Qingyun Wang


2024

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Language + Molecules
Carl Edwards | Qingyun Wang | Heng Ji
Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics: Tutorial Abstracts

Climate change, access to food and water, pandemics–the world faces an enormous number of problems in the coming decades on scales of complexity never-before-seen. To address these issues, development of scientific solutions which are scalable, flexible, and inexpensive are critical. Over the last couple years, considerable interest has arisen for applying natural language-driven solutions to these problems. Particularly, the chemistry field is posed to be substantially accelerated by language+molecule models. This tutorial is designed to provide an introduction to this area of research. It requires no knowledge outside mainstream NLP, and it will enable participants to begin exploring relevant research. By discussing cutting-edge work, we will highlight the key roles language can fill for 1) abstract, compositional control of generative models, 2) bridging different biochemical modalities, 3) planning experimental procedures, and 4) broadening access to computational approaches. Beyond this, language models have also seen considerable success when applied to proteins or molecule structures, which can be considered as ‘exotic’ languages, and computational linguistics researchers’ expertise can be highly valuable for these impactful, possibly life-saving tasks.

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Named Entity Recognition Under Domain Shift via Metric Learning for Life Sciences
Hongyi Liu | Qingyun Wang | Payam Karisani | Heng Ji
Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers)

Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the applicability of transfer learning for enhancing a named entity recognition model trained in the biomedical domain (the source domain) to be used in the chemical domain (the target domain). A common practice for training such a model in a few-shot learning setting is to pretrain the model on the labeled source data, and then, to finetune it on a hand-full of labeled target examples. In our experiments, we observed that such a model is prone to mislabeling the source entities, which can often appear in the text, as the target entities. To alleviate this problem, we propose a model to transfer the knowledge from the source domain to the target domain, but, at the same time, to project the source entities and target entities into separate regions of the feature space. This diminishes the risk of mislabeling the source entities as the target entities. Our model consists of two stages: 1) entity grouping in the source domain, which incorporates knowledge from annotated events to establish relations between entities, and 2) entity discrimination in the target domain, which relies on pseudo labeling and contrastive learning to enhance discrimination between the entities in the two domains. We conduct our extensive experiments across three source and three target datasets, demonstrating that our method outperforms the baselines by up to 5% absolute value. Code, data, and resources are publicly available for research purposes: https://github.com/Lhtie/Bio-Domain-Transfer .

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Chem-FINESE: Validating Fine-Grained Few-shot Entity Extraction through Text Reconstruction
Qingyun Wang | Zixuan Zhang | Hongxiang Li | Xuan Liu | Jiawei Han | Huimin Zhao | Heng Ji
Findings of the Association for Computational Linguistics: EACL 2024

Fine-grained few-shot entity extraction in the chemical domain faces two unique challenges. First, compared with entity extraction tasks in the general domain, sentences from chemical papers usually contain more entities. Moreover, entity extraction models usually have difficulty extracting entities of long-tailed types. In this paper, we propose Chem-FINESE, a novel sequence-to-sequence (seq2seq) based few-shot entity extraction approach, to address these two challenges. Our Chem-FINESE has two components: a seq2seq entity extractor to extract named entities from the input sentence and a seq2seq self-validation module to reconstruct the original input sentence from extracted entities. Inspired by the fact that a good entity extraction system needs to extract entities faithfully, our new self-validation module leverages entity extraction results to reconstruct the original input sentence. Besides, we design a new contrastive loss to reduce excessive copying during the extraction process. Finally, we release ChemNER+, a new fine-grained chemical entity extraction dataset that is annotated by domain experts with the ChemNER schema. Experiments in few-shot settings with both ChemNER+ and CHEMET datasets show that our newly proposed framework has contributed up to 8.26% and 6.84% absolute F1-score gains respectively.

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Towards a Human-Computer Collaborative Scientific Paper Lifecycle: A Pilot Study and Hands-On Tutorial
Qingyun Wang | Carl Edwards | Heng Ji | Tom Hope
Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024): Tutorial Summaries

Due to the rapid growth of publications varying in quality, there exists a pressing need to help scientists digest and evaluate relevant papers, thereby facilitating scientific discovery. This creates a number of urgent questions; however, computer-human collaboration in the scientific paper lifecycle is still in the exploratory stage and lacks a unified framework for analyzing the relevant tasks. Additionally, with the recent significant success of large language models (LLMs), they have increasingly played an important role in academic writing. In this cutting-edge tutorial, we aim to provide an all-encompassing overview of the paper lifecycle, detailing how machines can augment every stage of the research process for the scientist, including scientific literature understanding, experiment development, manuscript draft writing, and finally draft evaluation. This tutorial is devised for researchers interested in this rapidly-developing field of NLP-augmented paper writing. The tutorial will also feature a session of hands-on exercises during which participants can guide machines in generating ideas and automatically composing key paper elements. Furthermore, we will address current challenges, explore future directions, and discuss potential ethical issues. A toolkit designed for human-computer collaboration throughout the paper lifecycle will also be made publically available.

