Functional groups (FGs) serve as a foundation for analyzing chemical properties of organic molecules. Automatic discovery of FGs will impact various fields of research, including medicinal chemistry, by reducing the amount of lab experiments required for discovery or synthesis of new molecules. Here, we investigate methods based on graph convolutional neural networks (GCNNs) for localizing FGs that contribute to specific chemical properties. Molecules are modeled as undirected graphs with atoms as nodes and bonds as edges. Using this graph structure, we trained GCNNs in a supervised way on experimentally-validated molecular training sets to predict specific chemical properties, e.g., toxicity. Upon learning a GCNN, we analyzed its activation patterns to automatically identify FGs using four different methods: gradient-based saliency maps, Class Activation Mapping (CAM), gradient-weighted CAM (Grad-CAM), and Excitation Back-Propagation. We evaluated the contrastive power of these methods with respect to the specificity of the identified molecular substructures and their relevance for chemical functions. Grad- CAM had the highest contrastive power and generated qualitatively the best FGs. This work paves the way for automatic analysis and design of new molecules.
The most straight-forward approach for generating a sensitivity map over the input data to discover the importance of the underlying substructures is to calculate a gradient map within a layer by considering the norm of the gradient vector with respect to an input for each network weight @cite_14 . However, gradient maps are known to be noisy and smoothening these maps might be necessary @cite_18 . More advanced techniques include Class Activation Mapping (CAM) @cite_16 , Gradient-weighted Class Activation Mapping (Grad-CAM) @cite_19 , and Excitation Back-Propagation (EB) @cite_2 techniques that improve gradient maps by taking into account some notion of context. These techniques have been shown to be effective on CNNs and can identify highly abstract notions in images.
@cite_18 @cite_14 @cite_19 @cite_2 @cite_16
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We propose a technique for making Convolutional Neural Network (CNN)-based models more transparent by visualizing input regions that are 'important' for predictions -- or visual explanations. Our approach, called Gradient-weighted Class Activation Mapping (Grad-CAM), uses class-specific gradient information to localize important regions. These localizations are combined with existing pixel-space visualizations to create a novel high-resolution and class-discriminative visualization called Guided Grad-CAM. These methods help better understand CNN-based models, including image captioning and visual question answering (VQA) models. We evaluate our visual explanations by measuring their ability to discriminate between classes, to inspire trust in humans, and their correlation with occlusion maps. Grad-CAM provides a new way to understand CNN-based models. We have released code, an online demo hosted on CloudCV, and a full version of this extended abstract. Explaining the output of a deep network remains a challenge. In the case of an image classifier, one type of explanation is to identify pixels that strongly influence the final decision. A starting point for this strategy is the gradient of the class score function with respect to the input image. This gradient can be interpreted as a sensitivity map, and there are several techniques that elaborate on this basic idea. This paper makes two contributions: it introduces SmoothGrad, a simple method that can help visually sharpen gradient-based sensitivity maps, and it discusses lessons in the visualization of these maps. We publish the code for our experiments and a website with our results. We propose a novel method called deep convolutional decision jungle (CDJ) and its learning algorithm for image classification. The CDJ maintains the structure of standard convolutional neural networks (CNNs), i.e. multiple layers of multiple response maps fully connected. Each response map-or node-in both the convolutional and fully-connected layers selectively respond to class labels s.t. each data sample travels via a specific soft route of those activated nodes. The proposed method CDJ automatically learns features, whereas decision forests and jungles require pre-defined feature sets. Compared to CNNs, the method embeds the benefits of using data-dependent discriminative functions, which better handles multi-modal heterogeneous data; further,the method offers more diverse sparse network responses, which in turn can be used for cost-effective learning classification. The network is learnt by combining conventional softmax and proposed entropy losses in each layer. The entropy loss,as used in decision tree growing, measures the purity of data activation according to the class label distribution. The back-propagation rule for the proposed loss function is derived from stochastic gradient descent (SGD) optimization of CNNs. We show that our proposed method outperforms state-of-the-art methods on three public image classification benchmarks and one face verification dataset. We also demonstrate the use of auxiliary data labels, when available, which helps our method to learn more discriminative routing and representations and leads to improved classification. For crowded scenes, the accuracy of object-based computer vision methods declines when the images are low-resolution and objects have severe occlusions. Taking counting methods for example, almost all the recent state-of-the-art counting methods bypass explicit detection and adopt regression-based methods to directly count the objects of interest. Among regression-based methods, density map estimation, where the number of objects inside a subregion is the integral of the density map over that subregion, is especially promising because it preserves spatial information, which makes it useful for both counting and localization (detection and tracking). With the power of deep convolutional neural networks (CNNs) the counting performance has improved steadily. The goal of this paper is to evaluate density maps generated by density estimation methods on a variety of crowd analysis tasks, including counting, detection, and tracking. Most existing CNN methods produce density maps with resolution that is smaller than the original images, due to the downsample strides in the convolution pooling operations. To produce an original-resolution density map, we also evaluate a classical CNN that uses a sliding window regressor to predict the density for every pixel in the image. We also consider a fully convolutional (FCNN) adaptation, with skip connections from lower convolutional layers to compensate for loss in spatial information during upsampling. In our experiments, we found that the lower-resolution density maps sometimes have better counting performance. In contrast, the original-resolution density maps improved localization tasks, such as detection and tracking, compared to bilinear upsampling the lower-resolution density maps. Finally, we also propose several metrics for measuring the quality of a density map, and relate them to experiment results on counting and localization.