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Pre-trained language models induce dense entity representations that offer strong performance on entity-centric NLP tasks, but such representations are not immediately interpretable. This can be a barrier to model uptake in important domains such as biomedicine. There has been recent work on general interpretable representation learning (Onoe and Durrett, 2020), but these domain-agnostic representations do not readily transfer to the important domain of biomedicine. In this paper, we create a new entity type system and training set from a large corpus of biomedical texts by mapping entities to concepts in a medical ontology, and from these to Wikipedia pages whose categories are our types. From this mapping we derive Biomedical Interpretable Entity Representations BIERs), in which dimensions correspond to fine-grained entity types, and values are predicted probabilities that a given entity is of the corresponding type. We propose a novel method that exploits BIER&#39;s final sparse and intermediate dense representations to facilitate model and entity type debugging. We show that BIERs achieve strong performance in biomedical tasks including named entity disambiguation and entity linking, and we provide error analysis to highlight the utility of their interpretability, particularly in low-supervision settings. Finally, we provide our induced 68K biomedical type system, the corresponding 37 million triples of derived data used to train BIER models and our best performing model.

IJCNLP-AACL 2021

Biomedical Interpretable Entity Representations

interpretablity

entity representations

biomedical

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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).

Pre-trained language models induce dense entity representations that offer strong performance on entity-centric NLP tasks, but such representations are not immediately interpretable. This can be a barrier to model uptake in important domains such as biomedicine. There has been recent work on general interpretable representation learning (Onoe and Durrett, 2020), but these domain-agnostic representations do not readily transfer to the important domain of biomedicine. In this paper, we create a new entity type system and training set from a large corpus of biomedical texts by mapping entities to concepts in a medical ontology, and from these to Wikipedia pages whose categories are our types. From this mapping we derive Biomedical Interpretable Entity Representations BIERs), in which dimensions correspond to fine-grained entity types, and values are predicted probabilities that a given entity is of the corresponding type. We propose a novel method that exploits BIER's final sparse and intermediate dense representations to facilitate model and entity type debugging. We show that BIERs achieve strong performance in biomedical tasks including named entity disambiguation and entity linking, and we provide error analysis to highlight the utility of their interpretability, particularly in low-supervision settings. Finally, we provide our induced 68K biomedical type system, the corresponding 37 million triples of derived data used to train BIER models and our best performing model.

technical paper

The recent GPT-3 model (Brown et al., 2020) achieves remarkable few-shot performance solely by leveraging a natural-language prompt and a few task demonstrations as input context. Inspired by their findings, we study few-shot learning in a more practical scenario, where we use smaller language models for which fine-tuning is computationally efficient. We present LM-BFF—better few-shot fine-tuning of language models—a suite of simple and complementary techniques for fine-tuning language models on a small number of annotated examples. Our approach includes (1) prompt-based fine-tuning together with a novel pipeline for automating prompt generation; and (2) a refined strategy for dynamically and selectively incorporating demonstrations into each context. Finally, we present a systematic evaluation for analyzing few-shot performance on a range of NLP tasks, including classification and regression. Our experiments demonstrate that our methods combine to dramatically outperform standard fine-tuning procedures in this low resource setting, achieving up to 30% absolute improvement, and 11% on average across all tasks. Our approach makes minimal assumptions on task resources and domain expertise, and hence constitutes a strong task-agnostic method for few-shot learning.

Making Pre-trained Language Models Better Few-shot Learners

Event language models represent plausible sequences of events. Most existing approaches train autoregressive models on text, which successfully capture event co-occurrence but unfortunately constrain the model to follow the discourse order in which events are presented. Other domains may employ different discourse orders, and for many applications, we may care about different notions of ordering (e.g., temporal) or not care about ordering at all (e.g., when predicting related events in a schema). We propose a simple yet surprisingly effective strategy for improving event language models by perturbing event sequences so we can relax model dependence on text order. Despite generating completely synthetic event orderings, we show that this technique improves the performance of the event language models on both applications and out-of-domain events data.

