Biomedical Event Extraction with Hierarchical Knowledge Graphs

Biomedical event extraction is critical in understanding biomolecular interactions described in scientific corpus. One of the main challenges is to identify nested structured events that are associated with non-indicative trigger words. We propose to incorporate domain knowledge from Unified Medical Language System (UMLS) to a pre-trained language model via Graph Edge-conditioned Attention Networks (GEANet) and hierarchical graph representation. To better recognize the trigger words, each sentence is first grounded to a sentence graph based on a jointly modeled hierarchical knowledge graph from UMLS. The grounded graphs are then propagated by GEANet, a novel graph neural networks for enhanced capabilities in inferring complex events. On BioNLP 2011 GENIA Event Extraction task, our approach achieved 1.41% F1 and 3.19% F1 improvements on all events and complex events, respectively. Ablation studies confirm the importance of GEANet and hierarchical KG.

Deep Structured Neural Network for Event Temporal Relation Extraction

We propose a novel deep structured learning framework for event temporal relation extraction. The model consists of 1) a recurrent neural network (RNN) to learn scoring functions for pair-wise relations, and 2) a structured support vector machine (SSVM) to make joint predictions. The neural network automatically learns representations that account for long-term contexts to provide robust features for the structured model, while the SSVM incorporates domain knowledge such as transitive closure of temporal relations as constraints to make better globally consistent decisions. By jointly training the two components, our model combines the benefits of both data-driven learning and knowledge exploitation. Experimental results on three high-quality event temporal relation datasets (TCR, MATRES, and TB-Dense) demonstrate that incorporated with pre-trained contextualized embeddings, the proposed model achieves significantly better performances than the state-of-the-art methods on all three datasets. We also provide thorough ablation studies to investigate our model.

Spoken Language Intent Detection using Confusion2Vec

Decoding speaker's intent is a crucial part of spoken language understanding (SLU). The presence of noise or errors in the text transcriptions, in real life scenarios make the task more challenging. In this paper, we address the spoken language intent detection under noisy conditions imposed by automatic speech recognition (ASR) systems. We propose to employ confusion2vec word feature representation to compensate for the errors made by ASR and to increase the robustness of the SLU system. The confusion2vec, motivated from human speech production and perception, models acoustic relationships between words in addition to the semantic and syntactic relations of words in human language. We hypothesize that ASR often makes errors relating to acoustically similar words, and the confusion2vec with inherent model of acoustic relationships between words is able to compensate for the errors. We demonstrate through experiments on the ATIS benchmark dataset, the robustness of the proposed model to achieve state-of-the-art results under noisy ASR conditions. Our system reduces classification error rate (CER) by 20.84% and improves robustness by 37.48% (lower CER degradation) relative to the previous state-of-the-art going from clean to noisy transcripts. Improvements are also demonstrated when training the intent detection models on noisy transcripts.

Deep Hybrid Scattering Image Learning

A well-trained deep neural network is shown to gain capability of simultaneously restoring two kinds of images, which are completely destroyed by two distinct scattering medias respectively. The network, based on the U-net architecture, can be trained by blended dataset of speckles-reference images pairs. We experimentally demonstrate the power of the network in reconstructing images which are strongly diffused by glass diffuser or multi-mode fiber. The learning model further shows good generalization ability to reconstruct images that are distinguished from the training dataset. Our work facilitates the study of optical transmission and expands machine learning's application in optics.