Designing a new drug is a lengthy and expensive process. As the space of potential molecules is very large (10 23 - 10 60 ), a common technique during drug discovery is to start from a molecule which already has some of the desired properties. An interdisciplinary team of scientists generates hypothesis about the required changes to the prototype. In this work, we develop an algorithmic unsupervised-approach that automatically generates potential drug molecules given a prototype drug. We show that the molecules generated by the system are valid molecules and significantly different from the prototype drug. Out of the compounds generated by the system, we identified 35 FDA-approved drugs. As an example, our system generated Isoniazid - one of the main drugs for Tuberculosis. The system is currently being deployed for use in collaboration with pharmaceutical companies to further analyze the additional generated molecules.
Over the past decade, deep neural networks (DNN) has been a game changer in various areas of machine learning research, such as computer vision @cite_31 @cite_29 , natural language processing @cite_33 and speech recognition @cite_1 . Deep neural network most prominent success stories are observed in domains with access to large, raw (unprocessed) datasets. In such scenarios deep learning was able to achieve above human level performance. Compared with those domains, DNN in chemistry relies heavily on engineered features representing a molecule @cite_21 @cite_16 @cite_13 . Such approaches are semi optimal as they restrict the space of potential representations through the assumptions made by limiting to the chosen features @cite_0 .
@cite_33 @cite_29 @cite_21 @cite_1 @cite_0 @cite_31 @cite_16 @cite_13
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With access to large datasets, deep neural networks (DNN) have achieved human-level accuracy in image and speech recognition tasks. However, in chemistry, availability of large standardized and labelled datasets is scarce, and many chemical properties of research interest, chemical data is inherently small and fragmented. In this work, we explore transfer learning techniques in conjunction with the existing Chemception CNN model, to create a transferable and generalizable deep neural network for small-molecule property prediction. Our latest model, ChemNet learns in a semi-supervised manner from inexpensive labels computed from the ChEMBL database. When fine-tuned to the Tox21, HIV and FreeSolv dataset, which are 3 separate chemical properties that ChemNet was not originally trained on, we demonstrate that ChemNet exceeds the performance of existing Chemception models and other contemporary DNN models. Furthermore, as ChemNet has been pre-trained on a large diverse chemical database, it can be used as a general-purpose plug-and-play deep neural network for the prediction of novel small-molecule chemical properties. Abstract Deep Neural Network (DNN) has recently achieved outstanding performance in a variety of computer vision tasks, including facial attribute classification. The great success of classifying facial attributes with DNN often relies on a massive amount of labelled data. However, in real-world applications, labelled data are only provided for some commonly used attributes (such as age, gender); whereas, unlabelled data are available for other attributes (such as attraction, hairline). To address the above problem, we propose a novel deep transfer neural network method based on multi-label learning for facial attribute classification, termed FMTNet, which consists of three sub-networks: the Face detection Network (FNet), the Multi-label learning Network (MNet) and the Transfer learning Network (TNet). Firstly, based on the Faster Region-based Convolutional Neural Network (Faster R-CNN), FNet is fine-tuned for face detection. Then, MNet is fine-tuned by FNet to predict multiple attributes with labelled data, where an effective loss weight scheme is developed to explicitly exploit the correlation between facial attributes based on attribute grouping. Finally, based on MNet, TNet is trained by taking advantage of unsupervised domain adaptation for unlabelled facial attribute classification. The three sub-networks are tightly coupled to perform effective facial attribute classification. A distinguishing characteristic of the proposed FMTNet method is that the three sub-networks (FNet, MNet and TNet) are constructed in a similar network structure. Extensive experimental results on challenging face datasets demonstrate the effectiveness of our proposed method compared with several state-of-the-art methods. Deep neural networks (DNNs) have recently been achieving state-of-the-art performance on a variety of pattern-recognition tasks, most notably visual classification problems. Given that DNNs are now able to classify objects in images with near-human-level performance, questions naturally arise as to what differences remain between computer and human vision. A recent study [30] revealed that changing an image (e.g. of a lion) in a way imperceptible to humans can cause a DNN to label the image as something else entirely (e.g. mislabeling a lion a library). Here we show a related result: it is easy to produce images that are completely unrecognizable to humans, but that state-of-the-art DNNs believe to be recognizable objects with 99.99 confidence (e.g. labeling with certainty that white noise static is a lion). Specifically, we take convolutional neural networks trained to perform well on either the ImageNet or MNIST datasets and then find images with evolutionary algorithms or gradient ascent that DNNs label with high confidence as belonging to each dataset class. It is possible to produce images totally unrecognizable to human eyes that DNNs believe with near certainty are familiar objects, which we call “fooling images” (more generally, fooling examples). Our results shed light on interesting differences between human vision and current DNNs, and raise questions about the generality of DNN computer vision. Deep Neural Networks (DNNs) have recently been shown to significantly outperform existing machine learning techniques in several pattern recognition tasks. DNNs are the state-of-the-art models used in image recognition, object detection, classification and tracking, and speech and language processing applications. The biggest drawback to DNNs has been the enormous cost in computation and time taken to train the parameters of the networks - often a tenfold increase relative to conventional technologies. Such training time costs can be mitigated by the application of parallel computing algorithms and architectures. However, these algorithms often run into difficulties because of the cost of inter-processor communication bottlenecks. In this paper, we describe how to enable Parallel Deep Neural Network Training on the IBM Blue Gene Q (BG Q) computer system. Specifically, we explore DNN training using the data parallel Hessian-free 2nd order optimization algorithm. Such an algorithm is particularly well-suited to parallelization across a large set of loosely coupled processors. BG Q, with its excellent inter-processor communication characteristics, is an ideal match for this type of algorithm. The paper discusses how issues regarding programming model and data-dependent imbalances are addressed. Results on large-scale speech tasks show that the performance on BG Q scales linearly up to 4096 processes with no loss in accuracy. This allows us to train neural networks using billions of training examples in a few hours.