Don't Let Discourse Confine Your Model: Sequence Perturbations for Improved Event Language Models

Topic models have been widely used to learn text representations and gain insight into document corpora. To perform topic discovery, most existing neural models either take document bag-of-words (BoW) or sequence of tokens as input followed by variational inference and BoW reconstruction to learn topic-word distribution. However, leveraging topic-word distribution for learning better features during document encoding has not been explored much. To this end, we develop a framework TAN-NTM, which processes document as a sequence of tokens through a LSTM whose contextual outputs are attended in a topic-aware manner. We propose a novel attention mechanism which factors in topic-word distribution to enable the model to attend on relevant words that convey topic related cues. The output of topic attention module is then used to carry out variational inference. We perform extensive ablations and experiments resulting in ~9-15 percentage improvement over score of existing SOTA topic models in NPMI coherence on several benchmark datasets - 20Newsgroups, Yelp Review Polarity and AGNews. Further, we show that our method learns better latent document-topic features compared to existing topic models through improvement on two downstream tasks: document classification and topic guided keyphrase generation.

TAN-NTM: Topic Attention Networks for Neural Topic Modeling

paper proposes an approach to cross-language sentence selection in a low-resource setting. It uses data augmentation and negative sampling techniques on noisy parallel sentence data to directly learn a cross-lingual embedding-based query relevance model. Results show that this approach performs as well as or better than multiple state-of-the-art machine translation + monolingual retrieval systems trained on the same parallel data. Moreover, when a rationale training secondary objective is applied to encourage the model to match word alignment hints from a phrase-based statistical machine translation model, consistent improvements are seen across three language pairs (English-Somali, English-Swahili and English-Tagalog) over a variety of state-of-the-art baselines.

Cross-language Sentence Selection via Data Augmentation and Rationale Training

Question answering (QA) systems for large document collections typically use pipelines that (i) retrieve possibly relevant documents, (ii) re-rank them, (iii) rank paragraphs or other snippets of the top-ranked documents, and (iv) select spans of the top-ranked snippets as exact answers. Pipelines are conceptually simple, but errors propagate from one component to the next, without later components being able to revise earlier decisions. We present an architecture for joint document and snippet ranking, the two middle stages, which leverages the intuition that relevant documents have good snippets and good snippets come from relevant documents. The architecture is general and can be used with any neural text relevance ranker. We experiment with two main instantiations of the architecture, based on POSIT-DRMM (PDRMM) and a BERT-based ranker. Experiments on biomedical data from BIOASQ show that our joint models vastly outperform the pipelines in snippet retrieval, the main goal for QA, with fewer trainable parameters, also remaining competitive in document retrieval. Furthermore, our joint PDRMM-based model is competitive with BERT-based models, despite using orders of magnitude fewer parameters. These claims are also supported by human evaluation on two test batches of BIOASQ. To test our key findings on another dataset, we modified the Natural Questions dataset so that it can also be used for document and snippet retrieval. Our joint PDRMM-based model again outperforms the corresponding pipeline in snippet retrieval on the modified Natural Questions dataset, even though it performs worse than the pipeline in document retrieval. We make our code and the modified Natural Questions dataset publicly available.

A Neural Model for Joint Document and Snippet Ranking in Question Answering for Large Document Collections

Information Retrieval using dense low-dimensional representations recently became popular and showed out-performance to traditional sparse-representations like BM25. However, no previous work investigated how dense representations perform with large index sizes. We show theoretically and empirically that the performance for dense representations decreases quicker than sparse representations for increasing index sizes. In extreme cases, this can even lead to a tipping point where at a certain index size sparse representations outperform dense representations. We show that this behavior is tightly connected to the number of dimensions of the representations: The lower the dimension, the higher the chance for false positives, i.e. returning irrelevant documents

