Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userHybrid Attentional Memory Network for Computational drug repositioning
368
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Drug repositioning is designed to discover new uses of known drugs, which is an important and efficient method of drug discovery. Researchers only use one certain type of Collaborative Filtering (CF) models for drug repositioning currently, like the neighborhood based approaches which are good at mining the local information contained in few strong drug-disease associations, or the latent factor based models which are effectively capture the global information shared by a majority of drug-disease associations. Few researchers have combined these two types of CF models to derive a hybrid model with the advantages of both of them. Besides, the cold start problem has always been a major challenge in the field of computational drug repositioning, which restricts the inference ability of relevant models. Inspired by the memory network, we propose the Hybrid Attentional Memory Network (HAMN) model, a deep architecture combines two classes of CF model in a nonlinear manner. Firstly, the memory unit and the attention mechanism are combined to generate the neighborhood contribution representation to capture the local structure of few strong drug-disease associations. Then a variant version of the autoencoder is used to extract the latent factor of drugs and diseases to capture the overall information shared by a majority of drug-disease associations. In that process, ancillary information of drugs and diseases can help to alleviate the cold start problem. Finally, in the prediction stage, the neighborhood contribution representation is combined with the drug latent factor and disease latent factor to produce the predicted value. Comprehensive experimental results on two real data sets show that our proposed HAMN model is superior to other comparison models according to the AUC, AUPR and HR indicators.
rate research
Read More
Computational drug repositioning aims to discover new therapeutic diseases for marketed drugs and has the advantages of low cost, short development cycle, and high controllability compared to traditional drug development. The matrix factorization model has become a mainstream cornerstone technique for computational drug repositioning due to its ease of implementation and excellent scalability. However, the matrix factorization model uses the inner product operation to represent the association between drugs and diseases, which is lacking in expressive ability. Moreover, the degree of similarity of drugs or diseases could not be implied on their respective latent factor vectors, which is not satisfy the common sense of drug discovery. Therefore, a neural metric factorization model for computational drug repositioning is proposed in this work. We novelly consider the latent factor vector of drugs and diseases as a point in a high-dimensional coordinate system and propose a generalized Euclidean distance to represent the association between drugs and diseases to compensate for the shortcomings of the inner product operation. Furthermore, by embedding multiple drug and disease metrics information into the encoding space of the latent factor vector, the latent factor vectors of similar drugs or diseases are made closer. Finally, we conduct wide analysis experiments on two real datasets to demonstrate the effectiveness of the above improvement points and the superiority of the NMF model.
Training convolutional neural network models is memory intensive since back-propagation requires storing activations of all intermediate layers. This presents a practical concern when seeking to deploy very deep architectures in production, especially when models need to be frequently re-trained on updated datasets. In this paper, we propose a new implementation for back-propagation that significantly reduces memory usage, by enabling the use of approximations with negligible computational cost and minimal effect on training performance. The algorithm reuses common buffers to temporarily store full activations and compute the forward pass exactly. It also stores approximate per-layer copies of activations, at significant memory savings, that are used in the backward pass. Compared to simply approximating activations within standard back-propagation, our method limits accumulation of errors across layers. This allows the use of much lower-precision approximations without affecting training accuracy. Experiments on CIFAR-10, CIFAR-100, and ImageNet show that our method yields performance close to exact training, while storing activations compactly with as low as 4-bit precision.
In recent years, we have witnessed an increased interest in temporal modeling of patient records from large scale Electronic Health Records (EHR). While simpler RNN models have been used for such problems, memory networks, which in other domains were found to generalize well, are underutilized. Traditional memory networks involve diffused and non-linear operations where influence of past events on outputs are not readily quantifiable. We posit that this lack of interpretability makes such networks not applicable for EHR analysis. While networks with explicit memory have been proposed recently, the discontinuities imposed by the discrete operations make such networks harder to train and require more supervision. The problem is further exacerbated in the limited data setting of EHR studies. In this paper, we propose a novel memory architecture that is more interpretable than traditional memory networks while being easier to train than explicit memory banks. Inspired by well-known models of human cognition, we propose partitioning the external memory space into (a) a primary explicit memory block to store exact replicas of recent events to support interpretations, followed by (b) a secondary blurred memory block that accumulates salient aspects of past events dropped from the explicit block as higher level abstractions and allow training with less supervision by stabilize the gradients. We apply the model for 3 learning problems on ICU records from the MIMIC III database spanning millions of data points. Our model performs comparably to the state-of the art while also, crucially, enabling ready interpretation of the results.
The Corona Virus Disease 2019 (COVID-19) belongs to human coronaviruses (HCoVs), which spreads rapidly around the world. Compared with new drug development, drug repurposing may be the best shortcut for treating COVID-19. Therefore, we constructed a comprehensive heterogeneous network based on the HCoVs-related target proteins and use the previously proposed deepDTnet, to discover potential drug candidates for COVID-19. We obtain high performance in predicting the possible drugs effective for COVID-19 related proteins. In summary, this work utilizes a powerful heterogeneous network-based deep learning method, which may be beneficial to quickly identify candidate repurposable drugs toward future clinical trials for COVID-19. The code and data are available at https://github.com/stjin-XMU/HnDR-COVID.
User response prediction, which aims to predict the probability that a user will provide a predefined positive response in a given context such as clicking on an ad or purchasing an item, is crucial to many industrial applications such as online advertising, recommender systems, and search ranking. However, due to the high dimensionality and super sparsity of the data collected in these tasks, handcrafting cross features is inevitably time expensive. Prior studies in predicting user response leveraged the feature interactions by enhancing feature vectors with products of features to model second-order or high-order cross features, either explicitly or implicitly. Nevertheless, these existing methods can be hindered by not learning sufficient cross features due to model architecture limitations or modeling all high-order feature interactions with equal weights. This work aims to fill this gap by proposing a novel architecture Deep Cross Attentional Product Network (DCAP), which keeps cross networks benefits in modeling high-order feature interactions explicitly at the vector-wise level. Beyond that, it can differentiate the importance of different cross features in each network layer inspired by the multi-head attention mechanism and Product Neural Network (PNN), allowing practitioners to perform a more in-depth analysis of user behaviors. Additionally, our proposed model can be easily implemented and train in parallel. We conduct comprehensive experiments on three real-world datasets. The results have robustly demonstrated that our proposed model DCAP achieves superior prediction performance compared with the state-of-the-art models. Public codes are available at https://github.com/zachstarkk/DCAP.
suggested questions
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
