Entity Structure Within and Throughout: Modeling Mention Dependencies for Document-Level Relation Extraction

Entities, as the essential elements in relation extraction tasks, exhibit certain structure. In this work, we formulate such structure as distinctive dependencies between mention pairs. We then propose SSAN, which incorporates these structural dependencies within the standard self-attention mechanism and throughout the overall encoding stage. Specifically, we design two alternative transformation modules inside each self-attention building block to produce attentive biases so as to adaptively regularize its attention flow. Our experiments demonstrate the usefulness of the proposed entity structure and the effectiveness of SSAN. It significantly outperforms competitive baselines, achieving new state-of-the-art results on three popular document-level relation extraction datasets. We further provide ablation and visualization to show how the entity structure guides the model for better relation extraction. Our code is publicly available.Comment: Accepted to AAAI 202

Exploiting graph kernels for high performance biomedical relation extraction

BACKGROUND: Relation extraction from biomedical publications is an important task in the area of semantic mining of text. Kernel methods for supervised relation extraction are often preferred over manual feature engineering methods, when classifying highly ordered structures such as trees and graphs obtained from syntactic parsing of a sentence. Tree kernels such as the Subset Tree Kernel and Partial Tree Kernel have been shown to be effective for classifying constituency parse trees and basic dependency parse graphs of a sentence. Graph kernels such as the All Path Graph kernel (APG) and Approximate Subgraph Matching (ASM) kernel have been shown to be suitable for classifying general graphs with cycles, such as the enhanced dependency parse graph of a sentence. In this work, we present a high performance Chemical-Induced Disease (CID) relation extraction system. We present a comparative study of kernel methods for the CID task and also extend our study to the Protein-Protein Interaction (PPI) extraction task, an important biomedical relation extraction task. We discuss novel modifications to the ASM kernel to boost its performance and a method to apply graph kernels for extracting relations expressed in multiple sentences. RESULTS: Our system for CID relation extraction attains an F-score of 60%, without using external knowledge sources or task specific heuristic or rules. In comparison, the state of the art Chemical-Disease Relation Extraction system achieves an F-score of 56% using an ensemble of multiple machine learning methods, which is then boosted to 61% with a rule based system employing task specific post processing rules. For the CID task, graph kernels outperform tree kernels substantially, and the best performance is obtained with APG kernel that attains an F-score of 60%, followed by the ASM kernel at 57%. The performance difference between the ASM and APG kernels for CID sentence level relation extraction is not significant. In our evaluation of ASM for the PPI task, ASM performed better than APG kernel for the BioInfer dataset, in the Area Under Curve (AUC) measure (74% vs 69%). However, for all the other PPI datasets, namely AIMed, HPRD50, IEPA and LLL, ASM is substantially outperformed by the APG kernel in F-score and AUC measures. CONCLUSIONS: We demonstrate a high performance Chemical Induced Disease relation extraction, without employing external knowledge sources or task specific heuristics. Our work shows that graph kernels are effective in extracting relations that are expressed in multiple sentences. We also show that the graph kernels, namely the ASM and APG kernels, substantially outperform the tree kernels. Among the graph kernels, we showed the ASM kernel as effective for biomedical relation extraction, with comparable performance to the APG kernel for datasets such as the CID-sentence level relation extraction and BioInfer in PPI. Overall, the APG kernel is shown to be significantly more accurate than the ASM kernel, achieving better performance on most datasets

Exploiting graph kernels for high performance biomedical relation extraction

BACKGROUND: Relation extraction from biomedical publications is an important task in the area of semantic mining of text. Kernel methods for supervised relation extraction are often preferred over manual feature engineering methods, when classifying highly ordered structures such as trees and graphs obtained from syntactic parsing of a sentence. Tree kernels such as the Subset Tree Kernel and Partial Tree Kernel have been shown to be effective for classifying constituency parse trees and basic dependency parse graphs of a sentence. Graph kernels such as the All Path Graph kernel (APG) and Approximate Subgraph Matching (ASM) kernel have been shown to be suitable for classifying general graphs with cycles, such as the enhanced dependency parse graph of a sentence. In this work, we present a high performance Chemical-Induced Disease (CID) relation extraction system. We present a comparative study of kernel methods for the CID task and also extend our study to the Protein-Protein Interaction (PPI) extraction task, an important biomedical relation extraction task. We discuss novel modifications to the ASM kernel to boost its performance and a method to apply graph kernels for extracting relations expressed in multiple sentences. RESULTS: Our system for CID relation extraction attains an F-score of 60%, without using external knowledge sources or task specific heuristic or rules. In comparison, the state of the art Chemical-Disease Relation Extraction system achieves an F-score of 56% using an ensemble of multiple machine learning methods, which is then boosted to 61% with a rule based system employing task specific post processing rules. For the CID task, graph kernels outperform tree kernels substantially, and the best performance is obtained with APG kernel that attains an F-score of 60%, followed by the ASM kernel at 57%. The performance difference between the ASM and APG kernels for CID sentence level relation extraction is not significant. In our evaluation of ASM for the PPI task, ASM performed better than APG kernel for the BioInfer dataset, in the Area Under Curve (AUC) measure (74% vs 69%). However, for all the other PPI datasets, namely AIMed, HPRD50, IEPA and LLL, ASM is substantially outperformed by the APG kernel in F-score and AUC measures. CONCLUSIONS: We demonstrate a high performance Chemical Induced Disease relation extraction, without employing external knowledge sources or task specific heuristics. Our work shows that graph kernels are effective in extracting relations that are expressed in multiple sentences. We also show that the graph kernels, namely the ASM and APG kernels, substantially outperform the tree kernels. Among the graph kernels, we showed the ASM kernel as effective for biomedical relation extraction, with comparable performance to the APG kernel for datasets such as the CID-sentence level relation extraction and BioInfer in PPI. Overall, the APG kernel is shown to be significantly more accurate than the ASM kernel, achieving better performance on most datasets

Unmasking The Language Of Science Through Textual Analyses On Biomedical Preprints And Published Papers

Scientific communication is essential for science as it enables the field to grow. This task is often accomplished through a written form such as preprints and published papers. We can obtain a high-level understanding of science and how scientific trends adapt over time by analyzing these resources. This thesis focuses on conducting multiple analyses using biomedical preprints and published papers. In Chapter 2, we explore the language contained within preprints and examine how this language changes due to the peer-review process. We find that token differences between published papers and preprints are stylistically based, suggesting that peer-review results in modest textual changes. We also discovered that preprints are eventually published and adopted quickly within the life science community. Chapter 3 investigates how biomedical terms and tokens change their meaning and usage through time. We show that multiple machine learning models can correct for the latent variation contained within the biomedical text. Also, we provide the scientific community with a listing of over 43,000 potential change points. Tokens with notable changepoints such as “sars” and “cas9” appear within our listing, providing some validation for our approach. In Chapter 4, we use the weak supervision paradigm to examine the possibility of speeding up the labeling function generation process for multiple biomedical relationship types. We found that the language used to describe a biomedical relationship is often distinct, leading to a modest performance in terms of transferability. An exception to this trend is Compound-binds-Gene and Gene-interacts-Gene relationship types