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SciMON: Scientific Inspiration Machines Optimized for Novelty
Qingyun Wang | Doug Downey | Heng Ji | Tom Hope
Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

We explore and enhance the ability of neural language models to generate novel scientific directions grounded in literature. Work on literature-based hypothesis generation has traditionally focused on binary link prediction—severely limiting the expressivity of hypotheses. This line of work also does not focus on optimizing novelty. We take a dramatic departure with a novel setting in which models use as input background contexts (e.g., problems, experimental settings, goals), and output natural language ideas grounded in literature. We present SciMON, a modeling framework that uses retrieval of “inspirations” from past scientific papers, and explicitly optimizes for novelty by iteratively comparing to prior papers and updating idea suggestions until sufficient novelty is achieved. Comprehensive evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our methods partially mitigate this issue. Our work represents a first step toward evaluating and developing language models that generate new ideas derived from the scientific literature. Code, data, and resources are publicly available for research purposes: https://github.com/eaglew/clbd.

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Proceedings of the 1st Workshop on Language + Molecules (L+M 2024)
Carl Edwards | Qingyun Wang | Manling Li | Lawrence Zhao | Tom Hope | Heng Ji
Proceedings of the 1st Workshop on Language + Molecules (L+M 2024)

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L+M-24: Building a Dataset for Language+Molecules @ ACL 2024
Carl Edwards | Qingyun Wang | Lawrence Zhao | Heng Ji
Proceedings of the 1st Workshop on Language + Molecules (L+M 2024)

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction

2023

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Multimedia Generative Script Learning for Task Planning
Qingyun Wang | Manling Li | Hou Pong Chan | Lifu Huang | Julia Hockenmaier | Girish Chowdhary | Heng Ji
Findings of the Association for Computational Linguistics: ACL 2023

Goal-oriented generative script learning aims to generate subsequent steps to reach a particular goal, which is an essential task to assist robots or humans in performing stereotypical activities. An important aspect of this process is the ability to capture historical states visually, which provides detailed information that is not covered by text and will guide subsequent steps. Therefore, we propose a new task, Multimedia Generative Script Learning, to generate subsequent steps by tracking historical states in both text and vision modalities, as well as presenting the first benchmark containing 5,652 tasks and 79,089 multimedia steps. This task is challenging in three aspects: the multimedia challenge of capturing the visual states in images, the induction challenge of performing unseen tasks, and the diversity challenge of covering different information in individual steps. We propose to encode visual state changes through a selective multimedia encoder to address the multimedia challenge, transfer knowledge from previously observed tasks using a retrieval-augmented decoder to overcome the induction challenge, and further present distinct information at each step by optimizing a diversity-oriented contrastive learning objective. We define metrics to evaluate both generation and inductive quality. Experiment results demonstrate that our approach significantly outperforms strong baselines.

2021

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COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation
Qingyun Wang | Manling Li | Xuan Wang | Nikolaus Parulian | Guangxing Han | Jiawei Ma | Jingxuan Tu | Ying Lin | Ranran Haoran Zhang | Weili Liu | Aabhas Chauhan | Yingjun Guan | Bangzheng Li | Ruisong Li | Xiangchen Song | Yi Fung | Heng Ji | Jiawei Han | Shih-Fu Chang | James Pustejovsky | Jasmine Rah | David Liem | Ahmed ELsayed | Martha Palmer | Clare Voss | Cynthia Schneider | Boyan Onyshkevych
Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: Demonstrations

To combat COVID-19, both clinicians and scientists need to digest the vast amount of relevant biomedical knowledge in literature to understand the disease mechanism and the related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities, relations and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence. All of the data, KGs, reports.

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Knowledge-Enriched Natural Language Generation
Wenhao Yu | Meng Jiang | Zhiting Hu | Qingyun Wang | Heng Ji | Nazneen Rajani
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing: Tutorial Abstracts

Knowledge-enriched text generation poses unique challenges in modeling and learning, driving active research in several core directions, ranging from integrated modeling of neural representations and symbolic information in the sequential/hierarchical/graphical structures, learning without direct supervisions due to the cost of structured annotation, efficient optimization and inference with massive and global constraints, to language grounding on multiple modalities, and generative reasoning with implicit commonsense knowledge and background knowledge. In this tutorial we will present a roadmap to line up the state-of-the-art methods to tackle these challenges on this cutting-edge problem. We will dive deep into various technical components: how to represent knowledge, how to feed knowledge into a generation model, how to evaluate generation results, and what are the remaining challenges?

