Saadullah Amin


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MedDistant19: Towards an Accurate Benchmark for Broad-Coverage Biomedical Relation Extraction
Saadullah Amin | Pasquale Minervini | David Chang | Pontus Stenetorp | Guenter Neumann
Proceedings of the 29th International Conference on Computational Linguistics

Relation extraction in the biomedical domain is challenging due to the lack of labeled data and high annotation costs, needing domain experts. Distant supervision is commonly used to tackle the scarcity of annotated data by automatically pairing knowledge graph relationships with raw texts. Such a pipeline is prone to noise and has added challenges to scale for covering a large number of biomedical concepts. We investigated existing broad-coverage distantly supervised biomedical relation extraction benchmarks and found a significant overlap between training and test relationships ranging from 26% to 86%. Furthermore, we noticed several inconsistencies in the data construction process of these benchmarks, and where there is no train-test leakage, the focus is on interactions between narrower entity types. This work presents a more accurate benchmark MedDistant19 for broad-coverage distantly supervised biomedical relation extraction that addresses these shortcomings and is obtained by aligning the MEDLINE abstracts with the widely used SNOMED Clinical Terms knowledge base. Lacking thorough evaluation with domain-specific language models, we also conduct experiments validating general domain relation extraction findings to biomedical relation extraction.

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Few-Shot Cross-lingual Transfer for Coarse-grained De-identification of Code-Mixed Clinical Texts
Saadullah Amin | Noon Pokaratsiri Goldstein | Morgan Wixted | Alejandro Garcia-Rudolph | Catalina Martínez-Costa | Guenter Neumann
Proceedings of the 21st Workshop on Biomedical Language Processing

Despite the advances in digital healthcare systems offering curated structured knowledge, much of the critical information still lies in large volumes of unlabeled and unstructured clinical texts. These texts, which often contain protected health information (PHI), are exposed to information extraction tools for downstream applications, risking patient identification. Existing works in de-identification rely on using large-scale annotated corpora in English, which often are not suitable in real-world multilingual settings. Pre-trained language models (LM) have shown great potential for cross-lingual transfer in low-resource settings. In this work, we empirically show the few-shot cross-lingual transfer property of LMs for named entity recognition (NER) and apply it to solve a low-resource and real-world challenge of code-mixed (Spanish-Catalan) clinical notes de-identification in the stroke domain. We annotate a gold evaluation dataset to assess few-shot setting performance where we only use a few hundred labeled examples for training. Our model improves the zero-shot F1-score from 73.7% to 91.2% on the gold evaluation set when adapting Multilingual BERT (mBERT) (CITATION) from the MEDDOCAN (CITATION) corpus with our few-shot cross-lingual target corpus. When generalized to an out-of-sample test set, the best model achieves a human-evaluation F1-score of 97.2%.

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Temporal Knowledge Graph Reasoning with Low-rank and Model-agnostic Representations
Ioannis Dikeoulias | Saadullah Amin | Günter Neumann
Proceedings of the 7th Workshop on Representation Learning for NLP

Temporal knowledge graph completion (TKGC) has become a popular approach for reasoning over the event and temporal knowledge graphs, targeting the completion of knowledge with accurate but missing information. In this context, tensor decomposition has successfully modeled interactions between entities and relations. Their effectiveness in static knowledge graph completion motivates us to introduce Time-LowFER, a family of parameter-efficient and time-aware extensions of the low-rank tensor factorization model LowFER. Noting several limitations in current approaches to represent time, we propose a cycle-aware time-encoding scheme for time features, which is model-agnostic and offers a more generalized representation of time. We implement our methods in a unified temporal knowledge graph embedding framework, focusing on time-sensitive data processing. The experiments show that our proposed methods perform on par or better than the state-of-the-art semantic matching models on two benchmarks.


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AutoEQA: Auto-Encoding Questions for Extractive Question Answering
Stalin Varanasi | Saadullah Amin | Guenter Neumann
Findings of the Association for Computational Linguistics: EMNLP 2021

There has been a significant progress in the field of Extractive Question Answering (EQA) in the recent years. However, most of them are reliant on annotations of answer-spans in the corresponding passages. In this work, we address the problem of EQA when no annotations are present for the answer span, i.e., when the dataset contains only questions and corresponding passages. Our method is based on auto-encoding of the question that performs a question answering task during encoding and a question generation task during decoding. We show that our method performs well in a zero-shot setting and can provide an additional loss to boost performance for EQA.

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T2NER: Transformers based Transfer Learning Framework for Named Entity Recognition
Saadullah Amin | Guenter Neumann
Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: System Demonstrations

Recent advances in deep transformer models have achieved state-of-the-art in several natural language processing (NLP) tasks, whereas named entity recognition (NER) has traditionally benefited from long-short term memory (LSTM) networks. In this work, we present a Transformers based Transfer Learning framework for Named Entity Recognition (T2NER) created in PyTorch for the task of NER with deep transformer models. The framework is built upon the Transformers library as the core modeling engine and supports several transfer learning scenarios from sequential transfer to domain adaptation, multi-task learning, and semi-supervised learning. It aims to bridge the gap between the algorithmic advances in these areas by combining them with the state-of-the-art in transformer models to provide a unified platform that is readily extensible and can be used for both the transfer learning research in NER, and for real-world applications. The framework is available at:


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CopyBERT: A Unified Approach to Question Generation with Self-Attention
Stalin Varanasi | Saadullah Amin | Guenter Neumann
Proceedings of the 2nd Workshop on Natural Language Processing for Conversational AI

Contextualized word embeddings provide better initialization for neural networks that deal with various natural language understanding (NLU) tasks including Question Answering (QA) and more recently, Question Generation(QG). Apart from providing meaningful word representations, pre-trained transformer models (Vaswani et al., 2017), such as BERT (Devlin et al., 2019) also provide self-attentions which encode syntactic information that can be probed for dependency parsing (Hewitt and Manning, 2019) and POStagging (Coenen et al., 2019). In this paper, we show that the information from selfattentions of BERT are useful for language modeling of questions conditioned on paragraph and answer phrases. To control the attention span, we use semi-diagonal mask and utilize a shared model for encoding and decoding, unlike sequence-to-sequence. We further employ copy-mechanism over self-attentions to acheive state-of-the-art results for Question Generation on SQuAD v1.1 (Rajpurkar et al., 2016).

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A Data-driven Approach for Noise Reduction in Distantly Supervised Biomedical Relation Extraction
Saadullah Amin | Katherine Ann Dunfield | Anna Vechkaeva | Guenter Neumann
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing

Fact triples are a common form of structured knowledge used within the biomedical domain. As the amount of unstructured scientific texts continues to grow, manual annotation of these texts for the task of relation extraction becomes increasingly expensive. Distant supervision offers a viable approach to combat this by quickly producing large amounts of labeled, but considerably noisy, data. We aim to reduce such noise by extending an entity-enriched relation classification BERT model to the problem of multiple instance learning, and defining a simple data encoding scheme that significantly reduces noise, reaching state-of-the-art performance for distantly-supervised biomedical relation extraction. Our approach further encodes knowledge about the direction of relation triples, allowing for increased focus on relation learning by reducing noise and alleviating the need for joint learning with knowledge graph completion.