Search for: All records

Abstract Proteins are inherently dynamic, and their conformational ensembles are functionally important in biology. Large-scale motions may govern protein structure–function relationship, and numerous transient but stable conformations of intrinsically disordered proteins (IDPs) can play a crucial role in biological function. Investigating conformational ensembles to understand regulations and disease-related aggregations of IDPs is challenging both experimentally and computationally. In this paper we first introduced an unsupervised deep learning-based model, termed Internal Coordinate Net (ICoN), which learns the physical principles of conformational changes from molecular dynamics (MD) simulation data. Second, we selected interpolating data points in the learned latent space that rapidly identify novel synthetic conformations with sophisticated and large-scale sidechains and backbone arrangements. Third, with the highly dynamic amyloid-β_1-42(Aβ42) monomer, our deep learning model provided a comprehensive sampling of Aβ42’s conformational landscape. Analysis of these synthetic conformations revealed conformational clusters that can be used to rationalize experimental findings. Additionally, the method can identify novel conformations with important interactions in atomistic details that are not included in the training data. New synthetic conformations showed distinct sidechain rearrangements that are probed by our EPR and amino acid substitution studies. This approach is highly transferable and can be used for any available data for training. The work also demonstrated the ability for deep learning to utilize learned natural atomistic motions in protein conformation sampling. 

To understand the genuine emotions expressed by humans during social interactions, it is necessary to recognize the subtle changes on the face (micro-expressions) demonstrated by an individual. Facial micro-expressions are brief, rapid, spontaneous gestures and non-voluntary facial muscle movements beneath the skin. Therefore, it is a challenging task to classify facial micro-expressions. This paper presents an end-to-end novel three-stream graph attention network model to capture the subtle changes on the face and recognize micro-expressions (MEs) by exploiting the relationship between optical flow magnitude, optical flow direction, and the node locations features. A facial graph representational structure is used to extract the spatial and temporal information using three frames. The varying dynamic patch size of optical flow features is used to extract the local texture information across each landmark point. The network only utilizes the landmark points location features and optical flow information across these points and generates good results for the classification of MEs. A comprehensive evaluation of SAMM and the CASME II datasets demonstrates the high efficacy, efficiency, and generalizability of the proposed approach and achieves better results than the state-of-the-art methods. 

Facial micro-expressions are brief, rapid, spontaneous gestures of the facial muscles that express an individual's genuine emotions. Because of their short duration and subtlety, detecting and classifying these micro-expressions by humans and machines is difficult. In this paper, a novel approach is proposed that exploits relationships between landmark points and the optical flow patch for the given landmark points. It consists of a two-stream graph attention convolutional network that extracts the relationships between the landmark points and local texture using an optical flow patch. A graph structure is built to draw out temporal information using the triplet of frames. One stream is for node feature location, and the other one is for a patch of optical-flow information. These two streams (node location stream and optical flow stream) are fused for classification. The results are shown on, CASME II and SAMM, publicly available datasets, for three classes and five classes of micro-expressions. The proposed approach outperforms the state-of-the-art methods for 3 and 5 categories of expressions. 

Facial micro-expressions are spontaneous, subtle, involuntary muscle movements occurring briefly on the face. The spotting and recognition of these expressions are difficult due to the subtle behavior, and the time duration of these expressions is about half a second, which makes it difficult for humans to identify them. These micro-expressions have many applications in our daily life, such as in the field of online learning, game playing, lie detection, and therapy sessions. Traditionally, researchers use RGB images/videos to spot and classify these micro-expressions, which pose challenging problems, such as illumination, privacy concerns and pose variation. The use of depth videos solves these issues to some extent, as the depth videos are not susceptible to the variation in illumination. This paper describes the collection of a first RGB-D dataset for the classification of facial micro-expressions into 6 universal expressions: Anger, Happy, Sad, Fear, Disgust, and Surprise. This paper shows the comparison between the RGB and Depth videos for the classification of facial micro-expressions. Further, a comparison of results shows that depth videos alone can be used to classify facial micro-expressions correctly in a decision tree structure by using the traditional and deep learning approaches with good classification accuracy. The dataset will be released to the public in the near future. 

Recent advances in Convolutional Neural Network (CNN) model interpretability have led to impressive progress in visualizing and understanding model predictions. In particular, gradient-based visual attention methods have driven much recent effort in using visual attention maps as a means for visual explanations. A key problem, however, is these methods are designed for classification and categorization tasks, and their extension to explaining generative models, e.g., variational autoencoders (VAE) is not trivial. In this work, we take a step towards bridging this crucial gap, proposing the first technique to visually explain VAEs by means of gradient-based attention. We present methods to generate visual attention from the learned latent space, and also demonstrate such attention explanations serve more than just explaining VAE predictions. We show how these attention maps can be used to localize anomalies in images, demonstrating state-of-the-art performance on the MVTec-AD dataset. We also show how they can be infused into model training, helping bootstrap the VAE into learning improved latent space disentanglement, demonstrated on the Dsprites dataset.