Yannis Papanikolaou


pdf bib
Slot Filling for Biomedical Information Extraction
Yannis Papanikolaou | Marlene Staib | Justin Joshua Grace | Francine Bennett
Proceedings of the 21st Workshop on Biomedical Language Processing

Information Extraction (IE) from text refers to the task of extracting structured knowledge from unstructured text. The task typically consists of a series of sub-tasks such as Named Entity Recognition and Relation Extraction. Sourcing entity and relation type specific training data is a major bottleneck in domains with limited resources such as biomedicine. In this work we present a slot filling approach to the task of biomedical IE, effectively replacing the need for entity and relation-specific training data, allowing us to deal with zero-shot settings. We follow the recently proposed paradigm of coupling a Tranformer-based bi-encoder, Dense Passage Retrieval, with a Transformer-based reading comprehension model to extract relations from biomedical text. We assemble a biomedical slot filling dataset for both retrieval and reading comprehension and conduct a series of experiments demonstrating that our approach outperforms a number of simpler baselines. We also evaluate our approach end-to-end for standard as well as zero-shot settings. Our work provides a fresh perspective on how to solve biomedical IE tasks, in the absence of relevant training data. Our code, models and datasets are available at https://github.com/tba.

pdf bib
Neural Embedding Allocation: Distributed Representations of Topic Models
Kamrun Naher Keya | Yannis Papanikolaou | James R. Foulds
Computational Linguistics, Volume 48, Issue 4 - December 2022

We propose a method that uses neural embeddings to improve the performance of any given LDA-style topic model. Our method, called neural embedding allocation (NEA), deconstructs topic models (LDA or otherwise) into interpretable vector-space embeddings of words, topics, documents, authors, and so on, by learning neural embeddings to mimic the topic model. We demonstrate that NEA improves coherence scores of the original topic model by smoothing out the noisy topics when the number of topics is large. Furthermore, we show NEA’s effectiveness and generality in deconstructing and smoothing LDA, author-topic models, and the recent mixed membership skip-gram topic model and achieve better performance with the embeddings compared to several state-of-the-art models.


pdf bib
Deep Bidirectional Transformers for Relation Extraction without Supervision
Yannis Papanikolaou | Ian Roberts | Andrea Pierleoni
Proceedings of the 2nd Workshop on Deep Learning Approaches for Low-Resource NLP (DeepLo 2019)

We present a novel framework to deal with relation extraction tasks in cases where there is complete lack of supervision, either in the form of gold annotations, or relations from a knowledge base. Our approach leverages syntactic parsing and pre-trained word embeddings to extract few but precise relations, which are then used to annotate a larger corpus, in a manner identical to distant supervision. The resulting data set is employed to fine tune a pre-trained BERT model in order to perform relation extraction. Empirical evaluation on four data sets from the biomedical domain shows that our method significantly outperforms two simple baselines for unsupervised relation extraction and, even if not using any supervision at all, achieves slightly worse results than the state-of-the-art in three out of four data sets. Importantly, we show that it is possible to successfully fine tune a large pretrained language model with noisy data, as opposed to previous works that rely on gold data for fine tuning.