Artificial Intelligence in Drug Discovery:Applications and Techniques

Artificial intelligence has transformed the practice of drug discovery in the past decade. Various artificial intelligence techniques have been used in a wide range of applications. In this perspective, we present major applications of AI in drug discovery and discuss the relevant AI techniques, covering most recent progress in AI-driven drug discovery. We expect that the perspective will serve as a guide for researchers who are interested in working at this intersected area of artificial intelligence and drug discovery. We also provide a GitHub repository summarizing the surveyed papers as a learning resource, which will be regularly updated.

Hierarchical Proxy-based Loss for Deep Metric Learning

Proxy-based metric learning losses are superior to pair-based losses due to their fast convergence and low training complexity. However, existing proxy-based losses focus on learning class-discriminative features while overlooking the commonalities shared across classes which are potentially useful in describing and matching samples. Moreover, they ignore the implicit hierarchy of categories in real-world datasets, where similar subordinate classes can be grouped together. In this paper, we present a framework that leverages this implicit hierarchy by imposing a hierarchical structure on the proxies and can be used with any existing proxy-based loss. This allows our model to capture both class-discriminative features and class-shared characteristics without breaking the implicit data hierarchy. We evaluate our method on five established image retrieval datasets such as In-Shop and SOP. Results demonstrate that our hierarchical proxy-based loss framework improves the performance of existing proxy-based losses, especially on large datasets which exhibit strong hierarchical structure.

Topology-Aware Segmentation Using Discrete Morse Theory

In the segmentation of fine-scale structures from natural and biomedical images, per-pixel accuracy is not the only metric of concern. Topological correctness, such as vessel connectivity and membrane closure, is crucial for downstream analysis tasks. In this paper, we propose a new approach to train deep image segmentation networks for better topological accuracy. In particular, leveraging the power of discrete Morse theory (DMT), we identify global structures, including 1D skeletons and 2D patches, which are important for topological accuracy. Trained with a novel loss based on these global structures, the network performance is significantly improved especially near topologically challenging locations (such as weak spots of connections and membranes). On diverse datasets, our method achieves superior performance on both the DICE score and topological metrics.

Physics-based Shadow Image Decomposition for Shadow Removal

We propose a novel deep learning method for shadow removal. Inspired by physical models of shadow formation, we use a linear illumination transformation to model the shadow effects in the image that allows the shadow image to be expressed as a combination of the shadow-free image, the shadow parameters, and a matte layer. We use two deep networks, namely SP-Net and M-Net, to predict the shadow parameters and the shadow matte respectively. This system allows us to remove the shadow effects from images. We then employ an inpainting network, I-Net, to further refine the results. We train and test our framework on the most challenging shadow removal dataset (ISTD). Our method improves the state-of-the-art in terms of root mean square error (RMSE) for the shadow area by 20\%. Furthermore, this decomposition allows us to formulate a patch-based weakly-supervised shadow removal method. This model can be trained without any shadow-free images (that are cumbersome to acquire) and achieves competitive shadow removal results compared to state-of-the-art methods that are trained with fully paired shadow and shadow-free images. Last, we introduce SBU-Timelapse, a video shadow removal dataset for evaluating shadow removal methods.

FaceDet3D: Facial Expressions with 3D Geometric Detail Prediction

Facial Expressions induce a variety of high-level details on the 3D face geometry. For example, a smile causes the wrinkling of cheeks or the formation of dimples, while being angry often causes wrinkling of the forehead. Morphable Models (3DMMs) of the human face fail to capture such fine details in their PCA-based representations and consequently cannot generate such details when used to edit expressions. In this work, we introduce FaceDet3D, a first-of-its-kind method that generates - from a single image - geometric facial details that are consistent with any desired target expression. The facial details are represented as a vertex displacement map and used then by a Neural Renderer to photo-realistically render novel images of any single image in any desired expression and view. The project website is: http://shahrukhathar.github.io/2020/12/14/FaceDet3D.html

Localization in the Crowd with Topological Constraints

We address the problem of crowd localization, i.e., the prediction of dots corresponding to people in a crowded scene. Due to various challenges, a localization method is prone to spatial semantic errors, i.e., predicting multiple dots within a same person or collapsing multiple dots in a cluttered region. We propose a topological approach targeting these semantic errors. We introduce a topological constraint that teaches the model to reason about the spatial arrangement of dots. To enforce this constraint, we define a persistence loss based on the theory of persistent homology. The loss compares the topographic landscape of the likelihood map and the topology of the ground truth. Topological reasoning improves the quality of the localization algorithm especially near cluttered regions. On multiple public benchmarks, our method outperforms previous localization methods. Additionally, we demonstrate the potential of our method in improving the performance in the crowd counting task.

Modeling Deep Learning Based Privacy Attacks on Physical Mail

Mail privacy protection aims to prevent unauthorized access to hidden content within an envelope since normal paper envelopes are not as safe as we think. In this paper, for the first time, we show that with a well designed deep learning model, the hidden content may be largely recovered without opening the envelope. We start by modeling deep learning-based privacy attacks on physical mail content as learning the mapping from the camera-captured envelope front face image to the hidden content, then we explicitly model the mapping as a combination of perspective transformation, image dehazing and denoising using a deep convolutional neural network, named Neural-STE (See-Through-Envelope). We show experimentally that hidden content details, such as texture and image structure, can be clearly recovered. Finally, our formulation and model allow us to design envelopes that can counter deep learning-based privacy attacks on physical mail.

Intrinsic Decomposition of Document Images In-the-Wild

Automatic document content processing is affected by artifacts caused by the shape of the paper, non-uniform and diverse color of lighting conditions. Fully-supervised methods on real data are impossible due to the large amount of data needed. Hence, the current state of the art deep learning models are trained on fully or partially synthetic images. However, document shadow or shading removal results still suffer because: (a) prior methods rely on uniformity of local color statistics, which limit their application on real-scenarios with complex document shapes and textures and; (b) synthetic or hybrid datasets with non-realistic, simulated lighting conditions are used to train the models. In this paper we tackle these problems with our two main contributions. First, a physically constrained learning-based method that directly estimates document reflectance based on intrinsic image formation which generalizes to challenging illumination conditions. Second, a new dataset that clearly improves previous synthetic ones, by adding a large range of realistic shading and diverse multi-illuminant conditions, uniquely customized to deal with documents in-the-wild. The proposed architecture works in a self-supervised manner where only the synthetic texture is used as a weak training signal (obviating the need for very costly ground truth with disentangled versions of shading and reflectance). The proposed approach leads to a significant generalization of document reflectance estimation in real scenes with challenging illumination. We extensively evaluate on the real benchmark datasets available for intrinsic image decomposition and document shadow removal tasks. Our reflectance estimation scheme, when used as a pre-processing step of an OCR pipeline, shows a 26% improvement of character error rate (CER), thus, proving the practical applicability.