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Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders

arXiv.org Artificial Intelligence

In line with recent advances in neural drug design 1.1 Motivation and sensitivity prediction, we propose a novel Discovery of novel compounds with a desired efficacy and architecture for interpretable prediction of anticancer improving existing therapies are key bottlenecks in the pharmaceutical compound sensitivity using a multimodal industry, which fuel the largest R&D business attention-based convolutional encoder. Our model spending of any industry and account for 19% of the total is based on the three key pillars of drug sensitivity: R&D spending worldwide (Petrova, 2014; Goh et al., compounds' structure in the form of a SMILES 2017). Anticancer compounds, in particular, take the lion's sequence, gene expression profiles of tumors and share of drug discovery R&D efforts, with over 34% of all prior knowledge on intracellular interactions from drugs in the global R&D pipeline in 2018 (5,212 of 15,267 protein-protein interaction networks. We demonstrate drugs) (Lloyd et al., 2017). Despite enormous scientific that our multiscale convolutional attentionbased and technological advances in recent years, serendipity still (MCA) encoder significantly outperforms a plays a major role in anticancer drug discovery (Hargrave-baseline model trained on Morgan fingerprints, a Thomas et al., 2012) without a systematic way to accumulate selection of encoders based on SMILES as well and leverage years of R&D to achieve higher success as previously reported state of the art for multimodal rates in drug discovery. On the other hand, there is strong drug sensitivity prediction (R2 0.86 evidence that the response to anticancer therapy is highly dependent and RMSE 0.89).


Optimal Approach for Image Recognition using Deep Convolutional Architecture

arXiv.org Artificial Intelligence

In the recent time deep learning has achieved huge popularity due to its performance in various machine learning algorithms. Deep learning as hierarchical or structured learning attempts to model high level abstractions in data by using a group of processing layers. The foundation of deep learning architectures is inspired by the understanding of information processing and neural responses in human brain. The architectures are created by stacking multiple linear or non-linear operations. The article mainly focuses on the state-of-art deep learning models and various real world applications specific training methods. Selecting optimal architecture for specific problem is a challenging task, at a closing stage of the article we proposed optimal approach to deep convolutional architecture for the application of image recognition.


Debunking The Myths And Reality Of Artificial Intelligence

#artificialintelligence

Intelligence should be "distributed" where "knowledge" is created and "decisions" are made A few years ago, it was hard to find anyone to have a serious discussion about Artificial Intelligence (AI) outside academic institutions. Like any new major technology trend, the new wave of making AI and intelligent systems a reality is creating curiosity and enthusiasm. People are jumping on its bandwagon adding not only great ideas but also in many cases a lot of false promises and sometimes misleading opinions. Built by giant thinkers and academic researchers, AI adoption by industries and further development in academia around the globe is progressing at a faster rate than anyone had excepted. Accelerated by the strong belief that our biological limitations are increasingly becoming a major obstacle towards creating smart systems and machines that work with us to better use our biological cognitive capabilities to achieve higher goals. This is driving an overwhelming wave of demands and investments across industries to apply AI technologies to solve real-world problems and create smarter machines and new businesses.


The utility of a convolutional neural network for generating a myelin volume index map from rapid simultaneous relaxometry imaging

arXiv.org Artificial Intelligence

Background and Purpose: A current algorithm to obtain a synthetic myelin volume fraction map (SyMVF) from rapid simultaneous relaxometry imaging (RSRI) has a potential problem, that it does not incorporate information from surrounding pixels. The purpose of this study was to develop a method that utilizes a convolutional neural network (CNN) to overcome this problem. Methods: RSRI and magnetization transfer images from 20 healthy volunteers were included. A CNN was trained to reconstruct RSRI-related metric maps into a myelin volume-related index (generated myelin volume index: GenMVI) map using the myelin volume index map calculated from magnetization transfer images (MTMVI) as reference. The SyMVF and GenMVI maps were statistically compared by testing how well they correlated with the MTMVI map. The correlations were evaluated based on: (i) averaged values obtained from 164 atlas-based ROIs, and (ii) pixel-based comparison for ROIs defined in four different tissue types (cortical and subcortical gray matter, white matter, and whole brain). Results: For atlas-based ROIs, the overall correlation with the MTMVI map was higher for the GenMVI map than for the SyMVF map. In the pixel-based comparison, correlation with the MTMVI map was stronger for the GenMVI map than for the SyMVF map, and the difference in the distribution for the volunteers was significant (Wilcoxon sign-rank test, P<.001) in all tissue types. Conclusion: The proposed method is useful, as it can incorporate more specific information about local tissue properties than the existing method.


A Self-Attentive Emotion Recognition Network

arXiv.org Machine Learning

Modern deep learning approaches have achieved groundbreaking performance in modeling and classifying sequential data. Specifically, attention networks constitute the state-of-the-art paradigm for capturing long temporal dynamics. This paper examines the efficacy of this paradigm in the challenging task of emotion recognition in dyadic conversations. In contrast to existing approaches, our work introduces a novel attention mechanism capable of inferring the immensity of the effect of each past utterance on the current speaker emotional state. The proposed attention mechanism performs this inference procedure without the need of a decoder network; this is achieved by means of innovative self-attention arguments. Our self-attention networks capture the correlation patterns among consecutive encoder network states, thus allowing to robustly and effectively model temporal dynamics over arbitrary long temporal horizons. Thus, we enable capturing strong affective patterns over the course of long discussions. We exhibit the effectiveness of our approach considering the challenging IEMOCAP benchmark. As we show, our devised methodology outperforms state-of-the-art alternatives and commonly used approaches, giving rise to promising new research directions in the context of Online Social Network (OSN) analysis tasks.


