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.
A long standing limitation of general deep neural networks has been the difficulty in interpreting and explaining the classification results. Recently, explainability methods have been devised for deep networks and specifically CNNs @cite_14 @cite_16 @cite_19 @cite_2 . These methods enable one to probe a CNN and identify the important substructures of the input data (as deemed by the network), which could be used as an explanatory tool or as a tool to discover unknown underlying substructures in the data. For example, in the area of medical imaging, in addition to classifying images having malignant lesions, they can be localized, as the CNN can provide reasoning for classifying an input image. Here, we are interested in measuring the potential of these methods for discovery of FGs in organic molecules.
@cite_19 @cite_14 @cite_16 @cite_2
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Most convolutional neural networks (CNNs) lack midlevel layers that model semantic parts of objects. This limits CNN-based methods from reaching their full potential in detecting and utilizing small semantic parts in recognition. Introducing such mid-level layers can facilitate the extraction of part-specific features which can be utilized for better recognition performance. This is particularly important in the domain of fine-grained recognition. In this paper, we propose a new CNN architecture that integrates semantic part detection and abstraction (SPDACNN) for fine-grained classification. The proposed network has two sub-networks: one for detection and one for recognition. The detection sub-network has a novel top-down proposal method to generate small semantic part candidates for detection. The classification sub-network introduces novel part layers that extract features from parts detected by the detection sub-network, and combine them for recognition. As a result, the proposed architecture provides an end-to-end network that performs detection, localization of multiple semantic parts, and whole object recognition within one framework that shares the computation of convolutional filters. Our method outperforms state-of-theart methods with a large margin for small parts detection (e.g. our precision of 93.40 vs the best previous precision of 74.00 for detecting the head on CUB-2011). It also compares favorably to the existing state-of-the-art on finegrained classification, e.g. it achieves 85.14 accuracy on CUB-2011. Automatically detecting illustrations is needed for the target system.Deep Convolutional Neural Networks have been successful in computer vision tasks.DCNN with fine-tuning outperformed the other models including handcrafted features. Systems for aggregating illustrations require a function for automatically distinguishing illustrations from photographs as they crawl the network to collect images. A previous attempt to implement this functionality by designing basic features that were deemed useful for classification achieved an accuracy of only about 58 . On the other hand, deep neural networks had been successful in computer vision tasks, and convolutional neural networks (CNNs) had performed good at extracting such useful image features automatically. We evaluated alternative methods to implement this classification functionality with focus on deep neural networks. As the result of experiments, the method that fine-tuned deep convolutional neural network (DCNN) acquired 96.8 accuracy, outperforming the other models including the custom CNN models that were trained from scratch. We conclude that DCNN with fine-tuning is the best method for implementing a function for automatically distinguishing illustrations from photographs. Deep convolutional neural networks (CNN) have seen tremendous success in large-scale generic object recognition. In comparison with generic object recognition, fine-grained image classification (FGIC) is much more challenging because (i) fine-grained labeled data is much more expensive to acquire (usually requiring domain expertise); (ii) there exists large intra-class and small inter-class variance. Most recent work exploiting deep CNN for image recognition with small training data adopts a simple strategy: pre-train a deep CNN on a large-scale external dataset (e.g., ImageNet) and fine-tune on the small-scale target data to fit the specific classification task. In this paper, beyond the fine-tuning strategy, we propose a systematic framework of learning a deep CNN that addresses the challenges from two new perspectives: (i) identifying easily annotated hyper-classes inherent in the fine-grained data and acquiring a large number of hyper-class-labeled images from readily available external sources (e.g., image search engines), and formulating the problem into multitask learning; (ii) a novel learning model by exploiting a regularization between the fine-grained recognition model and the hyper-class recognition model. We demonstrate the success of the proposed framework on two small-scale fine-grained datasets (Stanford Dogs and Stanford Cars) and on a large-scale car dataset that we collected. Deep Convolutional Neural Networks (CNNs) have demonstrated excellent performance in image classification, but still show room for improvement in object-detection tasks with many categories, in particular for cluttered scenes and occlusion. Modern detection algorithms like Regions with CNNs (, 2014) rely on Selective Search (, 2013) to propose regions which with high probability represent objects, where in turn CNNs are deployed for classification. Selective Search represents a family of sophisticated algorithms that are engineered with multiple segmentation, appearance and saliency cues, typically coming with a significant run-time overhead. Furthermore, (, 2014) have shown that most methods suffer from low reproducibility due to unstable superpixels, even for slight image perturbations. Although CNNs are subsequently used for classification in top-performing object-detection pipelines, current proposal methods are agnostic to how these models parse objects and their rich learned representations. As a result they may propose regions which may not resemble high-level objects or totally miss some of them. To overcome these drawbacks we propose a boosting approach which directly takes advantage of hierarchical CNN features for detecting regions of interest fast. We demonstrate its performance on ImageNet 2013 detection benchmark and compare it with state-of-the-art methods.