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.
We will first directly feed the concatenated fingerprint feature representation into a multilayer perceptron (MLP) with a two hidden dense layers of size 128, each with ReLU activation. Before the output layer, we include a dropout layer for regularization. The output layer is a dense layer of size 2 - corresponding to the two possible labels - with softmax activation for a probability prediction for each label. The MLP architecture is summarized in Figure . We use binary cross entropy as the loss function, as given in the following equation: @math where @math is the loss, @math is the current set of model parameters, @math is the total number of data samples, @math is true label (0 or 1) for data sample @math , and @math is predicted probability output by the model that the label for data sample @math is 1. Adam is a gradient descent algorithm with an adaptive learning rate that in practice yields quicker model convergence than vanilla stochastic gradient descent, so we use Adam to optimize our model @cite_3 . We set the initial learning rate to @math , minibatch size to 32, and dropout probability to @math .
@cite_3
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In this paper, we study the problem of training large-scale face identification model with imbalanced training data. This problem naturally exists in many real scenarios including large-scale celebrity recognition, movie actor annotation, etc. Our solution contains two components. First, we build a face feature extraction model, and improve its performance, especially for the persons with very limited training samples, by introducing a regularizer to the cross entropy loss for the multi-nomial logistic regression (MLR) learning. This regularizer encourages the directions of the face features from the same class to be close to the direction of their corresponding classification weight vector in the logistic regression. Second, we build a multi-class classifier using MLR on top of the learned face feature extraction model. Since the standard MLR has poor generalization capability for the one-shot classes even if these classes have been oversampled, we propose a novel supervision signal called underrepresented-classes promotion loss, which aligns the norms of the weight vectors of the one-shot classes (a.k.a. underrepresented-classes) to those of the normal classes. In addition to the original cross entropy loss, this new loss term effectively promotes the underrepresented classes in the learned model and leads to a remarkable improvement in face recognition performance. We test our solution on the MS-Celeb-1M low-shot learning benchmark task. Our solution recognizes 94.89 of the test images at the precision of 99 for the one-shot classes. To the best of our knowledge, this is the best performance among all the published methods using this benchmark task with the same setup, including all the participants in the recent MS-Celeb-1M challenge at ICCV 2017. Multi-layer neural networks have lead to remarkable performance on many kinds of benchmark tasks in text, speech and image processing. Nonlinear parameter estimation in hierarchical models is known to be subject to overfitting and misspecification. One approach to these estimation and related problems (local minima, colinearity, feature discovery etc.) is called Dropout (Hinton, et al 2012, 2016). The Dropout algorithm removes hidden units according to a Bernoulli random variable with probability @math prior to each update, creating random "shocks" to the network that are averaged over updates. In this paper we will show that Dropout is a special case of a more general model published originally in 1990 called the Stochastic Delta Rule, or SDR (Hanson, 1990). SDR redefines each weight in the network as a random variable with mean @math and standard deviation @math . Each weight random variable is sampled on each forward activation, consequently creating an exponential number of potential networks with shared weights. Both parameters are updated according to prediction error, thus resulting in weight noise injections that reflect a local history of prediction error and local model averaging. SDR therefore implements a more sensitive local gradient-dependent simulated annealing per weight converging in the limit to a Bayes optimal network. Tests on standard benchmarks (CIFAR) using a modified version of DenseNet shows the SDR outperforms standard Dropout in test error by approx. @math with DenseNet-BC 250 on CIFAR-100 and approx. @math in smaller networks. We also show that SDR reaches the same accuracy that Dropout attains in 100 epochs in as few as 35 epochs. 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. We consider the problem of learning a one-hidden-layer neural network: we assume the input @math is from Gaussian distribution and the label @math , where @math is a nonnegative vector in @math with @math , @math is a full-rank weight matrix, and @math is a noise vector. We first give an analytic formula for the population risk of the standard squared loss and demonstrate that it implicitly attempts to decompose a sequence of low-rank tensors simultaneously. Inspired by the formula, we design a non-convex objective function @math whose landscape is guaranteed to have the following properties: 1. All local minima of @math are also global minima. 2. All global minima of @math correspond to the ground truth parameters. 3. The value and gradient of @math can be estimated using samples. With these properties, stochastic gradient descent on @math provably converges to the global minimum and learn the ground-truth parameters. We also prove finite sample complexity result and validate the results by simulations.