Biological data are extremely diverse, complex but also quite sparse. The recent developments in deep learning methods are offering new possibilities for the analysis of complex data. However, it is easy to be get a deep learning model that seems to have good results but is in fact either overfitting the training data or the validation data. In particular, the fact to overfit the validation data, called "information leak", is almost never treated in papers proposing deep learning models to predict protein-protein interactions (PPI). In this work, we compare two carefully designed deep learning models and show pitfalls to avoid while predicting PPIs through machine learning methods. Our best model predicts accurately more than 78 of human PPI, in very strict conditions both for training and testing. The methodology we propose here allow us to have strong confidences about the ability of a model to scale up on larger datasets. This would allow sharper models when larger datasets would be available, rather than current models prone to information leaks. Our solid methodological foundations shall be applicable to more organisms and whole proteome networks predictions.
Finally, @cite_10 present a fully connected model regulated by dropouts. Like @cite_0 , they use composition-transition-distribution descriptors as features. They apply a 5-fold cross validation and have no separated test sets.
@cite_0 @cite_10
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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. Recently, dropout has seen increasing use in deep learning. For deep convolutional neural networks, dropout is known to work well in fully-connected layers. However, its effect in convolutional and pooling layers is still not clear. This paper demonstrates that max-pooling dropout is equivalent to randomly picking activation based on a multinomial distribution at training time. In light of this insight, we advocate employing our proposed probabilistic weighted pooling, instead of commonly used max-pooling, to act as model averaging at test time. Empirical evidence validates the superiority of probabilistic weighted pooling. We also empirically show that the effect of convolutional dropout is not trivial, despite the dramatically reduced possibility of over-fitting due to the convolutional architecture. Elaborately designing dropout training simultaneously in max-pooling and fully-connected layers, we achieve state-of-the-art performance on MNIST, and very competitive results on CIFAR-10 and CIFAR-100, relative to other approaches without data augmentation. Finally, we compare max-pooling dropout and stochastic pooling, both of which introduce stochasticity based on multinomial distributions at pooling stage. Compositional embedding models build a representation (or embedding) for a linguistic structure based on its component word embeddings. We propose a Feature-rich Compositional Embedding Model (FCM) for relation extraction that is expressive, generalizes to new domains, and is easy-to-implement. The key idea is to combine both (unlexicalized) handcrafted features with learned word embeddings. The model is able to directly tackle the difficulties met by traditional compositional embeddings models, such as handling arbitrary types of sentence annotations and utilizing global information for composition. We test the proposed model on two relation extraction tasks, and demonstrate that our model outperforms both previous compositional models and traditional feature rich models on the ACE 2005 relation extraction task, and the SemEval 2010 relation classification task. The combination of our model and a loglinear classifier with hand-crafted features gives state-of-the-art results. We made our implementation available for general use 1 . Compositional embedding models build a representation (or embedding) for a linguistic structure based on its component word embeddings. We propose a Feature-rich Compositional Embedding Model (FCM) for relation extraction that is expressive, generalizes to new domains, and is easy-to-implement. The key idea is to combine both (unlexicalized) hand-crafted features with learned word embeddings. The model is able to directly tackle the difficulties met by traditional compositional embeddings models, such as handling arbitrary types of sentence annotations and utilizing global information for composition. We test the proposed model on two relation extraction tasks, and demonstrate that our model outperforms both previous compositional models and traditional feature rich models on the ACE 2005 relation extraction task, and the SemEval 2010 relation classification task. The combination of our model and a log-linear classifier with hand-crafted features gives state-of-the-art results.