Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text

We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction system when compared to a baseline that relies solely on surface- and syntax-based features; (ii) In contrast with previous approaches that infer relations on a sentence-by-sentence basis, we expand our framework to enable consistent predictions over sets of sentences (documents); (iii) We further modify and expand a graph kernel learning framework to enable concurrent exploitation of automatically induced AMR (semantic) and dependency structure (syntactic) representations. Our experiments show that our approach yields interaction extraction systems that are more robust in environments where there is a significant mismatch between training and test conditions.Comment: Appearing in Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence (AAAI-16

Guiding AMR Parsing with Reverse Graph Linearization

Abstract Meaning Representation (AMR) parsing aims to extract an abstract semantic graph from a given sentence. The sequence-to-sequence approaches, which linearize the semantic graph into a sequence of nodes and edges and generate the linearized graph directly, have achieved good performance. However, we observed that these approaches suffer from structure loss accumulation during the decoding process, leading to a much lower F1-score for nodes and edges decoded later compared to those decoded earlier. To address this issue, we propose a novel Reverse Graph Linearization (RGL) enhanced framework. RGL defines both default and reverse linearization orders of an AMR graph, where most structures at the back part of the default order appear at the front part of the reversed order and vice versa. RGL incorporates the reversed linearization to the original AMR parser through a two-pass self-distillation mechanism, which guides the model when generating the default linearizations. Our analysis shows that our proposed method significantly mitigates the problem of structure loss accumulation, outperforming the previously best AMR parsing model by 0.8 and 0.5 Smatch scores on the AMR 2.0 and AMR 3.0 dataset, respectively. The code are available at https://github.com/pkunlp-icler/AMR_reverse_graph_linearization.Comment: Findings of EMNLP202

Incorporating Graph Information in Transformer-based AMR Parsing

Abstract Meaning Representation (AMR) is a Semantic Parsing formalism that aims at providing a semantic graph abstraction representing a given text. Current approaches are based on autoregressive language models such as BART or T5, fine-tuned through Teacher Forcing to obtain a linearized version of the AMR graph from a sentence. In this paper, we present LeakDistill, a model and method that explores a modification to the Transformer architecture, using structural adapters to explicitly incorporate graph information into the learned representations and improve AMR parsing performance. Our experiments show how, by employing word-to-node alignment to embed graph structural information into the encoder at training time, we can obtain state-of-the-art AMR parsing through self-knowledge distillation, even without the use of additional data. We release the code at \url{http://www.github.com/sapienzanlp/LeakDistill}.Comment: ACL 2023. Please cite authors correctly using both lastnames ("Mart\'inez Lorenzo", "Huguet Cabot"