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Numerous tools have been recently developed to predict disease phenotypes using single-cell RNA sequencing (RNA-seq) data. CloudPred is an end-to-end differentiable learning algorithm coupled with a biologically informed mixture model,…

Genomics · Quantitative Biology 2024-02-20 Hossein Moghimianavval , Baharan Meghdadi , Tasmine Clement , Man I Wu

The Learning Rate (LR) has a high impact on deep learning training performance. A common practice is to train a Deep Neural Network (DNN) multiple times with different LR policies to find the optimal LR policy, which has been widely…

Machine Learning · Computer Science 2024-10-11 Hongpeng Jin , Yanzhao Wu

Chemotherapeutic response of cancer cells to a given compound is one of the most fundamental information one requires to design anti-cancer drugs. Recent advances in producing large drug screens against cancer cell lines provided an…

Genomics · Quantitative Biology 2018-07-17 Mehmet Tan , Ozan Fırat Özgül , Batuhan Bardak , Işıksu Ekşioğlu , Suna Sabuncuoğlu

Snapshot compressive imaging (SCI) can record the 3D information by a 2D measurement and from this 2D measurement to reconstruct the original 3D information by reconstruction algorithm. As we can see, the reconstruction algorithm plays a…

Image and Video Processing · Electrical Eng. & Systems 2022-08-23 Chengshuai Yang , Shiyu Zhang , Xin Yuan

Machine learning has made tremendous progress in recent years, with models matching or even surpassing humans on a series of specialized tasks. One key element behind the progress of machine learning in recent years has been the ability to…

Machine Learning · Computer Science 2020-06-30 Giorgi Nadiradze , Ilia Markov , Bapi Chatterjee , Vyacheslav Kungurtsev , Dan Alistarh

Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in…

Genomics · Quantitative Biology 2016-11-17 Yaniv Erlich , Assaf Gordon , Michael Brand , Gregory J. Hannon , Partha P. Mitra

Handwritten digit recognition remains a fundamental challenge in computer vision, with applications ranging from postal code reading to document digitization. This paper presents an ensemble-based approach that combines Convolutional Neural…

Computer Vision and Pattern Recognition · Computer Science 2025-03-11 Syed Sajid Ullah , Li Gang , Mudassir Riaz , Ahsan Ashfaq , Salman Khan , Sajawal Khan

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is…

Populations and Evolution · Quantitative Biology 2018-03-28 Melia E. Bonomo , Michael W. Deem

Leveraging artificial intelligence (AI)-driven electronic design and automation (EDA) tools, high-performance computing, and parallelized algorithms are essential for next-generation microprocessor innovation, ensuring continued progress in…

Hardware Architecture · Computer Science 2025-07-21 Riadul Islam , Dhandeep Challagundla

Continual learning (CL) in deep neural networks (DNNs) involves incrementally accumulating knowledge in a DNN from a growing data stream. A major challenge in CL is that non-stationary data streams cause catastrophic forgetting of…

Machine Learning · Computer Science 2024-05-02 Md Yousuf Harun , Jhair Gallardo , Junyu Chen , Christopher Kanan

Ensemble learning is a process by which multiple base learners are strategically generated and combined into one composite learner. There are two features that are essential to an ensemble's performance, the individual accuracies of the…

Machine Learning · Computer Science 2021-09-30 Wenjing Li , Randy C. Paffenroth , David Berthiaume

Targeting RNA with small molecules offers significant therapeutic potential. Machine learning could substantially accelerate preclinical drug discovery, from hit identification to lead optimization. Yet a fundamental limitation emerges:…

Biomolecules · Quantitative Biology 2025-12-18 Wissam Karroucha , Carlos Oliver , Veronique Stoven , Vincent Mallet

Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…

Genomics · Quantitative Biology 2025-09-23 Siying Yang , Neng Huang , Heng Li

In many machine learning tasks, models are trained to predict structure data such as graphs. For example, in natural language processing, it is very common to parse texts into dependency trees or abstract meaning representation (AMR)…

Computation and Language · Computer Science 2022-01-25 Hoang Thanh Lam , Gabriele Picco , Yufang Hou , Young-Suk Lee , Lam M. Nguyen , Dzung T. Phan , Vanessa López , Ramon Fernandez Astudillo

Ensemble learning has been a focal point of machine learning research due to its potential to improve predictive performance. This study revisits the foundational work on ensemble error decomposition, historically confined to…

Machine Learning · Computer Science 2024-02-13 João Mendes-Moreira , Tiago Mendes-Neves

CRISPR-based diagnostics have gained increasing attention as biosensing tools able to address limitations in contemporary molecular diagnostic tests. To maximise the performance of CRISPR-based assays, much effort has focused on optimizing…

Quantitative Methods · Quantitative Biology 2025-01-09 Nathan Khosla , Jake M. Lesinski , Marcus Haywood-Alexander , Andrew J. deMello , Daniel A. Richards

Obtaining high certainty in predictive models is crucial for making informed and trustworthy decisions in many scientific and engineering domains. However, extensive experimentation required for model accuracy can be both costly and…

Machine Learning · Computer Science 2024-12-17 Giorgio Morales , John Sheppard

Convolutional Neural Networks (CNNs) have demonstrated great results for the single-image super-resolution (SISR) problem. Currently, most CNN algorithms promote deep and computationally expensive models to solve SISR. However, we propose a…

Computer Vision and Pattern Recognition · Computer Science 2018-08-28 Vandit Jain , Prakhar Bansal , Abhinav Kumar Singh , Rajeev Srivastava

Recently, deep learning-based models have been widely studied for click-through rate (CTR) prediction and lead to improved prediction accuracy in many industrial applications. However, current research focuses primarily on building complex…

Machine Learning · Computer Science 2023-07-06 Jieming Zhu , Jinyang Liu , Weiqi Li , Jincai Lai , Xiuqiang He , Liang Chen , Zibin Zheng

Addressing biases in AI models is crucial for ensuring fair and accurate predictions. However, obtaining large, unbiased datasets for training can be challenging. This paper proposes a comprehensive approach using multiple methods to remove…

Machine Learning · Computer Science 2024-02-15 Ahmed Radwan , Layan Zaafarani , Jetana Abudawood , Faisal AlZahrani , Fares Fourati