Abdul Wahab

Ehtisham Fazal, Muhammad Sohail Ibrahim, Seongyong Park et al.

Cancer is one of the most challenging diseases because of its complexity, variability, and diversity of causes. It has been one of the major research topics over the past decades, yet it is still poorly understood. To this end, multifaceted therapeutic frameworks are indispensable. \emph{Anticancer peptides} (ACPs) are the most promising treatment option, but their large-scale identification and synthesis require reliable prediction methods, which is still a problem. In this paper, we present an intuitive classification strategy that differs from the traditional \emph{black box} method and is based on the well-known statistical theory of \emph{sparse-representation classification} (SRC). Specifically, we create over-complete dictionary matrices by embedding the \emph{composition of the K-spaced amino acid pairs} (CKSAAP). Unlike the traditional SRC frameworks, we use an efficient \emph{matching pursuit} solver instead of the computationally expensive \emph{basis pursuit} solver in this strategy. Furthermore, the \emph{kernel principal component analysis} (KPCA) is employed to cope with non-linearity and dimension reduction of the feature space whereas the \emph{synthetic minority oversampling technique} (SMOTE) is used to balance the dictionary. The proposed method is evaluated on two benchmark datasets for well-known statistical parameters and is found to outperform the existing methods. The results show the highest sensitivity with the most balanced accuracy, which might be beneficial in understanding structural and chemical aspects and developing new ACPs. The Google-Colab implementation of the proposed method is available at the author's GitHub page (\href{https://github.com/ehtisham-Fazal/ACP-Kernel-SRC}{https://github.com/ehtisham-fazal/ACP-Kernel-SRC}).

Jaejun Yoo, Younghoon Jung, Mikyoung Lim et al.

A robust algorithm is proposed to reconstruct the spatial support and the Lamé parameters of multiple inclusions in a homogeneous background elastic material using a few measurements of the displacement field over a finite collection of boundary points. The algorithm does not require any linearization or iterative update of Green's function but still allows very accurate reconstruction. The breakthrough comes from a novel interpretation of Lippmann-Schwinger type integral representation of the displacement field in terms of unknown densities having common sparse support on the location of inclusions. Accordingly, the proposed algorithm consists of a two-step approach. First, the localization problem is recast as a joint sparse recovery problem that renders the densities and the inclusion support simultaneously. Then, a noise robust constrained optimization problem is formulated for the reconstruction of elastic parameters. An efficient algorithm is designed for numerical implementation using the Multiple Sparse Bayesian Learning (M-SBL) for joint sparse recovery problem and the Constrained Split Augmented Lagrangian Shrinkage Algorithm (C-SALSA) for the constrained optimization problem. The efficacy of the proposed framework is manifested through extensive numerical simulations. To the best of our knowledge, this is the first algorithm tailored for parameter reconstruction problems in elastic media using highly under-sampled data in the sense of Nyquist rate.

Tasawar Abbas, Shujaat Khan, Muhammad Sajid et al.

The aim of this article is to present and rigorously analyze topological sensitivity based algorithms for detection of diametrically small inclusions in an isotropic homogeneous elastic formation using single and multiple measurements of the far-field scattering amplitudes. A $L^2-$cost functional is considered and a location indicator is constructed from its topological derivative. The performance of the indicator is analyzed in terms of the topological sensitivity for location detection and stability with respect to measurement and medium noises. It is established that the location indicator does not guarantee inclusion detection and achieves only a low resolution when there is mode-conversion in an elastic formation. Accordingly, a weighted location indicator is designed to tackle the mode-conversion phenomenon. It is substantiated that the weighted function renders the location of an inclusion stably with resolution as per Rayleigh criterion.

Abdul Wahab, Raksha Kumaraswamy, Martha White

Optimistic value estimates provide one mechanism for directed exploration in reinforcement learning (RL). The agent acts greedily with respect to an estimate of the value plus what can be seen as a value bonus. The value bonus can be learned by estimating a value function on reward bonuses, propagating local uncertainties around rewards. However, this approach only increases the value bonus for an action retroactively, after seeing a higher reward bonus from that state and action. Such an approach does not encourage the agent to visit a state and action for the first time. In this work, we introduce an algorithm for exploration called Value Bonuses with Ensemble errors (VBE), that maintains an ensemble of random action-value functions (RQFs). VBE uses the errors in the estimation of these RQFs to design value bonuses that provide first-visit optimism and deep exploration. The key idea is to design the rewards for these RQFs in such a way that the value bonus can decrease to zero. We show that VBE outperforms Bootstrap DQN and two reward bonus approaches (RND and ACB) on several classic environments used to test exploration and provide demonstrative experiments that it can scale easily to more complex environments like Atari.

Seongyong Park, Shujaat Khan, Abdul Wahab

Understanding E3 ligase and target substrate interactions are important for cell biology and therapeutic development. However, experimental identification of E3 target relationships is not an easy task due to the labor-intensive nature of the experiments. In this article, a sequence-based E3-target prediction model is proposed for the first time. The proposed framework utilizes composition of k-spaced amino acid pairs (CKSAAP) to learn the relationship between E3 ligases and their target protein. A class separable latent space encoding scheme is also devised that provides a compressed representation of feature space. A thorough ablation study is performed to identify an optimal gap size for CKSAAP and the number of latent variables that can represent the E3-target relationship successfully. The proposed scheme is evaluated on an independent dataset for a variety of standard quantitative measures. In particular, it achieves an average accuracy of $70.63\%$ on an independent dataset. The source code and datasets used in the study are available at the author's GitHub page (https://github.com/psychemistz/E3targetPred).

Abdul Wahab, Shujaat Khan, Imran Naseem et al.

Fractional learning algorithms are trending in signal processing and adaptive filtering recently. However, it is unclear whether the proclaimed superiority over conventional algorithms is well-grounded or is a myth as their performance has never been extensively analyzed. In this article, a rigorous analysis of fractional variants of the least mean squares and steepest descent algorithms is performed. Some critical schematic kinks in fractional learning algorithms are identified. Their origins and consequences on the performance of the learning algorithms are discussed and swift ready-witted remedies are proposed. Apposite numerical experiments are conducted to discuss the convergence and efficiency of the fractional learning algorithms in stochastic environments.

Jaejun Yoo, Abdul Wahab, Jong Chul Ye

An inverse elastic source problem with sparse measurements is of concern. A generic mathematical framework is proposed which incorporates a low- dimensional manifold regularization in the conventional source reconstruction algorithms thereby enhancing their performance with sparse datasets. It is rigorously established that the proposed framework is equivalent to the so-called \emph{deep convolutional framelet expansion} in machine learning literature for inverse problems. Apposite numerical examples are furnished to substantiate the efficacy of the proposed framework.