Xiaojun Xu

Cheng Ge, Yi Lu, Jia Qu et al.

De novo peptide sequencing from mass spectrometry data is an important method for protein identification. Recently, various deep learning approaches were applied for de novo peptide sequencing and DeepNovoV2 is one of the represetative models. In this study, we proposed an enhanced model, DePS, which can improve the accuracy of de novo peptide sequencing even with missing signal peaks or large number of noisy peaks in tandem mass spectrometry data. It is showed that, for the same test set of DeepNovoV2, the DePS model achieved excellent results of 74.22%, 74.21% and 41.68% for amino acid recall, amino acid precision and peptide recall respectively. Furthermore, the results suggested that DePS outperforms DeepNovoV2 on the cross species dataset.

Xiaohua Lu, Liangxu Xie, Lei Xu et al.

Accurately predicting molecular properties is a challenging but essential task in drug discovery. Recently, many mono-modal deep learning methods have been successfully applied to molecular property prediction. However, the inherent limitation of mono-modal learning arises from relying solely on one modality of molecular representation, which restricts a comprehensive understanding of drug molecules and hampers their resilience against data noise. To overcome the limitations, we construct multimodal deep learning models to cover different molecular representations. We convert drug molecules into three molecular representations, SMILES-encoded vectors, ECFP fingerprints, and molecular graphs. To process the modal information, Transformer-Encoder, bi-directional gated recurrent units (BiGRU), and graph convolutional network (GCN) are utilized for feature learning respectively, which can enhance the model capability to acquire complementary and naturally occurring bioinformatics information. We evaluated our triple-modal model on six molecule datasets. Different from bi-modal learning models, we adopt five fusion methods to capture the specific features and leverage the contribution of each modal information better. Compared with mono-modal models, our multimodal fused deep learning (MMFDL) models outperform single models in accuracy, reliability, and resistance capability against noise. Moreover, we demonstrate its generalization ability in the prediction of binding constants for protein-ligand complex molecules in the refined set of PDBbind. The advantage of the multimodal model lies in its ability to process diverse sources of data using proper models and suitable fusion methods, which would enhance the noise resistance of the model while obtaining data diversity.

Huichen Li, Xiaojun Xu, Chang Liu et al.

Malicious calls, i.e., telephony spams and scams, have been a long-standing challenging issue that causes billions of dollars of annual financial loss worldwide. This work presents the first machine learning-based solution without relying on any particular assumptions on the underlying telephony network infrastructures. The main challenge of this decade-long problem is that it is unclear how to construct effective features without the access to the telephony networks' infrastructures. We solve this problem by combining several innovations. We first develop a TouchPal user interface on top of a mobile App to allow users tagging malicious calls. This allows us to maintain a large-scale call log database. We then conduct a measurement study over three months of call logs, including 9 billion records. We design 29 features based on the results, so that machine learning algorithms can be used to predict malicious calls. We extensively evaluate different state-of-the-art machine learning approaches using the proposed features, and the results show that the best approach can reduce up to 90% unblocked malicious calls while maintaining a precision over 99.99% on the benign call traffic. The results also show the models are efficient to implement without incurring a significant latency overhead. We also conduct ablation analysis, which reveals that using 10 out of the 29 features can reach a performance comparable to using all features.

Rui Luo, Weinan Zhang, Xiaojun Xu et al.

In this paper, we show that the recent integration of statistical models with deep recurrent neural networks provides a new way of formulating volatility (the degree of variation of time series) models that have been widely used in time series analysis and prediction in finance. The model comprises a pair of complementary stochastic recurrent neural networks: the generative network models the joint distribution of the stochastic volatility process; the inference network approximates the conditional distribution of the latent variables given the observables. Our focus here is on the formulation of temporal dynamics of volatility over time under a stochastic recurrent neural network framework. Experiments on real-world stock price datasets demonstrate that the proposed model generates a better volatility estimation and prediction that outperforms mainstream methods, e.g., deterministic models such as GARCH and its variants, and stochastic models namely the MCMC-based model \emph{stochvol} as well as the Gaussian process volatility model \emph{GPVol}, on average negative log-likelihood.

Xiaojun Xu, Xinyun Chen, Chang Liu et al.

Adversarial attacks are known to succeed on classifiers, but it has been an open question whether more complex vision systems are vulnerable. In this paper, we study adversarial examples for vision and language models, which incorporate natural language understanding and complex structures such as attention, localization, and modular architectures. In particular, we investigate attacks on a dense captioning model and on two visual question answering (VQA) models. Our evaluation shows that we can generate adversarial examples with a high success rate (i.e., > 90%) for these models. Our work sheds new light on understanding adversarial attacks on vision systems which have a language component and shows that attention, bounding box localization, and compositional internal structures are vulnerable to adversarial attacks. These observations will inform future work towards building effective defenses.