In this talk, I will show how these materials are used in organic electrochemical transistors (OECTs) to detect biological species in physiological media. I will introduce two types of OECT based sensors; one that detects Alzheimer’s disease biomarkers with performance exceeding the state-of-the-art,1,2 and the other that detects coronavirus spike proteins at the physical limit.3 Having challenged these sensors with patient samples, I will discuss areas where proof-of-concept organic biosensor platforms may fail. By tackling each of these problems, we improve device performance to a level that marks a considerable step toward biochemical sensing of infectious and noninfectious disease biomarkers. I will highlight how computational methods can aid in sensor development and organic semiconductor research.

Abstract

The life sciences have invested significant resources in the development and application

The Artificial Intelligence Initiative (AII) at KAUST cordially invites you to attend the KAUST Conference on Artificial Intelligence to be held on April 28-29, 2021. The conference is a two full-day event that will bring together KAUST faculty and researchers to highlight exciting AI research being done on campus. It will feature the broad AI landscape at KAUST by delving into topics on machine learning, AI theory and foundations, systems, and the many applications of AI in various scientific fields ranging from healthcare and biology to automation and visual computing.

Dynamic programming is an efficient technique to solve optimization problems. It is based on decomposing the initial problem into simpler ones and solving these sub-problems beginning from the simplest ones. A conventional dynamic programming algorithm returns an optimal object from a given set of objects. We developed extensions of dynamic programming which allow us (i) to describe the set of objects under consideration, (ii) to perform a multi-stage optimization of objects relative to different criteria, (iii) to count the number of optimal objects, (iv) to find the set of Pareto optimal points for the bi-criteria optimization problem, and (v) to study the relationships between two criteria. The considered applications include optimization of decision trees and decision rule systems as algorithms for problem-solving, as ways for knowledge representation, and as classifiers, optimization of element partition trees for rectangular meshes which are used in finite element methods for solving PDEs, and multi-stage optimization for such classic combinatorial optimization problems as matrix chain multiplication, binary search trees, global sequence alignment, and shortest paths.

In this talk, I will present our recent works on reducing the beam pointing error for improved free-space optical communication (FSO) link performance. Specifically, I will discuss a robust control strategy that reduces the beam alignment error under controlled weak turbulence conditions for FSO systems. Then, I will discuss localization and tracking control of a mobile target ship with an autonomous underwater vehicle (AUV) in underwater environment. The framework is designed using a hybrid acoustic-optical underwater communication to drive the AUV to the maximum achievable data rate angle. The acoustic link is used for non-line-of-sight localization, and the optical link is for line-of-sight transmission. I will conclude the talk by providing recent results on estimating the alignment angle through a novel estimation-based reference trajectory control algorithm for an LED-based optical communication model.

COVID-19 has caused a global pandemic and become the most urgent threat to the entire world. Tremendous efforts and resources have been invested in developing diagnosis. Despite the various, urgent advances in developing artificial intelligence (AI)-based computer-aided systems for CT-based COVID-19 diagnosis, most of the existing methods can only perform classification, whereas the state-of-the-art segmentation method requires a high level of human intervention. In this talk, I will introduce our recent work on a fully-automatic, rapid, accurate, and machine-agnostic method that can segment and quantify the infection regions on CT scans from different sources. Our method is founded upon three innovations: 1) an embedding method that projects any arbitrary CT scan to a same, standard space, so that the trained model becomes robust and generalizable; 2) the first CT scan simulator for COVID-19, by fitting the dynamic change of real patients’ data measured at different time points, which greatly alleviates the data scarcity issue; and 3) a novel deep learning algorithm to solve the large-scene-small-object problem, which decomposes the 3D segmentation problem into three 2D ones, and thus reduces the model complexity by an order of magnitude and, at the same time, significantly improves the segmentation accuracy. Comprehensive experimental results over multi-country, multi-hospital, and multi-machine datasets demonstrate the superior performance of our method over the existing ones and suggest its important application value in combating the disease.

In this talk, I will first give an overview of the research activities in Structural and Functional Bioinformatics Group (http://sfb.kaust.edu.sa). I will then focus on our efforts on developing computational methods to tackle key open problems in Nanopore sequencing. In particular, I will introduce our recent works on developing a collection of computational methods to decode raw electrical current signal sequences into DNA sequences, to simulate raw signals of Nanopore, and to efficiently and accurately align electrical current signal sequences with DNA sequences. I will further introduce their applications in biomedicine and healthcare.

This talk will introduce two novel models we developed for automatic HG generation in two different settings, positive-negative learning and positive-unlabeled learning. We demonstrate the efficacy of the proposed model on three real-world datasets constructed from biomedical publications.

