Potential function of simplified protein models for discriminating native proteins from decoys: Combining contact interaction and local sequence-dependent geometry

An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only $C_\alpha$ atoms need to be specified, an accurate potential function is important. Such a simplified model is essential for efficient search of conformational space. In this work, we present a formulation of potential function for simplified representations of protein structures. It is based on the combination of descriptors derived from residue-residue contact and sequence-dependent local geometry. The optimal weight coefficients for contact and local geometry is obtained through optimization by maximizing margins among native and decoy structures. The latter are generated by chain growth and by gapless threading. The performance of the potential function in blind test of discriminating native protein structures from decoys is evaluated using several benchmark decoy sets. This potential function have comparable or better performance than several residue-based potential functions that require in addition coordinates of side chain centers or coordinates of all side chain atoms.Comment: 4 pages, 2 figures, Accepted by 26th IEEE-EMBS Conference, San Francisc

Attacking Visual Language Grounding with Adversarial Examples: A Case Study on Neural Image Captioning

Visual language grounding is widely studied in modern neural image captioning systems, which typically adopts an encoder-decoder framework consisting of two principal components: a convolutional neural network (CNN) for image feature extraction and a recurrent neural network (RNN) for language caption generation. To study the robustness of language grounding to adversarial perturbations in machine vision and perception, we propose Show-and-Fool, a novel algorithm for crafting adversarial examples in neural image captioning. The proposed algorithm provides two evaluation approaches, which check whether neural image captioning systems can be mislead to output some randomly chosen captions or keywords. Our extensive experiments show that our algorithm can successfully craft visually-similar adversarial examples with randomly targeted captions or keywords, and the adversarial examples can be made highly transferable to other image captioning systems. Consequently, our approach leads to new robustness implications of neural image captioning and novel insights in visual language grounding.Comment: Accepted by 56th Annual Meeting of the Association for Computational Linguistics (ACL 2018). Hongge Chen and Huan Zhang contribute equally to this wor

Is Robustness the Cost of Accuracy? -- A Comprehensive Study on the Robustness of 18 Deep Image Classification Models

The prediction accuracy has been the long-lasting and sole standard for comparing the performance of different image classification models, including the ImageNet competition. However, recent studies have highlighted the lack of robustness in well-trained deep neural networks to adversarial examples. Visually imperceptible perturbations to natural images can easily be crafted and mislead the image classifiers towards misclassification. To demystify the trade-offs between robustness and accuracy, in this paper we thoroughly benchmark 18 ImageNet models using multiple robustness metrics, including the distortion, success rate and transferability of adversarial examples between 306 pairs of models. Our extensive experimental results reveal several new insights: (1) linear scaling law - the empirical $\ell_2$ and $\ell_\infty$ distortion metrics scale linearly with the logarithm of classification error; (2) model architecture is a more critical factor to robustness than model size, and the disclosed accuracy-robustness Pareto frontier can be used as an evaluation criterion for ImageNet model designers; (3) for a similar network architecture, increasing network depth slightly improves robustness in $\ell_\infty$ distortion; (4) there exist models (in VGG family) that exhibit high adversarial transferability, while most adversarial examples crafted from one model can only be transferred within the same family. Experiment code is publicly available at \url{https://github.com/huanzhang12/Adversarial_Survey}.Comment: Accepted by the European Conference on Computer Vision (ECCV) 201