The Curse of Dense Low-Dimensional Information Retrieval for Large Index Sizes

Using multiple treebanks to improve parsing performance has shown positive results. However, to what extent similar, yet competing annotation decisions play in parser behavior is unclear. We investigate this within a multi-task learning (MTL) dependency parser setup on two parallel treebanks, UD and SUD, which, while possessing similar annotation schemes, differ in specific linguistic annotation preferences. We perform a set of experiments with different MTL architectural choices, comparing performance across various input embeddings. We find languages tend to pattern in lose typological associations, but generally the performance within an MTL setting is lower than single model baseline parsers for each annotation scheme. The main contributing factor seems to be the competing syntactic annotation information shared between treebanks in an MTL setting, which is shown in experiments against differently annotated treebanks.This suggests that the impact of how the signal is encoded for annotations and its influence on possible negative transfer is more important than that of the input embeddings in an MTL setting.

Annotations Matter: Leveraging Multi-task Learning to Parse UD and SUD

The purpose of an argumentative text is to support a certain conclusion. Yet, they are often omitted, expecting readers to infer them rather. While appropriate when reading an individual text, this rhetorical device limits accessibility when browsing many texts (e.g., on a search engine or on social media). In these scenarios, an explicit conclusion makes for a good candidate summary of an argumentative text. This is especially true if the conclusion is informative, emphasizing specific concepts from the text. With this paper we introduce the task of generating informative conclusions: First, Webis-ConcluGen-21 is compiled, a large-scale corpus of 136,996 samples of argumentative texts and their conclusions. Second, two paradigms for conclusion generation are investigated; one extractive, the other abstractive in nature. The latter exploits argumentative knowledge that augment the data via control codes and finetuning the BART model on several subsets of the corpus. Third, insights are provided into the suitability of our corpus for the task, the differences between the two generation paradigms, the trade-off between informativeness and conciseness, and the impact of encoding argumentative knowledge. The corpus, code, and the trained models are publicly available.

Generating Informative Conclusions for Argumentative Texts

We study a family of data augmentation methods, substructure substitution (SUB2), that generalizes prior methods. SUB2 generates new examples by substituting substructures (e.g., subtrees or subsequences) with others having the same label. This idea can be applied to many structured NLP tasks such as part-of-speech tagging and parsing. For more general tasks (e.g., text classification) which do not have explicitly annotated substructures, we present variations of SUB2 based on text spans or parse trees, introducing structure-aware data augmentation methods to general NLP tasks. For most cases, training with a dataset augmented by SUB2 achieves better performance than training with the original training set. Further experiments show that SUB2 has more consistent performance than other investigated augmentation methods, across different tasks and sizes of the seed dataset.

Substructure Substitution: Structured Data Augmentation for NLP

In challenging economic times, obtaining value for money by ensuring financial integrity and fairer distribution of services are among the top priorities for social and health-care systems globally. However, healthcare billing policies are complex and identifying non-compliance is often narrow-scope, manual and expensive. Maintaining ‘integrity’ is a challenge - ensuring that scarce resources get to those in need and are not lost to fraud and waste. Our approach fuses recent advances in dependency parsing with a policy ontology to convert the content of regulatory healthcare policy into human-friendly policy rules, that are amenable to machine-execution, with human oversight. We describe the ontology-guided transformation of textual patterns into a semantically-meaningful knowledge graph of rules, outline our experiments and evaluate results against policy rules obtained from professional investigators. The aim is to make a policy-compliance ‘landscape’ visible to healthcare programs - helping them identify Fraud, Waste or Abuse.

Biomedical Interpretable Entity Representations

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Making Pre-trained Language Models Better Few-shot Learners

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Biomedical Interpretable Entity Representations

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Making Pre-trained Language Models Better Few-shot Learners

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A Neural Model for Joint Document and Snippet Ranking in Question Answering for Large Document Collections

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

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RESOURCES

Downloads