Showing papers by "Mihai Surdeanu published in 2022"

SuMe: A Dataset Towards Summarizing Biomedical Mechanisms

Abstract: Can language models read biomedical texts and explain the biomedical mechanisms discussed? In this work we introduce a biomedical mechanism summarization task. Biomedical studies often investigate the mechanisms behind how one entity (e.g., a protein or a chemical) affects another in a biological context. The abstracts of these publications often include a focused set of sentences that present relevant supporting statements regarding such relationships, associated experimental evidence, and a concluding sentence that summarizes the mechanism underlying the relationship. We leverage this structure and create a summarization task, where the input is a collection of sentences and the main entities in an abstract, and the output includes the relationship and a sentence that summarizes the mechanism. Using a small amount of manually labeled mechanism sentences, we train a mechanism sentence classifier to filter a large biomedical abstract collection and create a summarization dataset with 22k instances. We also introduce conclusion sentence generation as a pretraining task with 611k instances. We benchmark the performance of large bio-domain language models. We find that while the pretraining task help improves performance, the best model produces acceptable mechanism outputs in only 32% of the instances, which shows the task presents significant challenges in biomedical language understanding and summarization.

It Takes Two Flints to Make a Fire: Multitask Learning of Neural Relation and Explanation Classifiers

Abstract: Abstract We propose an explainable approach for relation extraction that mitigates the tension between generalization and explainability by jointly training for the two goals. Our approach uses a multi-task learning architecture, which jointly trains a classifier for relation extraction, and a sequence model that labels words in the context of the relations that explain the decisions of the relation classifier. We also convert the model outputs to rules to bring global explanations to this approach. This sequence model is trained using a hybrid strategy: supervised, when supervision from pre-existing patterns is available, and semi-supervised otherwise. In the latter situation, we treat the sequence model’s labels as latent variables, and learn the best assignment that maximizes the performance of the relation classifier. We evaluate the proposed approach on the two datasets and show that the sequence model provides labels that serve as accurate explanations for the relation classifier’s decisions, and, importantly, that the joint training generally improves the performance of the relation classifier. We also evaluate the performance of the generated rules and show that the new rules are a great add-on to the manual rules and bring the rule-based system much closer to the neural models.

Do Transformer Networks Improve the Discovery of Rules from Text?

Abstract: With their Discovery of Inference Rules from Text (DIRT) algorithm, Lin and Pantel (2001) made a seminal contribution to the field of rule acquisition from text, by adapting the distributional hypothesis of Harris (1954) to rules that model binary relations such as X treat Y. DIRT’s relevance is renewed in today’s neural era given the recent focus on interpretability in the field of natural language processing. We propose a novel take on the DIRT algorithm, where we implement the distributional hypothesis using the contextualized embeddings provided by BERT, a transformer-network-based language model (Vaswani et al. 2017; Devlin et al. 2018). In particular, we change the similarity measure between pairs of slots (i.e., the set of words matched by a rule) from the original formula that relies on lexical items to a formula computed using contextualized embeddings. We empirically demonstrate that this new similarity method yields a better implementation of the distributional hypothesis, and this, in turn, yields rules that outperform the original algorithm in the question answering-based evaluation proposed by Lin and Pantel (2001).

Combining Extraction and Generation for Constructing Belief-Consequence Causal Links

Abstract: In this paper, we introduce and justify a new task—causal link extraction based on beliefs—and do a qualitative analysis of the ability of a large language model—InstructGPT-3—to generate implicit consequences of beliefs. With the language model-generated consequences being promising, but not consistent, we propose directions of future work, including data collection, explicit consequence extraction using rule-based and language modeling-based approaches, and using explicitly stated consequences of beliefs to fine-tune or prompt the language model to produce outputs suitable for the task.

A Compact Pretraining Approach for Neural Language Models

Abstract: Domain adaptation for large neural language models (NLMs) is coupled with massive amounts of unstructured data in the pretraining phase. In this study, however, we show that pretrained NLMs learn in-domain information more effectively and faster from a compact subset of the data that focuses on the key information in the domain. We construct these compact subsets from the unstructured data using a combination of abstractive summaries and extractive keywords. In particular, we rely on BART to generate abstractive summaries, and KeyBERT to extract keywords from these summaries (or the original unstructured text directly). We evaluate our approach using six different settings: three datasets combined with two distinct NLMs. Our results reveal that the task-specific classifiers trained on top of NLMs pretrained using our method outperform methods based on traditional pretraining, i.e., random masking on the entire data, as well as methods without pretraining. Further, we show that our strategy reduces pretraining time by up to five times compared to vanilla pretraining. The code for all of our experiments is publicly available at https://github.com/shahriargolchin/compact-pretraining.

