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Neoantigens play important roles in cancer immunotherapy. Current methods used for neoantigen prediction focus on the binding between human leukocyte antigens (HLAs) and peptides, which is insufficient for high-confidence neoantigen prediction. In this study, we apply deep learning techniques to predict neoantigens considering both the possibility of HLA-peptide binding (binding model) and the potential immunogenicity (immunogenicity model) of the peptide-HLA complex (pHLA). The binding model achieves comparable performance with other well-acknowledged tools on the latest Immune Epitope Database (IEDB) benchmark datasets and an independent mass spectrometry (MS) dataset. The immunogenicity model could significantly improve the prediction precision of neoantigens. The further application of our method to the mutations with pre-existing T-cell responses indicating its feasibility in clinical application. DeepHLApan is freely available at https://github.com/jiujiezz/deephlapan and http://biopharm.zju.edu.cn/deephlapan., (Copyright © 2019 Wu, Wang, Zhang, Zhou, Zhao, Su, Gu, Wu, Zhou and Chen.)

Predicting the biological properties of molecules is crucial in computer-aided drug development, yet it's often impeded by data scarcity and imbalance in many practical applications. Existing approaches are based on self-supervised learning or 3D data and using an increasing number of parameters to improve performance. These approaches may not take full advantage of established chemical knowledge and could inadvertently introduce noise into the respective model. In this study, we introduce a more elegant transformer-based framework with focused attention for molecular representation (TransFoxMol) to improve the understanding of artificial intelligence (AI) of molecular structure property relationships. TransFoxMol incorporates a multi-scale 2D molecular environment into a graph neural network + Transformer module and uses prior chemical maps to obtain a more focused attention landscape compared to that obtained using existing approaches. Experimental results show that TransFoxMol achieves state-of-the-art performance on MoleculeNet benchmarks and surpasses the performance of baselines that use self-supervised learning or geometry-enhanced strategies on small-scale datasets. Subsequent analyses indicate that TransFoxMol's predictions are highly interpretable and the clever use of chemical knowledge enables AI to perceive molecules in a simple but rational way, enhancing performance. [ABSTRACT FROM AUTHOR]

Nowadays, interactive recommendation systems (IRS) play a significant role in our daily life. Recently, reinforcement learning has shown great potential in solving challenging tasks in IRS, since it can focus on long-term profit and can capture the dynamic preference of users. However, existing RL methods for IRS have two typical deficiencies. First, most state representation models use left-to-right recurrent neural networks to capture the user dynamics, which usually fail to handle the long and noisy sequential data in real life. Second, an IRS always needs to handle millions of items, leading to a large discrete action space in RL settings, which has not been fully addressed by the inefficient existing works. To bridge these deficiencies, in this paper, we propose attention-based tree recommendation (ATRec), an efficient tree-structured policy with attention-based state representation for IRS. ATRec uses an attention-based state representation model to effectively capture the user's dynamic preference hidden in the long and noisy sequence of behaviors. Moreover, to improve the learning efficiency, we propose an efficient tree-structured policy representation method, in which a complete tree is devised to represent the policy, and a novel parameter-sharing strategy is introduced. Extensive experiments are conducted on three real-world datasets and the results show the proposed ATRec obtains 42.3% improvement over some of the state of the arts methods in the hit rate and 21.4% improvement in the mean reciprocal rank of the top 30 ranked items. Additionally, the learning and decision efficiency can also be improved at an average of 35.5%. [ABSTRACT FROM AUTHOR]

Synthetic aperture radar (SAR) has become one of the most important means of information acquisition in today's society and shows great potential in many fields. Target identification and classification of SAR images are also the focus of research. With the vigorous development of deep learning, many researchers apply this method to SAR target classification to obtain a more automatic process and more accurate results. In this paper, a novel deep forest model constructed by multi-grained cascade forest (gcForest), which is different from the traditional neural network (NN) model, is employed to classify ten types of SAR targets in the moving and stationary target acquisition and recognition (MSTAR) dataset. Considering that the targets of input images may be off-center and of different sizes in practical applications, two improved models based on varying weights by image features have been put forward, and both obtain better results. A series of experiments have been conducted to optimize model parameters, and final results with the MSTAR dataset illustrate that the two improved models are both superior to the original gcForest model. This is the first attempt to classify SAR targets using the non-NN model. [ABSTRACT FROM AUTHOR]