Jie Hou

Nexhi Sula, Abhinav Kumar, Jie Hou et al.

With the continued advancement and widespread adoption of machine learning (ML) models across various domains, ensuring user privacy and data security has become a paramount concern. In compliance with data privacy regulations, such as GDPR, a secure machine learning framework should not only grant users the right to request the removal of their contributed data used for model training but also facilitates the elimination of sensitive data fingerprints within machine learning models to mitigate potential attack - a process referred to as machine unlearning. In this study, we present a novel unlearning mechanism designed to effectively remove the impact of specific data samples from a neural network while considering the performance of the unlearned model on the primary task. In achieving this goal, we crafted a novel loss function tailored to eliminate privacy-sensitive information from weights and activation values of the target model by combining target classification loss and membership inference loss. Our adaptable framework can easily incorporate various privacy leakage approximation mechanisms to guide the unlearning process. We provide empirical evidence of the effectiveness of our unlearning approach with a theoretical upper-bound analysis through a membership inference mechanism as a proof of concept. Our results showcase the superior performance of our approach in terms of unlearning efficacy and latency as well as the fidelity of the primary task, across four datasets and four deep learning architectures.

Yinglin Duan, Tianyang Shi, Zhengxia Zou et al.

Music-to-dance translation is a brand-new and powerful feature in recent role-playing games. Players can now let their characters dance along with specified music clips and even generate fan-made dance videos. Previous works of this topic consider music-to-dance as a supervised motion generation problem based on time-series data. However, these methods suffer from limited training data pairs and the degradation of movements. This paper provides a new perspective for this task where we re-formulate the translation problem as a piece-wise dance phrase retrieval problem based on the choreography theory. With such a design, players are allowed to further edit the dance movements on top of our generation while other regression based methods ignore such user interactivity. Considering that the dance motion capture is an expensive and time-consuming procedure which requires the assistance of professional dancers, we train our method under a semi-supervised learning framework with a large unlabeled dataset (20x than labeled data) collected. A co-ascent mechanism is introduced to improve the robustness of our network. Using this unlabeled dataset, we also introduce self-supervised pre-training so that the translator can understand the melody, rhythm, and other components of music phrases. We show that the pre-training significantly improves the translation accuracy than that of training from scratch. Experimental results suggest that our method not only generalizes well over various styles of music but also succeeds in expert-level choreography for game players.

Jie Hou, Badri Adhikari, Jianlin Cheng

Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to classify protein sequences into a small number of folds due to methodological limitations, which are not generally useful in practice. Results We develop a deep 1D-convolution neural network (DeepSF) to directly classify any protein se quence into one of 1195 known folds, which is useful for both fold recognition and the study of se quence-structure relationship. Different from traditional sequence alignment (comparison) based methods, our method automatically extracts fold-related features from a protein sequence of any length and map it to the fold space. We train and test our method on the datasets curated from SCOP1.75, yielding a classification accuracy of 80.4%. On the independent testing dataset curated from SCOP2.06, the classification accuracy is 77.0%. We compare our method with a top profile profile alignment method - HHSearch on hard template-based and template-free modeling targets of CASP9-12 in terms of fold recognition accuracy. The accuracy of our method is 14.5%-29.1% higher than HHSearch on template-free modeling targets and 4.5%-16.7% higher on hard template-based modeling targets for top 1, 5, and 10 predicted folds. The hidden features extracted from sequence by our method is robust against sequence mutation, insertion, deletion and truncation, and can be used for other protein pattern recognition problems such as protein clustering, comparison and ranking.

Renzhi Cao, Debswapna Bhattacharya, Jie Hou et al.

Protein quality assessment (QA) by ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model pool consisting of mostly low-quality models, is still a largely unsolved problem. We introduce a novel single-model quality assessment method DeepQA based on deep belief network that utilizes a number of selected features describing the quality of a model from different perspectives, such as energy, physio-chemical characteristics, and structural information. The deep belief network is trained on several large datasets consisting of models from the Critical Assessment of Protein Structure Prediction (CASP) experiments, several publicly available datasets, and models generated by our in-house ab initio method. Our experiment demonstrate that deep belief network has better performance compared to Support Vector Machines and Neural Networks on the protein model quality assessment problem, and our method DeepQA achieves the state-of-the-art performance on CASP11 dataset. It also outperformed two well-established methods in selecting good outlier models from a large set of models of mostly low quality generated by ab initio modeling methods. DeepQA is a useful tool for protein single model quality assessment and protein structure prediction. The source code, executable, document and training/test datasets of DeepQA for Linux is freely available to non-commercial users at http://cactus.rnet.missouri.edu/DeepQA/.

Jie Hou, Gerhard Kramer

A security measure called effective security is defined that includes strong secrecy and stealth communication. Effective secrecy ensures that a message cannot be deciphered and that the presence of meaningful communication is hidden. To measure stealth we use resolvability and relate this to binary hypothesis testing. Results are developed for wire-tap channels and broadcast channels with confidential messages.