Cícero dos Santos

Payel Das, Kahini Wadhawan, Oscar Chang et al.

Given the emerging global threat of antimicrobial resistance, new methods for next-generation antimicrobial design are urgently needed. We report a peptide generation framework PepCVAE, based on a semi-supervised variational autoencoder (VAE) model, for designing novel antimicrobial peptide (AMP) sequences. Our model learns a rich latent space of the biological peptide context by taking advantage of abundant, unlabeled peptide sequences. The model further learns a disentangled antimicrobial attribute space by using the feedback from a jointly trained AMP classifier that uses limited labeled instances. The disentangled representation allows for controllable generation of AMPs. Extensive analysis of the PepCVAE-generated sequences reveals superior performance of our model in comparison to a plain VAE, as PepCVAE generates novel AMP sequences with higher long-range diversity, while being closer to the training distribution of biological peptides. These features are highly desired in next-generation antimicrobial design.

Mo Yu, Wenpeng Yin, Kazi Saidul Hasan et al.

Relation detection is a core component for many NLP applications including Knowledge Base Question Answering (KBQA). In this paper, we propose a hierarchical recurrent neural network enhanced by residual learning that detects KB relations given an input question. Our method uses deep residual bidirectional LSTMs to compare questions and relation names via different hierarchies of abstraction. Additionally, we propose a simple KBQA system that integrates entity linking and our proposed relation detector to enable one enhance another. Experimental results evidence that our approach achieves not only outstanding relation detection performance, but more importantly, it helps our KBQA system to achieve state-of-the-art accuracy for both single-relation (SimpleQuestions) and multi-relation (WebQSP) QA benchmarks.

Ming Tan, Cicero dos Santos, Bing Xiang et al.

In this paper, we apply a general deep learning (DL) framework for the answer selection task, which does not depend on manually defined features or linguistic tools. The basic framework is to build the embeddings of questions and answers based on bidirectional long short-term memory (biLSTM) models, and measure their closeness by cosine similarity. We further extend this basic model in two directions. One direction is to define a more composite representation for questions and answers by combining convolutional neural network with the basic framework. The other direction is to utilize a simple but efficient attention mechanism in order to generate the answer representation according to the question context. Several variations of models are provided. The models are examined by two datasets, including TREC-QA and InsuranceQA. Experimental results demonstrate that the proposed models substantially outperform several strong baselines.