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The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…

Computational Physics · Physics 2015-09-01 Alejandro Gil-Ley , Giovanni Bussi

Genome-Scale Metabolic Models (GEMs) describe the interactions between genes, proteins, and the biochemical reactions that underpin an organism's metabolism aiming to computationally simulate functions at the cellular level. While many…

The multiple knapsack problem with grouped items aims to maximize rewards by assigning groups of items among multiple knapsacks, considering knapsack capacities. Either all items in a group are assigned or none at all. We propose algorithms…

Data Structures and Algorithms · Computer Science 2020-06-02 Francisco Castillo-Zunino , Pinar Keskinocak

Understanding the anatomy of renal pathology is crucial for advancing disease diagnostics, treatment evaluation, and clinical research. The complex kidney system comprises various components across multiple levels, including regions…

Image and Video Processing · Electrical Eng. & Systems 2024-03-22 Ruining Deng , Quan Liu , Can Cui , Tianyuan Yao , Jialin Yue , Juming Xiong , Lining Yu , Yifei Wu , Mengmeng Yin , Yu Wang , Shilin Zhao , Yucheng Tang , Haichun Yang , Yuankai Huo

Collective communications are ubiquitous in parallel applications. We present two new algorithms for performing a reduction. The operation associated with our reduction needs to be associative and commutative. The two algorithms are…

Distributed, Parallel, and Cluster Computing · Computer Science 2013-10-18 Bradley R. Lowery , Julien Langou

Liver transplantation often faces fairness challenges across subgroups defined by sensitive attributes such as age group, gender, and race/ethnicity. Machine learning models for outcome prediction can introduce additional biases. Therefore,…

Machine Learning · Computer Science 2024-08-28 Can Li , Dejian Lai , Xiaoqian Jiang , Kai Zhang

With rapid increase of mobile computing and wireless network linkage, the information exchange between connected systems and within groups increases heavily. Exchanging confidential information within groups via unsecured communication…

Cryptography and Security · Computer Science 2020-02-26 Peter Hillmann , Marcus Knüpfer , Tobias Guggemos , Klement Streit

The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…

Statistical Mechanics · Physics 2025-06-04 Akie Kowaguchi , Katsuhiro Endo , Kentaro Nomura , Shuichi Kurabayashi , Paul E. Brumby , Kenji Yasuoka

The cooperative data exchange problem is studied for the fully connected network. In this problem, each node initially only possesses a subset of the $K$ packets making up the file. Nodes make broadcast transmissions that are received by…

Information Theory · Computer Science 2021-09-20 Su Li , Michael Gastpar

A theoretical quantum key distribution scheme using EPR pairs is presented. This scheme is efficient in that it uses all EPR pairs in distributing the key except those chosen for checking eavesdroppers. The high capacity is achieved because…

Quantum Physics · Physics 2009-11-06 Gui Lu Long , Xiao Shu Liu

Overconfidence in deep learning models poses a significant risk in high-stakes medical imaging tasks, particularly in multi-label classification of chest X-rays, where multiple co-occurring pathologies must be detected simultaneously. This…

Image and Video Processing · Electrical Eng. & Systems 2025-09-15 Yehudit Aperstein , Amit Tzahar , Alon Gottlib , Tal Verber , Ravit Shagan Damti , Alexander Apartsin

Basket designs are prospective clinical trials that are devised with the hypothesis that the presence of selected molecular features determine a patient's subsequent response to a particular "targeted" treatment strategy. Basket trials are…

Computation · Statistics 2019-08-05 Michael J. Kane , Nan Chen , Alexander M. Kaizer , Xun Jiang , H. Amy Xia , Brian P. Hobbs

Differential positivity and K-cooperativity, a special case of differential positivity, extend differential approaches to control to nonlinear systems with multiple equilibria, such as switches or multi-agent consensus. To apply this…

Optimization and Control · Mathematics 2020-05-12 Dimitris Kousoulidis , Fulvio Forni

In an observational study, matching aims to create many small sets of similar treated and control units from initial samples that may differ substantially in order to permit more credible causal inferences. The problem of constructing…

Methodology · Statistics 2024-06-28 Shichao Han , Samuel D. Pimentel

The kidney cancer is one of the most common cancer types. The treatment frequently include surgical intervention. However, surgery is in this case particularly challenging due to regional anatomical relations. Organ delineation can…

Image and Video Processing · Electrical Eng. & Systems 2022-08-09 David Jozef Hresko , Marek Kurej , Jakub Gazda , Peter Drotar

Reinforcement Learning algorithms aim to learn optimal control strategies through iterative interactions with an environment. A critical element in this process is the experience replay buffer, which stores past experiences, allowing the…

Machine Learning · Computer Science 2025-01-31 Hoda Yamani , Yuning Xing , Lee Violet C. Ong , Bruce A. MacDonald , Henry Williams

Reducing the shortage of organ donations to meet the demands of patients on the waiting list has being a major challenge in organ transplantation. Because of the shortage, organ matching decision is the most critical decision to assign the…

Machine Learning · Computer Science 2023-02-01 Parshin Shojaee , Xiaoyu Chen , Ran Jin

We consider single-source single-sink (ss-ss) multi-hop networks, with slow-fading links and single-antenna half-duplex relays. We identify two families of networks that are multi-hop generalizations of the well-studied two-hop network:…

Information Theory · Computer Science 2008-02-14 K. Sreeram , S. Birenjith , P. Vijay Kumar

The Coin Change problem, also known as the Change-Making problem, is a well-studied combinatorial optimization problem, which involves minimizing the number of coins needed to make a specific change amount using a given set of coin…

Computational Complexity · Computer Science 2024-11-28 Shreya Gupta , Boyang Huang , Russell Impagliazzo

Accurate cell nuclei segmentation is critical for downstream tasks in kidney pathology and remains a major challenge due to the morphological diversity and imaging variability of renal tissues. While our prior work has evaluated…