From Examples to Rules: Neural Guided Rule Synthesis for Information Extraction

Abstract: While deep learning approaches to information extraction have had many successes, they can be difficult to augment or maintain as needs shift. Rule-based methods, on the other hand, can be more easily modified. However, crafting rules requires expertise in linguistics and the domain of interest, making it infeasible for most users. Here we attempt to combine the advantages of these two directions while mitigating their drawbacks. We adapt recent advances from the adjacent field of program synthesis to information extraction, synthesizing rules from provided examples. We use a transformer-based architecture to guide an enumerative search, and show that this reduces the number of steps that need to be explored before a rule is found. Further, we show that without training the synthesis algorithm on the specific domain, our synthesized rules achieve state-of-the-art performance on the 1-shot scenario of a task that focuses on few-shot learning for relation classification, and competitive performance in the 5-shot scenario.

Better Retrieval May Not Lead to Better Question Answering

Abstract: Considerable progress has been made recently in open-domain question answering (QA) problems, which require Information Retrieval (IR) and Reading Comprehension (RC). A popular approach to improve the system's performance is to improve the quality of the retrieved context from the IR stage. In this work we show that for StrategyQA, a challenging open-domain QA dataset that requires multi-hop reasoning, this common approach is surprisingly ineffective -- improving the quality of the retrieved context hardly improves the system's performance. We further analyze the system's behavior to identify potential reasons.

BioNLI: Generating a Biomedical NLI Dataset Using Lexico-semantic Constraints for Adversarial Examples

Abstract: Natural language inference (NLI) is critical for complex decision-making in biomedical domain. One key question, for example, is whether a given biomedical mechanism is supported by experimental evidence. This can be seen as an NLI problem but there are no directly usable datasets to address this. The main challenge is that manually creating informative negative examples for this task is difficult and expensive. We introduce a novel semi-supervised procedure that bootstraps an NLI dataset from existing biomedical dataset that pairs mechanisms with experimental evidence in abstracts. We generate a range of negative examples using nine strategies that manipulate the structure of the underlying mechanisms both with rules, e.g., flip the roles of the entities in the interaction, and, more importantly, as perturbations via logical constraints in a neuro-logical decoding system. We use this procedure to create a novel dataset for NLI in the biomedical domain, called BioNLI and benchmark two state-of-the-art biomedical classifiers. The best result we obtain is around mid 70s in F1, suggesting the difficulty of the task. Critically, the performance on the different classes of negative examples varies widely, from 97% F1 on the simple role change negative examples, to barely better than chance on the negative examples generated using neuro-logic decoding.

PatternRank: Jointly Ranking Patterns and Extractions for Relation Extraction Using Graph-Based Algorithms

Abstract: In this paper we revisit the direction of using lexico-syntactic patterns for relation extraction instead of today’s ubiquitous neural classifiers. We propose a semi-supervised graph-based algorithm for pattern acquisition that scores patterns and the relations they extract jointly, using a variant of PageRank. We insert light supervision in the form of seed patterns or relations, and model it with several custom teleportation probabilities that bias random-walk scores of patterns/relations based on their proximity to correct information. We evaluate our approach on Few-Shot TACRED, and show that our method outperforms (or performs competitively with) more expensive and opaque deep neural networks. Lastly, we thoroughly compare our proposed approach with the seminal RlogF pattern acquisition algorithm of, showing that it outperforms it for all the hyper parameters tested, in all settings.

Validity Assessment of Legal Will Statements as Natural Language Inference

Abstract: This work introduces a natural language inference (NLI) dataset that focuses on the validity of statements in legal wills. This dataset is unique because: (a) each entailment decision requires three inputs: the statement from the will, the law, and the conditions that hold at the time of the testator's death; and (b) the included texts are longer than the ones in current NLI datasets. We trained eight neural NLI models in this dataset. All the models achieve more than 80% macro F1 and accuracy, which indicates that neural approaches can handle this task reasonably well. However, group accuracy, a stricter evaluation measure that is calculated with a group of positive and negative examples generated from the same statement as a unit, is in mid 80s at best, which suggests that the models' understanding of the task remains superficial. Further ablative analyses and explanation experiments indicate that all three text segments are used for prediction, but some decisions rely on semantically irrelevant tokens. This indicates that overfitting on these longer texts likely happens, and that additional research is required for this task to be solved.

A STEP towards Interpretable Multi-Hop Reasoning:Bridge Phrase Identification and Query Expansion

Abstract: We propose an unsupervised method for the identification of bridge phrases in multi-hop question answering (QA). Our method constructs a graph of noun phrases from the question and the available context, and applies the Steiner tree algorithm to identify the minimal sub-graph that connects all question phrases. Nodes in the sub-graph that bridge loosely-connected or disjoint subsets of question phrases due to low-strength semantic relations are extracted as bridge phrases. The identified bridge phrases are then used to expand the query based on the initial question, helping in increasing the relevance of evidence that has little lexical overlap or semantic relation with the question. Through an evaluation on HotpotQA, a popular dataset for multi-hop QA, we show that our method yields: (a) improved evidence retrieval, (b) improved QA performance when using the retrieved sentences; and (c) effective and faithful explanations when answers are provided.

