Deep learning for extracting protein-protein interactions from biomedical literature

State-of-the-art methods for protein-protein interaction (PPI) extraction are primarily feature-based or kernel-based by leveraging lexical and syntactic information. But how to incorporate such knowledge in the recent deep learning methods remains an open question. In this paper, we propose a multichannel dependency-based convolutional neural network model (McDepCNN). It applies one channel to the embedding vector of each word in the sentence, and another channel to the embedding vector of the head of the corresponding word. Therefore, the model can use richer information obtained from different channels. Experiments on two public benchmarking datasets, AIMed and BioInfer, demonstrate that McDepCNN compares favorably to the state-of-the-art rich-feature and single-kernel based methods. In addition, McDepCNN achieves 24.4% relative improvement in F1-score over the state-of-the-art methods on cross-corpus evaluation and 12% improvement in F1-score over kernel-based methods on "difficult" instances. These results suggest that McDepCNN generalizes more easily over different corpora, and is capable of capturing long distance features in the sentences.Comment: Accepted for publication in Proceedings of the 2017 Workshop on Biomedical Natural Language Processing, 10 pages, 2 figures, 6 table

Strategic Planning for Coastal Area of Pudong In Shanghai 2025 – Eastern Shanghai International Frontier Gateway District

To be an international economic, financial, trade, shipping center and a global city is an ultimate goal and long-term task for Shanghai. In the past 30 years, Shanghai has got a great development. In the meanwhile, as the center of Yangtze River Delta, Shanghai has also contributed a lot to the development of the surrounding area, which is growing to be one important metropolitan area in the world. Nowadays,around Shanghai, there has been three other Shanghais. One Western Shanghai includes Suzhou, Kunshan, Hangzhou which are based on cultural tourism and manufacture of technology; one Southern Shanghai includes Ningbo which is based on marine equipment and chemical industry, and one Northern Shanghai includes Nantong which is also based on marine equipment and chemical industry. In the future development, Shanghai and Yangtze River Delta will face more challeges and need to change the development path, laying more effort on improving the soft power in international service, scientific and technological innovation, cultural influence and livable ecology. In this paper, we have one envision for Shanghai 2025, that there will be one area playing the role of springboard for the transition,which need international ports and airports in the meantime, and land resources growing gradually. We believe that as the international gateway of Shanghai and Yangtze river delta, Coastal Area of Pudong including Jiuduansha wetland has a big chance to be the pivot, and the Eastern Shanghai in the near future. In this paper , we are going to depict the picture for Coastal Area of Pudong in 2025, and explain how it is going to be and why it can be

Ten computational challenges in human virome studies

In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent, primarily hindered by the absence of effective methods, particularly in the domain of computational tools. This perspective systematically outlines ten computational challenges spanning various phases of virome studies, ranging from virus identification, sequencing quality evaluation, genome assembly, annotation of viral taxonomy, genome and proteins, inference of biological properties, applications of the virome in disease diagnosis, interactions with other microbes, and associations with human diseases. The resolution of these challenges necessitates ongoing collaboration among computational scientists, virologists, and multidisciplinary experts. In essence, this perspective serves as a comprehensive guide for directing computational efforts in human virome studies, aiming to significantly propel the field forward.Comment: 16 pages, 1 figure