We explore multiple important choices that have not been analyzed in conjunction regarding active learning for token classification using transformer networks. These choices are: (i) how to select what to annotate, (ii) decide whether to annotate entire sentences or smaller sentence fragments, (iii) how to train with incomplete annotations at token-level, and (iv) how to select the initial seed dataset. We explore whether annotating at sub-sentence level can translate to an improved downstream performance by considering two different sub-sentence annotation strategies: (i) entity-level, and (ii) token-level. These approaches result in some sentences being only partially annotated. To address this issue, we introduce and evaluate multiple strategies to deal with partially-annotated sentences during the training process. We show that annotating at the sub-sentence level achieves comparable or better performance than sentence-level annotations with a smaller number of annotated tokens. We then explore the extent to which the performance gap remains once accounting for the annotation time and found that both annotation schemes perform similarly.

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.

We propose a neural-based approach for rule synthesis designed to help bridge the gap between the interpretability, precision and maintainability exhibited by rule-based information extraction systems with the scalability and convenience of statistical information extraction systems. This is achieved by avoiding placing the burden of learning another specialized language on domain experts and instead asking them to provide a small set of examples in the form of highlighted spans of text. We introduce a transformer-based architecture that drives a rule synthesis system that leverages a self-supervised approach for pre-training a large-scale language model complemented by an analysis of different loss functions and aggregation mechanisms for variable length sequences of user-annotated spans of text. The results are encouraging and point to different desirable properties, such as speed and quality, depending on the choice of loss and aggregation method.

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.

This paper explores an unsupervised approach to learning a compositional representation function for multi-word expressions (MWEs), and evaluates it on the Tratz dataset, which associates two-word expressions with the semantic relation between the compound constituents (e.g. the label employer is associated with the noun compound government agency) (Tratz, 2011). The composition function is based on recurrent neural networks, and is trained using the Skip-Gram objective to predict the words in the context of MWEs. Thus our approach can naturally leverage large unlabeled text sources. Further, our method can make use of provided MWEs when available, but can also function as a completely unsupervised algorithm, using MWE boundaries predicted by a single, domain-agnostic part-of-speech pattern. With pre-defined MWE boundaries, our method outperforms the previous state-of-the-art performance on the coarse-grained evaluation of the Tratz dataset (Tratz, 2011), with an F1 score of 50.4%. The unsupervised version of our method approaches the performance of the supervised one, and even outperforms it in some configurations.

We present Odinson, a rule-based information extraction framework, which couples a simple yet powerful pattern language that can operate over multiple representations of text, with a runtime system that operates in near real time. In the Odinson query language, a single pattern may combine regular expressions over surface tokens with regular expressions over graphs such as syntactic dependencies. To guarantee the rapid matching of these patterns, our framework indexes most of the necessary information for matching patterns, including directed graphs such as syntactic dependencies, into a custom Lucene index. Indexing minimizes the amount of expensive pattern matching that must take place at runtime. As a result, the runtime system matches a syntax-based graph traversal in 2.8 seconds in a corpus of over 134 million sentences, nearly 150,000 times faster than its predecessor.

Extending machine reading approaches to extract mathematical concepts and their descriptions is useful for a variety of tasks, ranging from mathematical information retrieval to increasing accessibility of scientific documents for the visually impaired. This entails segmenting mathematical formulae into identifiers and linking them to their natural language descriptions. We propose a rule-based approach for this task, which extracts LaTeX representations of formula identifiers and links them to their in-text descriptions, given only the original PDF and the location of the formula of interest. We also present a novel evaluation dataset for this task, as well as the tool used to create it.

We propose a simple yet accurate method for dependency parsing that treats parsing as tagging (PaT). That is, our approach addresses the parsing of dependency trees with a sequence model implemented with a bidirectional LSTM over BERT embeddings, where the “tag” to be predicted at each token position is the relative position of the corresponding head. For example, for the sentence John eats cake, the tag to be predicted for the token cake is -1 because its head (eats) occurs one token to the left. Despite its simplicity, our approach performs well. For example, our approach outperforms the state-of-the-art method of (Fernández-González and Gómez-Rodríguez, 2019) on Universal Dependencies (UD) by 1.76% unlabeled attachment score (UAS) for English, 1.98% UAS for French, and 1.16% UAS for German. On average, on 12 UD languages, our method with minimal tuning performs comparably with this state-of-the-art approach: better by 0.11% UAS, and worse by 0.58% LAS.

