: Multiple Synonyms Matching Network for Automatic ICD Coding

Triangular machine translation is a special case of low-resource machine translation where the language pair of interest has limited parallel data, but both languages have abundant parallel data with a pivot language. Naturally, the key to triangular machine translation is the successful exploitation of such auxiliary data. In this work, we propose a transfer-learning-based approach that utilizes all types of auxiliary data. As we train auxiliary source-pivot and pivot-target translation models, we initialize some parameters of the pivot side with a pre-trained language model and freeze them to encourage both translation models to work in the same pivot language space, so that they can be smoothly transferred to the source-target translation model. Experiments show that our approach can outperform previous ones.

Triangular Transfer: Freezing the Pivot for Triangular Machine Translation

Natural Language Inference (NLI) is the task of determining whether a premise entails a hypothesis. NLI with temporal order is a challenging task because tense and aspect are complex linguistic phenomena involving interactions with temporal adverbs and temporal connectives. To tackle this, temporal and aspectual inference has been analyzed in various ways in the field of formal semantics. However, a Japanese NLI system for temporal order based on the analysis of formal semantics has not been sufficiently developed. We present a logic-based NLI system that considers temporal order in Japanese based on compositional semantics via Combinatory Categorial Grammar (CCG) syntactic analysis. Our system performs inference involving temporal order by using axioms for temporal relations and automated theorem provers. We evaluate our system by experimenting with Japanese NLI datasets that involve temporal order. We show that our system outperforms previous logic-based systems as well as current deep learning-based models.

 Compositional Semantics and Inference System for Temporal Order based on Japanese CCG

Existing visual grounding datasets are artificially made, where every query regarding an entity must be able to be grounded to a corresponding image region, i.e., answerable. However, in real-world multimedia data such as news articles and social media, many entities in the text cannot be grounded to the image, i.e., unanswerable, due to the fact that the text is unnecessarily directly describing the accompanying image. A robust visual grounding model should be able to flexibly deal with both answerable and unanswerable visual grounding. To study this flexible visual grounding problem, we construct a pseudo dataset and a social media dataset including both answerable and unanswerable queries. In order to handle unanswerable visual grounding, we propose a novel method by adding a pseudo image region corresponding to a query that cannot be grounded. The model is then trained to ground to ground-truth regions for answerable queries and pseudo regions for unanswerable queries. In our experiments, we show that our model can flexibly process both answerable and unanswerable queries with high accuracy on our datasets.

 Flexible Visual Grounding

Recently, the Natural Language Inference (NLI) task has been studied for semi-structured tables that do not have a strict format. Although neural approaches have achieved high performance in various types of NLI, including NLI between semi-structured tables and texts, they still have difficulty in performing a numerical type of inference, such as counting. To handle a numerical type of inference, we propose a logical inference system for reasoning between semi-structured tables and texts. We use logical representations as meaning representations for tables and texts and use model checking to handle a numerical type of inference between texts and tables. To evaluate the extent to which our system can perform inference with numerical comparatives, we make an evaluation protocol that focuses on numerical understanding between semi-structured tables and texts in English. We show that our system can more robustly perform inference between tables and texts that requires numerical understanding compared with current neural approaches.

 Logical Inference for Counting on Semi-structured Tables

We tackle the tasks of image and text retrieval using a dual-encoder model in which images and text are encoded independently. This model has attracted attention as an approach that enables efficient offline inferences by connecting both vision and language in the same semantic space. However, whether an image encoder as part of a dual-encoder model can interpret scene-text, i.e., the textual information in images, is unclear. We propose pre-training methods that encourage a joint understanding of the scene-text and surrounding visual information. The experimental results demonstrate that our methods improve the retrieval performances of the dual-encoder models.

 Scene-Text Aware Image and Text Retrieval with Dual-Encoder

Indonesian and Malay are underrepresented in the development of natural language processing (NLP) technologies and available resources are difficult to find. A clear picture of existing work can invigorate and inform how researchers conceptualise worthwhile projects. Using an education sector project to motivate the study, we conducted a wide-ranging overview of Indonesian and Malay human language technologies and corpus work. We charted 657 included studies according to Hirschberg and Manning’s 2015 description of NLP, concluding that the field was dominated by exploratory corpus work, machine reading of text gathered from the Internet, and sentiment analysis. In this paper, we identify most published authors and research hubs, and make a number of recommendations to encourage future collaboration and efficiency within NLP in Indonesian and Malay.

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That Slepen Al the Nyght with Open Ye! Cross-era Sequence Segmentation with Switch-memory

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