Informal Persian Universal Dependency Treebank

Abstract: This paper presents the phonological, morphological, and syntactic distinctions between formal and informal Persian, showing that these two variants have fundamental differences that cannot be attributed solely to pronunciation discrepancies. Given that informal Persian exhibits particular characteristics, any computational model trained on formal Persian is unlikely to transfer well to informal Persian, necessitating the creation of dedicated treebanks for this variety. We thus detail the development of the open-source Informal Persian Universal Dependency Treebank, a new treebank annotated within the Universal Dependencies scheme. We then investigate the parsing of informal Persian by training two dependency parsers on existing formal treebanks and evaluating them on out-of-domain data, i.e. the development set of our informal treebank. Our results show that parsers experience a substantial performance drop when we move across the two domains, as they face more unknown tokens and structures and fail to generalize well. Furthermore, the dependency relations whose performance deteriorates the most represent the unique properties of the informal variant. The ultimate goal of this study that demonstrates a broader impact is to provide a stepping-stone to reveal the significance of informal variants of languages, which have been widely overlooked in natural language processing tools across languages.

Automatic Correction of Syntactic Dependency Annotation Differences

Abstract: Annotation inconsistencies between data sets can cause problems for low-resource NLP, where noisy or inconsistent data cannot be easily replaced. We propose a method for automatically detecting annotation mismatches between dependency parsing corpora, along with three related methods for automatically converting the mismatches. All three methods rely on comparing unseen examples in a new corpus with similar examples in an existing corpus. These three methods include a simple lexical replacement using the most frequent tag of the example in the existing corpus, a GloVe embedding-based replacement that considers related examples, and a BERT-based replacement that uses contextualized embeddings to provide examples fine-tuned to our data. We evaluate these conversions by retraining two dependency parsers—Stanza and Parsing as Tagging (PaT)—on the converted and unconverted data. We find that applying our conversions yields significantly better performance in many cases. Some differences observed between the two parsers are observed. Stanza has a more complex architecture with a quadratic algorithm, taking longer to train, but it can generalize from less data. The PaT parser has a simpler architecture with a linear algorithm, speeding up training but requiring more training data to reach comparable or better performance.

Taxonomy Builder: a Data-driven and User-centric Tool for Streamlining Taxonomy Construction

Abstract: An existing domain taxonomy for normalizing content is often assumed when discussing approaches to information extraction, yet often in real-world scenarios there is none.When one does exist, as the information needs shift, it must be continually extended. This is a slow and tedious task, and one which does not scale well.Here we propose an interactive tool that allows a taxonomy to be built or extended rapidly and with a human in the loop to control precision. We apply insights from text summarization and information extraction to reduce the search space dramatically, then leverage modern pretrained language models to perform contextualized clustering of the remaining concepts to yield candidate nodes for the user to review. We show this allows a user to consider as many as 200 taxonomy concept candidates an hour, to quickly build or extend a taxonomy to better fit information needs.

Learning Open Domain Multi-hop Search Using Reinforcement Learning

Abstract: We propose a method to teach an automated agent to learn how to search for multi-hop paths of relations between entities in an open domain. The method learns a policy for directing existing information retrieval and machine reading resources to focus on relevant regions of a corpus. The approach formulates the learning problem as a Markov decision process with a state representation that encodes the dynamics of the search process and a reward structure that minimizes the number of documents that must be processed while still finding multi-hop paths. We implement the method in an actor-critic reinforcement learning algorithm and evaluate it on a dataset of search problems derived from a subset of English Wikipedia. The algorithm finds a family of policies that succeeds in extracting the desired information while processing fewer documents compared to several baseline heuristic algorithms.

Low Resource Causal Event Detection from Biomedical Literature

Abstract: Recognizing causal precedence relations among the chemical interactions in biomedical literature is crucial to understanding the underlying biological mechanisms. However, detecting such causal relation can be hard because: (1) many times, such causal relations among events are not explicitly expressed by certain phrases but implicitly implied by very diverse expressions in the text, and (2) annotating such causal relation detection datasets requires considerable expert knowledge and effort. In this paper, we propose a strategy to address both challenges by training neural models with in-domain pre-training and knowledge distillation. We show that, by using very limited amount of labeled data, and sufficient amount of unlabeled data, the neural models outperform previous baselines on the causal precedence detection task, and are ten times faster at inference compared to the BERT base model.

A Human-machine Interface for Few-shot Rule Synthesis for Information Extraction

Abstract: We propose a system that assists a user in constructing transparent information extraction models, consisting of patterns (or rules) written in a declarative language, through program synthesis.Users of our system can specify their requirements through the use of examples,which are collected with a search interface.The rule-synthesis system proposes rule candidates and the results of applying them on a textual corpus; the user has the option to accept the candidate, request another option, or adjust the examples provided to the system.Through an interactive evaluation, we show that our approach generates high-precision rules even in a 1-shot setting. On a second evaluation on a widely-used relation extraction dataset (TACRED), our method generates rules that outperform considerably manually written patterns.Our code, demo, and documentation is available at https://clulab.github.io/odinsynth.