EBM-Fold: Fully-Differentiable Protein Folding Powered by Energy-based Models

Accurate protein structure prediction from amino-acid sequences is critical to better understanding the protein function. Recent advances in this area largely benefit from more precise inter-residue distance and orientation predictions, powered by deep neural networks. However, the structure optimization procedure is still dominated by traditional tools, e.g. Rosetta, where the structure is solved via minimizing a pre-defined statistical energy function (with optional prediction-based restraints). Such energy function may not be optimal in formulating the whole conformation space of proteins. In this paper, we propose a fully-differentiable approach for protein structure optimization, guided by a data-driven generative network. This network is trained in a denoising manner, attempting to predict the correction signal from corrupted distance matrices between Ca atoms. Once the network is well trained, Langevin dynamics based sampling is adopted to gradually optimize structures from random initialization. Extensive experiments demonstrate that our EBM-Fold approach can efficiently produce high-quality decoys, compared against traditional Rosetta-based structure optimization routines.

tFold-TR: Combining Deep Learning Enhanced Hybrid Potential Energy for Template-Based Modeling Structure Refinement

Protein structure prediction has been a grand challenge for over 50 years, owing to its broad scientific and application interests. There are two primary types of modeling algorithms, template-free modeling and template-based modeling. The latter one is suitable for easy prediction tasks and is widely adopted in computer-aided drug discoveries for drug design and screening. Although it has been several decades since its first edition, the current template-based modeling approach suffers from two critical problems: 1) there are many missing regions in the template-query sequence alignment, and 2) the accuracy of the distance pairs from different regions of the template varies, and this information is not well introduced into the modeling. To solve these two problems, we propose a structural optimization process based on template modeling, introducing two neural network models to predict the distance information of the missing regions and the accuracy of the distance pairs of different regions in the template modeling structure. The predicted distances and residue pairwise-specific deviations are incorporated into the potential energy function for structural optimization, which significantly improves the qualities of the original template modeling decoys.

tFold-TR: Combining Deep Learning Enhanced Hybrid Potential Energy for Template-Based Modelling Structure Refinement

Proteins structure prediction has long been a grand challenge over the past 50 years, owing to its broad scientific and application interests. There are two major types of modelling algorithms, template-free modelling and template-based modelling. The latter one is suitable for easy prediction tasks and is widely adopted in computer-aided drug discoveries for drug design and screening. Although it has been several decades since its first edition, the current template-based modeling approach suffers from two important problems: 1) there are many missing regions in the template-query sequence alignment, and 2) the accuracy of the distance pairs from different regions of the template varies, and this information is not well introduced into the modeling. To solve the two problems, we propose a structural optimization process based on template modelling, introducing two neural network models to predict the distance information of the missing regions and the accuracy of the distance pairs of different regions in the template modeling structure. The predicted distances and residue pairwise-specific deviations are incorporated into the potential energy function for structural optimization, which significantly improves the qualities of the original template modelling decoys.

Federated Face Recognition

Face recognition has been extensively studied in computer vision and artificial intelligence communities in recent years. An important issue of face recognition is data privacy, which receives more and more public concerns. As a common privacy-preserving technique, Federated Learning is proposed to train a model cooperatively without sharing data between parties. However, as far as we know, it has not been successfully applied in face recognition. This paper proposes a framework named FedFace to innovate federated learning for face recognition. Specifically, FedFace relies on two major innovative algorithms, Partially Federated Momentum (PFM) and Federated Validation (FV). PFM locally applies an estimated equivalent global momentum to approximating the centralized momentum-SGD efficiently. FV repeatedly searches for better federated aggregating weightings via testing the aggregated models on some private validation datasets, which can improve the model's generalization ability. The ablation study and extensive experiments validate the effectiveness of the FedFace method and show that it is comparable to or even better than the centralized baseline in performance.

Real-Time Semantic Segmentation via Auto Depth, Downsampling Joint Decision and Feature Aggregation

To satisfy the stringent requirements on computational resources in the field of real-time semantic segmentation, most approaches focus on the hand-crafted design of light-weight segmentation networks. Recently, Neural Architecture Search (NAS) has been used to search for the optimal building blocks of networks automatically, but the network depth, downsampling strategy, and feature aggregation way are still set in advance by trial and error. In this paper, we propose a joint search framework, called AutoRTNet, to automate the design of these strategies. Specifically, we propose hyper-cells to jointly decide the network depth and downsampling strategy, and an aggregation cell to achieve automatic multi-scale feature aggregation. Experimental results show that AutoRTNet achieves 73.9% mIoU on the Cityscapes test set and 110.0 FPS on an NVIDIA TitanXP GPU card with 768x1536 input images.

Disturbance-immune Weight Sharing for Neural Architecture Search

Neural architecture search (NAS) has gained increasing attention in the community of architecture design. One of the key factors behind the success lies in the training efficiency created by the weight sharing (WS) technique. However, WS-based NAS methods often suffer from a performance disturbance (PD) issue. That is, the training of subsequent architectures inevitably disturbs the performance of previously trained architectures due to the partially shared weights. This leads to inaccurate performance estimation for the previous architectures, which makes it hard to learn a good search strategy. To alleviate the performance disturbance issue, we propose a new disturbance-immune update strategy for model updating. Specifically, to preserve the knowledge learned by previous architectures, we constrain the training of subsequent architectures in an orthogonal space via orthogonal gradient descent. Equipped with this strategy, we propose a novel disturbance-immune training scheme for NAS. We theoretically analyze the effectiveness of our strategy in alleviating the PD risk. Extensive experiments on CIFAR-10 and ImageNet verify the superiority of our method.

Few Shot Network Compression via Cross Distillation

Model compression has been widely adopted to obtain light-weighted deep neural networks. Most prevalent methods, however, require fine-tuning with sufficient training data to ensure accuracy, which could be challenged by privacy and security issues. As a compromise between privacy and performance, in this paper we investigate few shot network compression: given few samples per class, how can we effectively compress the network with negligible performance drop? The core challenge of few shot network compression lies in high estimation errors from the original network during inference, since the compressed network can easily over-fits on the few training instances. The estimation errors could propagate and accumulate layer-wisely and finally deteriorate the network output. To address the problem, we propose cross distillation, a novel layer-wise knowledge distillation approach. By interweaving hidden layers of teacher and student network, layer-wisely accumulated estimation errors can be effectively reduced.The proposed method offers a general framework compatible with prevalent network compression techniques such as pruning. Extensive experiments on benchmark datasets demonstrate that cross distillation can significantly improve the student network's accuracy when only a few training instances are available.