Differentiable Pruning Method for Neural Networks

arXiv.org Machine Learning

Architecture optimization is a promising technique to find an efficient neural network to meet certain requirements, which is usually a problem of selections. This paper introduces a concept of a trainable gate function and proposes a channel pruning method which finds automatically the optimal combination of channels using a simple gradient descent training procedure. The trainable gate function, which confers a differentiable property to discrete-valued variables, allows us to directly optimize loss functions that include discrete values such as the number of parameters or FLOPs that are generally non-differentiable. Channel pruning can be applied simply by appending trainable gate functions to each intermediate output tensor followed by fine-tuning the overall model, using any gradient-based training methods. Our experiments show that the proposed method can achieve better compression results on various models. For instance, our proposed method compresses ResNet-56 on CIFAR-10 dataset by half in terms of the number of FLOPs without accuracy drop.


Forecasting in Big Data Environments: an Adaptable and Automated Shrinkage Estimation of Neural Networks (AAShNet)

arXiv.org Machine Learning

This paper considers improved forecasting in possibly nonlinear dynamic settings, with high-dimension predictors ("big data" environments). To overcome the curse of dimensionality and manage data and model complexity, we examine shrinkage estimation of a back-propagation algorithm of a deep neural net with skip-layer connections. We expressly include both linear and nonlinear components. This is a high-dimensional learning approach including both sparsity L1 and smoothness L2 penalties, allowing high-dimensionality and nonlinearity to be accommodated in one step. This approach selects significant predictors as well as the topology of the neural network. We estimate optimal values of shrinkage hyperparameters by incorporating a gradient-based optimization technique resulting in robust predictions with improved reproducibility. The latter has been an issue in some approaches. This is statistically interpretable and unravels some network structure, commonly left to a black box. An additional advantage is that the nonlinear part tends to get pruned if the underlying process is linear. In an application to forecasting equity returns, the proposed approach captures nonlinear dynamics between equities to enhance forecast performance. It offers an appreciable improvement over current univariate and multivariate models by RMSE and actual portfolio performance.


A Robust Approach for Securing Audio Classification Against Adversarial Attacks

arXiv.org Machine Learning

Adversarial audio attacks can be considered as a small perturbation unperceptive to human ears that is intentionally added to the audio signal and causes a machine learning model to make mistakes. This poses a security concern about the safety of machine learning models since the adversarial attacks can fool such models toward the wrong predictions. In this paper we first review some strong adversarial attacks that may affect both audio signals and their 2D representations and evaluate the resiliency of the most common machine learning model, namely deep learning models and support vector machines (SVM) trained on 2D audio representations such as short time Fourier transform (STFT), discrete wavelet transform (DWT) and cross recurrent plot (CRP) against several state-of-the-art adversarial attacks. Next, we propose a novel approach based on pre-processed DWT representation of audio signals and SVM to secure audio systems against adversarial attacks. The proposed architecture has several preprocessing modules for generating and enhancing spectrograms including dimension reduction and smoothing. We extract features from small patches of the spectrograms using speeded up robust feature (SURF) algorithm which are further used to generate a codebook using the K-Means++ algorithm. Finally, codewords are used to train a SVM on the codebook of the SURF-generated vectors. All these steps yield to a novel approach for audio classification that provides a good trade-off between accuracy and resilience. Experimental results on three environmental sound datasets show the competitive performance of proposed approach compared to the deep neural networks both in terms of accuracy and robustness against strong adversarial attacks.


Reducing The Search Space For Hyperparameter Optimization Using Group Sparsity

arXiv.org Machine Learning

We propose a new algorithm for hyperparameter selection in machine learning algorithms. The algorithm is a novel modification of Harmonica, a spectral hyperparameter selection approach using sparse recovery methods. In particular, we show that a special encoding of hyperparameter space enables a natural group-sparse recovery formulation, which when coupled with HyperBand (a multi-armed bandit strategy) leads to improvement over existing hyperparameter optimization methods such as Successive Halving and Random Search. Experimental results on image datasets such as CIFAR-10 confirm the benefits of our approach.


Wearable-based Parkinson's Disease Severity Monitoring using Deep Learning

arXiv.org Machine Learning

One major challenge in the medication of Parkinson's disease is that the severity of the disease, reflected in the patients' motor state, cannot be measured using accessible biomarkers. Therefore, we develop and examine a variety of statistical models to detect the motor state of such patients based on sensor data from a wearable device. We find that deep learning models consistently outperform a classical machine learning model applied on hand-crafted features in this time series classification task. Furthermore, our results suggest that treating this problem as a regression instead of an ordinal regression or a classification task is most appropriate. For consistent model evaluation and training, we adopt the leave-one-subject-out validation scheme to the training of deep learning models. We also employ a class-weighting scheme to successfully mitigate the problem of high multi-class imbalances in this domain. In addition, we propose a customized performance measure that reflects the requirements of the involved medical staff on the model. To solve the problem of limited availability of high quality training data, we propose a transfer learning technique which helps to improve model performance substantially. Our results suggest that deep learning techniques offer a high potential to autonomously detect motor states of patients with Parkinson's disease.