Word Recognition with Deep Conditional Random Fields

Recognition of handwritten words continues to be an important problem in document analysis and recognition. Existing approaches extract hand-engineered features from word images--which can perform poorly with new data sets. Recently, deep learning has attracted great attention because of the ability to learn features from raw data. Moreover they have yielded state-of-the-art results in classification tasks including character recognition and scene recognition. On the other hand, word recognition is a sequential problem where we need to model the correlation between characters. In this paper, we propose using deep Conditional Random Fields (deep CRFs) for word recognition. Basically, we combine CRFs with deep learning, in which deep features are learned and sequences are labeled in a unified framework. We pre-train the deep structure with stacked restricted Boltzmann machines (RBMs) for feature learning and optimize the entire network with an online learning algorithm. The proposed model was evaluated on two datasets, and seen to perform significantly better than competitive baseline models. The source code is available at https://github.com/ganggit/deepCRFs.Comment: 5 pages, published in ICIP 2016. arXiv admin note: substantial text overlap with arXiv:1412.339

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

Recently exciting progress has been made on protein contact prediction, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual networks. This deep neural network allows us to model very complex sequence-contact relationship as well as long-range inter-contact correlation. Our method greatly outperforms existing contact prediction methods and leads to much more accurate contact-assisted protein folding. Tested on three datasets of 579 proteins, the average top L long-range prediction accuracy obtained our method, the representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints can yield correct folds (i.e., TMscore>0.6) for 203 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 proteins, respectively. Further, our contact-assisted models have much better quality than template-based models. Using our predicted contacts as restraints, we can (ab initio) fold 208 of the 398 membrane proteins with TMscore>0.5. By contrast, when the training proteins of our method are used as templates, homology modeling can only do so for 10 of them. One interesting finding is that even if we do not train our prediction models with any membrane proteins, our method works very well on membrane protein prediction. Finally, in recent blind CAMEO benchmark our method successfully folded 5 test proteins with a novel fold