The current state of cancer therapeutics has been moving away from one-size-fits-all cytotoxic chemotherapy, and towards a more individualized and specific approach involving the targeting of each tumor's genetic vulnerabilities. Different tumors, even of the same type, may be more reliant on certain cellular pathways more than others. With modern advancements in our understanding of cancer genome sequencing, these pathways can be discovered. Investigating each of the millions of possible small molecule inhibitors for each kinase in vitro, however, would be extremely expensive and time consuming. This project focuses on predicting the inhibition activity of small molecules targeting 8 different kinases using multiple deep learning models. We trained fingerprint-based MLPs and simplified molecular-input line-entry specification (SMILES)-based recurrent neural networks (RNNs) and molecular graph convolutional networks (GCNs) to accurately predict inhibitory activity targeting these 8 kinases.
Essentially, a graph convolution layer, similar to a convolutional layer, represents each node as a combination of its neighbors, as shown in Figure . This is accomplished by feeding both atom features (-dimensional vectors for each atom) and pair features (-dimensional vectors for each pair of atoms) through Weave modules in series @cite_13 . Weave modules combine these atom and pair features (denoted @math and @math ) together to generate another set of atom and pair features, which can then be fed into another Weave module. The architecture of a Weave module is shown in Figure , and the definitions of each of the operations is shown below: where @math is an arbitrary, trainable function and @math is an arbitrary commutative function.
@cite_13
2963881378 2169488311 2788158258 1910657905
We present a novel and practical deep fully convolutional neural network architecture for semantic pixel-wise segmentation termed SegNet. This core trainable segmentation engine consists of an encoder network, a corresponding decoder network followed by a pixel-wise classification layer. The architecture of the encoder network is topologically identical to the 13 convolutional layers in the VGG16 network [1] . The role of the decoder network is to map the low resolution encoder feature maps to full input resolution feature maps for pixel-wise classification. The novelty of SegNet lies is in the manner in which the decoder upsamples its lower resolution input feature map(s). Specifically, the decoder uses pooling indices computed in the max-pooling step of the corresponding encoder to perform non-linear upsampling. This eliminates the need for learning to upsample. The upsampled maps are sparse and are then convolved with trainable filters to produce dense feature maps. We compare our proposed architecture with the widely adopted FCN [2] and also with the well known DeepLab-LargeFOV [3] , DeconvNet [4] architectures. This comparison reveals the memory versus accuracy trade-off involved in achieving good segmentation performance. SegNet was primarily motivated by scene understanding applications. Hence, it is designed to be efficient both in terms of memory and computational time during inference. It is also significantly smaller in the number of trainable parameters than other competing architectures and can be trained end-to-end using stochastic gradient descent. We also performed a controlled benchmark of SegNet and other architectures on both road scenes and SUN RGB-D indoor scene segmentation tasks. These quantitative assessments show that SegNet provides good performance with competitive inference time and most efficient inference memory-wise as compared to other architectures. We also provide a Caffe implementation of SegNet and a web demo at http: mi.eng.cam.ac.uk projects segnet . We propose an unsupervised method for learning multi-stage hierarchies of sparse convolutional features. While sparse coding has become an increasingly popular method for learning visual features, it is most often trained at the patch level. Applying the resulting filters convolutionally results in highly redundant codes because overlapping patches are encoded in isolation. By training convolutionally over large image windows, our method reduces the redudancy between feature vectors at neighboring locations and improves the efficiency of the overall representation. In addition to a linear decoder that reconstructs the image from sparse features, our method trains an efficient feed-forward encoder that predicts quasi-sparse features from the input. While patch-based training rarely produces anything but oriented edge detectors, we show that convolutional training produces highly diverse filters, including center-surround filters, corner detectors, cross detectors, and oriented grating detectors. We show that using these filters in multistage convolutional network architecture improves performance on a number of visual recognition and detection tasks. We present a network architecture for processing point clouds that directly operates on a collection of points represented as a sparse set of samples in a high-dimensional lattice. NaA¯vely applying convolutions on this lattice scales poorly, both in terms of memory and computational cost, as the size of the lattice increases. Instead, our network uses sparse bilateral convolutional layers as building blocks. These layers maintain efficiency by using indexing structures to apply convolutions only on occupied parts of the lattice, and allow flexible specifications of the lattice structure enabling hierarchical and spatially-aware feature learning, as well as joint 2D-3D reasoning. Both point-based and image-based representations can be easily incorporated in a network with such layers and the resulting model can be trained in an end-to-end manner. We present results on 3D segmentation tasks where our approach outperforms existing state-of-the-art techniques. We present a novel and practical deep fully convolutional neural network architecture for semantic pixel-wise segmentation termed SegNet. This core trainable segmentation engine consists of an encoder network, a corresponding decoder network followed by a pixel-wise classification layer. The architecture of the encoder network is topologically identical to the 13 convolutional layers in the VGG16 network. The role of the decoder network is to map the low resolution encoder feature maps to full input resolution feature maps for pixel-wise classification. The novelty of SegNet lies is in the manner in which the decoder upsamples its lower resolution input feature map(s). Specifically, the decoder uses pooling indices computed in the max-pooling step of the corresponding encoder to perform non-linear upsampling. This eliminates the need for learning to upsample. The upsampled maps are sparse and are then convolved with trainable filters to produce dense feature maps. We compare our proposed architecture with the widely adopted FCN and also with the well known DeepLab-LargeFOV, DeconvNet architectures. This comparison reveals the memory versus accuracy trade-off involved in achieving good segmentation performance. SegNet was primarily motivated by scene understanding applications. Hence, it is designed to be efficient both in terms of memory and computational time during inference. It is also significantly smaller in the number of trainable parameters than other competing architectures. We also performed a controlled benchmark of SegNet and other architectures on both road scenes and SUN RGB-D indoor scene segmentation tasks. We show that SegNet provides good performance with competitive inference time and more efficient inference memory-wise as compared to other architectures. We also provide a Caffe implementation of SegNet and a web demo at this http URL