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Stage-wise Fine-tuning for Graph-to-Text Generation
Qingyun Wang | Semih Yavuz | Xi Victoria Lin | Heng Ji | Nazneen Rajani
Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing: Student Research Workshop

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset.

2020

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ReviewRobot: Explainable Paper Review Generation based on Knowledge Synthesis
Qingyun Wang | Qi Zeng | Lifu Huang | Kevin Knight | Heng Ji | Nazneen Fatema Rajani
Proceedings of the 13th International Conference on Natural Language Generation

To assist human review process, we build a novel ReviewRobot to automatically assign a review score and write comments for multiple categories such as novelty and meaningful comparison. A good review needs to be knowledgeable, namely that the comments should be constructive and informative to help improve the paper; and explainable by providing detailed evidence. ReviewRobot achieves these goals via three steps: (1) We perform domain-specific Information Extraction to construct a knowledge graph (KG) from the target paper under review, a related work KG from the papers cited by the target paper, and a background KG from a large collection of previous papers in the domain. (2) By comparing these three KGs, we predict a review score and detailed structured knowledge as evidence for each review category. (3) We carefully select and generalize human review sentences into templates, and apply these templates to transform the review scores and evidence into natural language comments. Experimental results show that our review score predictor reaches 71.4%-100% accuracy. Human assessment by domain experts shows that 41.7%-70.5% of the comments generated by ReviewRobot are valid and constructive, and better than human-written ones for 20% of the time. Thus, ReviewRobot can serve as an assistant for paper reviewers, program chairs and authors.

2019

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PaperRobot: Incremental Draft Generation of Scientific Ideas
Qingyun Wang | Lifu Huang | Zhiying Jiang | Kevin Knight | Heng Ji | Mohit Bansal | Yi Luan
Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics

We present a PaperRobot who performs as an automatic research assistant by (1) conducting deep understanding of a large collection of human-written papers in a target domain and constructing comprehensive background knowledge graphs (KGs); (2) creating new ideas by predicting links from the background KGs, by combining graph attention and contextual text attention; (3) incrementally writing some key elements of a new paper based on memory-attention networks: from the input title along with predicted related entities to generate a paper abstract, from the abstract to generate conclusion and future work, and finally from future work to generate a title for a follow-on paper. Turing Tests, where a biomedical domain expert is asked to compare a system output and a human-authored string, show PaperRobot generated abstracts, conclusion and future work sections, and new titles are chosen over human-written ones up to 30%, 24% and 12% of the time, respectively.

2018

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Describing a Knowledge Base
Qingyun Wang | Xiaoman Pan | Lifu Huang | Boliang Zhang | Zhiying Jiang | Heng Ji | Kevin Knight
Proceedings of the 11th International Conference on Natural Language Generation

We aim to automatically generate natural language descriptions about an input structured knowledge base (KB). We build our generation framework based on a pointer network which can copy facts from the input KB, and add two attention mechanisms: (i) slot-aware attention to capture the association between a slot type and its corresponding slot value; and (ii) a new table position self-attention to capture the inter-dependencies among related slots. For evaluation, besides standard metrics including BLEU, METEOR, and ROUGE, we propose a KB reconstruction based metric by extracting a KB from the generation output and comparing it with the input KB. We also create a new data set which includes 106,216 pairs of structured KBs and their corresponding natural language descriptions for two distinct entity types. Experiments show that our approach significantly outperforms state-of-the-art methods. The reconstructed KB achieves 68.8% - 72.6% F-score.

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Paper Abstract Writing through Editing Mechanism
Qingyun Wang | Zhihao Zhou | Lifu Huang | Spencer Whitehead | Boliang Zhang | Heng Ji | Kevin Knight
Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers)

We present a paper abstract writing system based on an attentive neural sequence-to-sequence model that can take a title as input and automatically generate an abstract. We design a novel Writing-editing Network that can attend to both the title and the previously generated abstract drafts and then iteratively revise and polish the abstract. With two series of Turing tests, where the human judges are asked to distinguish the system-generated abstracts from human-written ones, our system passes Turing tests by junior domain experts at a rate up to 30% and by non-expert at a rate up to 80%.