Leveraging Full Dependency Parsing Graph Information For Biomedical Event Extraction

Many models are proposed in the literature on biomedical event extraction(BEE). Some of them use the shortest dependency path(SDP) information to represent the argument classification task. There is an issue with this representation since even missing one word from the dependency parsing graph may totally change the final prediction. To this end, the full adjacency matrix of the dependency graph is used to embed individual tokens using a graph convolutional network(GCN). An ablation study is also done to show the effect of the dependency graph on the overall performance. The results show a significant improvement when dependency graph information is used. The proposed model slightly outperforms state-of-the-art models on BEE over different datasets.

BioNCERE: Non-Contrastive Enhancement For Relation Extraction In Biomedical Texts

State-of-the-art models for relation extraction (RE) in the biomedical domain consider finetuning BioBERT using classification, but they may suffer from the anisotropy problem. Contrastive learning methods can reduce this anisotropy phenomena, and also help to avoid class collapse in any classification problem. In the present paper, a new training method called biological non-contrastive relation extraction (BioNCERE) is introduced for relation extraction without using any named entity labels for training to reduce annotation costs. BioNCERE uses transfer learning and non-contrastive learning to avoid full or dimensional collapse as well as bypass overfitting. It resolves RE in three stages by leveraging transfer learning two times. By freezing the weights learned in previous stages in the proposed pipeline and by leveraging non-contrastive learning in the second stage, the model predicts relations without any knowledge of named entities. Experiments have been done on SemMedDB that are almost similar to State-of-the-art performance on RE without using the information of named entities.

Transferring Neural Potentials For High Order Dependency Parsing

High order dependency parsing leverages high order features such as siblings or grandchildren to improve state of the art accuracy of current first order dependency parsers. The present paper uses biaffine scores to provide an estimate of the arc scores and is then propagated into a graphical model. The inference inside the graphical model is solved using dual decomposition. The present algorithm propagates biaffine neural scores to the graphical model and by leveraging dual decomposition inference, the overall circuit is trained end-to-end to transfer first order informations to the high order informations.

Semantic Tagging with LSTM-CRF

In the present paper, two models are presented namely LSTM-CRF and BERT-LSTM-CRF for semantic tagging of universal semantic tag dataset. The experiments show that the first model is much easier to converge while the second model that leverages BERT embedding, takes a long time to converge and needs a big dataset for semtagging to be effective.

Semantic Operator Prediction and Applications

In the present paper, semantic parsing challenges are briefly introduced and QDMR formalism in semantic parsing is implemented using sequence to sequence model with attention but uses only part of speech(POS) as a representation of words of a sentence to make the training as simple and as fast as possible and also avoiding curse of dimensionality as well as overfitting. It is shown how semantic operator prediction could be augmented with other models like the CopyNet model or the recursive neural net model.

A Bayesian Approach To Graph Partitioning

A new algorithm based on bayesian inference for learning local graph conductance based on Gaussian Process(GP) is given that uses advanced MCMC convergence ideas to create a scalable and fast algorithm for convergence to stationary distribution which is provided to learn the bahavior of conductance when traversing the indirected weighted graph. First metric embedding is used to represent the vertices of the graph. Then, uniform induced conductance is calculated for training points. Finally, in the learning step, a gaussian process is used to approximate the uniform induced conductance. MCMC is used to measure uncertainty of estimated hyper-parameters.