Many of the most pressing current research problems (e.g., public health, food security, or climate change) require multi-disciplinary collaborations. In order to facilitate this process, we propose a system that incorporates multi-domain extractions of causal interactions into a single searchable knowledge graph. Our system enables users to search iteratively over direct and indirect connections in this knowledge graph, and collaboratively build causal models in real time. To enable the aggregation of causal information from multiple languages, we extend an open-domain machine reader to Portuguese. The new Portuguese reader extracts over 600 thousand causal statements from 120 thousand Portuguese publications with a precision of 62%, which demonstrates the value of mining multilingual scientific information.

Building causal models of complicated phenomena such as food insecurity is currently a slow and labor-intensive manual process. In this paper, we introduce an approach that builds executable probabilistic models from raw, free text. The proposed approach is implemented through three systems: Eidos, INDRA, and Delphi. Eidos is an open-domain machine reading system designed to extract causal relations from natural language. It is rule-based, allowing for rapid domain transfer, customizability, and interpretability. INDRA aggregates multiple sources of causal information and performs assembly to create a coherent knowledge base and assess its reliability. This assembled knowledge serves as the starting point for modeling. Delphi is a modeling framework that assembles quantified causal fragments and their contexts into executable probabilistic models that respect the semantics of the original text, and can be used to support decision making.

We introduce a machine learning approach for the identification of “white spaces” in scientific knowledge. Our approach addresses this task as link prediction over a graph that contains over 2M influence statements such as “CTCF activates FOXA1”, which were automatically extracted using open-domain machine reading. We model this prediction task using graph-based features extracted from the above influence graph, as well as from a citation graph that captures scientific communities. We evaluated the proposed approach through backtesting. Although the data is heavily unbalanced (50 times more negative examples than positives), our approach predicts which influence links will be discovered in the “near future” with a F1 score of 27 points, and a mean average precision of 68%.

For many applications of question answering (QA), being able to explain why a given model chose an answer is critical. However, the lack of labeled data for answer justifications makes learning this difficult and expensive. Here we propose an approach that uses answer ranking as distant supervision for learning how to select informative justifications, where justifications serve as inferential connections between the question and the correct answer while often containing little lexical overlap with either. We propose a neural network architecture for QA that reranks answer justifications as an intermediate (and human-interpretable) step in answer selection. Our approach is informed by a set of features designed to combine both learned representations and explicit features to capture the connection between questions, answers, and answer justifications. We show that with this end-to-end approach we are able to significantly improve upon a strong IR baseline in both justification ranking (+9% rated highly relevant) and answer selection (+6% P@1).

Recent efforts in bioinformatics have achieved tremendous progress in the machine reading of biomedical literature, and the assembly of the extracted biochemical interactions into large-scale models such as protein signaling pathways. However, batch machine reading of literature at today’s scale (PubMed alone indexes over 1 million papers per year) is unfeasible due to both cost and processing overhead. In this work, we introduce a focused reading approach to guide the machine reading of biomedical literature towards what literature should be read to answer a biomedical query as efficiently as possible. We introduce a family of algorithms for focused reading, including an intuitive, strong baseline, and a second approach which uses a reinforcement learning (RL) framework that learns when to explore (widen the search) or exploit (narrow it). We demonstrate that the RL approach is capable of answering more queries than the baseline, while being more efficient, i.e., reading fewer documents.

We describe challenges and advantages unique to coreference resolution in the biomedical domain, and a sieve-based architecture that leverages domain knowledge for both entity and event coreference resolution. Domain-general coreference resolution algorithms perform poorly on biomedical documents, because the cues they rely on such as gender are largely absent in this domain, and because they do not encode domain-specific knowledge such as the number and type of participants required in chemical reactions. Moreover, it is difficult to directly encode this knowledge into most coreference resolution algorithms because they are not rule-based. Our rule-based architecture uses sequentially applied hand-designed “sieves”, with the output of each sieve informing and constraining subsequent sieves. This architecture provides a 3.2% increase in throughput to our Reach event extraction system with precision parallel to that of the stricter system that relies solely on syntactic patterns for extraction.

Odin is an information extraction framework that applies cascades of finite state automata over both surface text and syntactic dependency graphs. Support for syntactic patterns allow us to concisely define relations that are otherwise difficult to express in languages such as Common Pattern Specification Language (CPSL), which are currently limited to shallow linguistic features. The interaction of lexical and syntactic automata provides robustness and flexibility when writing extraction rules. This paper describes Odin’s declarative language for writing these cascaded automata.