In this presentation, I will give a short overview of the ongoing and future work in the Structural Biology and Engineering (StruBE) lab. I will show how structural biology has allowed us to obtain a first specific inhibitor for a currently uncontrollable parasitic plant; how we combine structural and computational biology to elucidate the evolution of novel protein functions; and how we use our capacity to engineer proteins to obtain a portable next-generation COVID19 detector with single-molecule sensitivity. I will also give a brief outlook on our planned projects, in particular, our efforts to further integrate computational and experimental structure-guided science. 


Transcription factors are an important family of proteins that control the transcription rate from DNAs to messenger RNAs through the binding to specific DNA sequences. Transcription factor regulation is thus fundamental to understanding not only the system-level behaviors of gene regulatory networks, but also the molecular mechanisms underpinning endogenous gene regulation. In this talk, I will introduce our efforts on developing novel optimization and deep learning methods to quantitatively understanding transcription factor regulation at network- and molecular-levels. Specifically, I will talk about how we estimate the kinetic parameters from sparse time-series readout of gene circuit models, and how we model the relationship between the transcription factor binding sites and their binding affinities.

We developed and expanded novel methods for representation learning, predicting protein functions and their loss of function phenotypes. We use deep neural network algorithm and combine them with symbolic inference into neural-symbolic algorithms. Our work significantly improves previously developed methods for predicting protein functions through methodological advances in machine learning, incorporation of broader data types that may be predictive of functions, and improved systems for neural-symbolic integration. The methods we developed are generic and can be applied to other domains in which similar types of structured and unstructured information exist. In future, our methods can be applied to prediction of protein function for metagenomic samples in order to evaluate the potential for discovery of novel proteins of industrial value.  Also our methods can be applied to the prediction of loss of function phenotypes in human genetics and incorporate the results in a variant prioritization tool that can be applied to diagnose patients with Mendelian disorders.

In my research I aim to understand how formalized knowledge bases can be used to systematically structure and integrate biological knowledge, and how to utilize these formalized knowledge bases as background knowledge to improve scientific discovery in biology and biomedicine.  To achieve these aims, I develop methods for representing, integrating, and analyzing data and knowledge with the specific aim to make the combination of data and formalized knowledge accessible to data analytics and machine learning in bioinformatics. Biomedicine, and life sciences in general, are an ideal domain for knowledge-driven data analysis methods due to the large number of formal knowledge bases that have been developed to capture the broad, diverse, and heterogeneous data and knowledge.

In this dissertation, I present the methods I have developed for prediction of promoters for different organisms. Instead of focusing on the classification accuracy of the discrimination between promoter and non-promoter sequences, I predict the exact positions of the TSS inside the genomic sequences, testing every possible location. The developed methods significantly outperform the previous promoter prediction programs by considerably reducing the number of false positive predictions. Specifically, to reduce the false positive rate, the models are adaptively and iteratively trained by changing the distribution of samples in the training set based on the false positive errors made in the previous iteration. The new methods are used to gain insights into the design principles of the core promoters. Using model analysis, I have identified the most important core promoter elements and their effect on the promoter activity. I have developed a novel general approach to detect long range interactions in the input of a deep learning model, which was used to find related positions inside the promoter region. The final model was applied to the genomes of different species without a significant drop in the performance, demonstrating a high generality of the developed method.

Computational Bioscience Research Center at King Abdullah University of Science and Technology is pleased to announce the KAUST Research Conference on Digital Health 2020.

I will present an overview of our activities around estimation problems for partial and fractional differential equations. I will present the methods and the algorithms we develop for the state, source and parameters estimation and illustrate the results with some simulations and real applications.

In this talk, I will discuss our work to create computational standards, platforms, and methods to wrangle knowledge into simple, but effective representations based on semantic web technologies that are maximally FAIR - Findable, Accessible, Interoperable, and Reuseable - and to further use these for biomedical knowledge discovery. But only with additional crucial developments will this emerging Internet of FAIR data and services enable automated scientific discovery on a global scale.

The goal of this thesis is to pave the way towards the next generation of recommendation systems tackling such real-world challenges to improve the user experience while giving good recommendations.

In this talk, I will first give an overview of the research activities in Structural and Functional Bioinformatics Group (http://sfb.kaust.edu.sa). I will then focus on our efforts on developing computational methods to tackle key open problems in Nanopore sequencing. In particular, I will introduce our recent works on developing a collection of computational methods to decode raw electrical current signal sequences into DNA sequences, to simulate raw signals of Nanopore, and to efficiently and accurately align electrical current signal sequences with DNA sequences. Then, I will further introduce their applications in clinical and environmental fields.

Abstract

The demand for a novel and robust m

With the advances in transcriptomic analysis, the monitoring of genome-wide gene expression provides a powerful approach for determining the action of drugs. In this thesis, we analyzed the transcriptional responses of cells treated with drugs either alone or in combinations to explore their effects in two different applications: breast cancer therapy and cell conversion.