Biomedical pathways have been extensively used to characterize the mechanism of complex diseases. One essential step in biomedical pathway analysis is to curate the description of a pathway based on its graph structure and node features. Neural text generation could be a plausible technique to circumvent the tedious manual curation. In this paper, we propose a new dataset Pathway2Text, which contains 2,367 pairs of biomedical pathways and textual descriptions. All pathway graphs are experimentally derived or manually curated. All textual descriptions are written by domain experts. We form this problem as a Graph2Text task and propose a novel graph-based text generation approach kNN-Graph2Text, which explicitly exploited descriptions of similar graphs to generate new descriptions. We observed substantial improvement of our method on both Graph2Text and the reverse task of Text2Graph. We further illustrated how our dataset can be used as a novel benchmark for biomedical named entity recognition. Collectively, we envision our method will become an important benchmark for evaluating Graph2Text methods and advance biomedical research for complex diseases.

Precisely defining the terminology is the first step in scientific communication. Developing neural text generation models for definition generation can circumvent the labor-intensity curation, further accelerating scientific discovery. Unfortunately, the lack of large-scale terminology definition dataset hinders the process toward definition generation. In this paper, we present a large-scale terminology definition dataset Graphine covering 2,010,648 terminology definition pairs, spanning 227 biomedical subdisciplines. Terminologies in each subdiscipline further form a directed acyclic graph, opening up new avenues for developing graph-aware text generation models. We then proposed a novel graph-aware definition generation model Graphex that integrates transformer with graph neural network. Our model outperforms existing text generation models by exploiting the graph structure of terminologies. We further demonstrated how Graphine can be used to evaluate pretrained language models, compare graph representation learning methods and predict sentence granularity. We envision Graphine to be a unique resource for definition generation and many other NLP tasks in biomedicine.

Training the generative models with minimal corpus is one of the critical challenges for building open-domain dialogue systems. Existing methods tend to use the meta-learning framework which pre-trains the parameters on all non-target tasks then fine-tunes on the target task. However, fine-tuning distinguishes tasks from the parameter perspective but ignores the model-structure perspective, resulting in similar dialogue models for different tasks. In this paper, we propose an algorithm that can customize a unique dialogue model for each task in the few-shot setting. In our approach, each dialogue model consists of a shared module, a gating module, and a private module. The first two modules are shared among all the tasks, while the third one will differentiate into different network structures to better capture the characteristics of the corresponding task. The extensive experiments on two datasets show that our method outperforms all the baselines in terms of task consistency, response quality, and diversity.