23 papers · ranked by Valyu relevance
Storm Slivkoff, Jack L. Gallant
Over the past few decades, neuroscience experiments have become increasingly complex and naturalistic. Experimental design has in turn become more challenging, as experiments must conform to an ever-increasing diversity of design constraints. In this article we demonstrate how this design process can be greatly…
Authors not listed
Automated chemistry platforms hold the potential to enable large-scale organic synthesis campaigns, such as producing a library of compounds for biological evaluation. The efficiency of such platforms will depend on the schedule according to which the synthesis operations are executed. In this work, we study the…
Tianxing Yang, Huigen Ye, Hua Xu
Mixed-Integer Linear Programming (MILP) is widely used in fields such as scheduling, logistics, and planning. Enhancing the performance of MILP solvers, particularly learning-based solvers, requires substantial amounts of high-quality data. However, existing methods for MILP instance generation typically necessitate…
Haoyu Wang, Jialin Liu, Xiaohan Chen, Xinshang Wang + 2 more
'Wotao Yin'] Mixed-integer linear programming (MILP) stands as a notable NP-hard problem pivotal to numerous crucial industrial applications. The development of effective algorithms, the tuning of solvers, and the training of machine learning models for MILP resolution all hinge on access to extensive, diverse, and…
Sirui Li, Janardhan Kulkarni, Ishai Menache, Cathy Wu + 1 more
Mixed Integer Linear Programming (MILP) is essential for modeling complex decision-making problems but faces challenges in computational tractability and requires expert formulation. Current deep learning approaches for MILP focus on specific problem classes and do not generalize to unseen classes. To address this…
Yidong Luo, Chenguang Wang, Jiahao Yang, Fanzeng Xia + 1 more
Mixed-Integer Linear Programming (MILP) is fundamental to solving complex decision-making problems. The proliferation of MILP instance generation methods, driven by machine learning's demand for diverse optimization datasets and the limitations of static benchmarks, has significantly outpaced standardized evaluation…
Martin Gonzalez, Jose J. López-Espín, Juan Aparicio, El-Ghazali Talbi + 1 more
'El-Ghazali Talbi' 'Nicholas Higham'] Mixed Integer Linear Programs (MILPs) are usually NP-hard mathematical programming problems, which present difficulties to obtain optimal solutions in a reasonable time for large scale models. Nowadays, metaheuristics are one of the potential tools for solving this type of problems…
Kexin Niu, Maxat Kulmanov, Robert Hoehndorf
Current machine learning methods for enzyme function prediction primarily treat proteins as independent entities, ignoring the metabolic context in which they operate. This reductionist approach often generates biologically implausible annotations that fail to satisfy stoichiometric or thermodynamic constraints. While…
Albert No
The size of the largest binary single deletion code has been unknown for more than 50 years. It is known that Varshamov-Tenengolts (VT) code is an optimum single deletion code for block length $n\leq10$; however, only a few upper bounds of the size of single deletion code are proposed for larger n. We provide improved…
Julia Blaurock, Thorsten Heuer, Kurt Gedrich, Lauri Byerley
Food Frequency Questionnaires (FFQs) are important instruments to assess dietary intake in large epidemiological studies. To determine dietary intake correctly, food lists need to be adapted depending on the study aim and the target population. The present work compiles food lists for an FFQ with Mixed Integer Linear…
Pierre Salvy, Vassily Hatzimanikatis
Since the introduction of metabolic models and flux balance analysis (FBA) in systems biology, several attempts have been made to supplement these formulations with expression information to form metabolic and expression models (ME-models). However, directly accounting for enzyme and mRNA production in the mathematical…
Zahra Khalilzadeh, Lizhi Wang
Corn planting and harvest scheduling is an important problem due to having a significant impact on corn yield, balancing the capacities for harvest, transport, and storage operations. Different corn hybrids also have different planting window and poor planting and harvest schedules may cause erratic weekly harvest…
Fangyan Chen, Xiangcheng Wu, Zhiming Wang, Weimin Qi + 5 more
Currently, wireless sensor networks (WSNs) have been mutually applied to environmental monitoring and industrial control due to their low-cost and low-energy sensor nodes. However, WSNs are composed of a large number of energy-limited sensor nodes, which requires balancing the relationship among energy consumption…
Satoshi Horikoshi, Seiya Sawada, Nick Serpone
The focus of this article rests on our discovery that a water-soluble polymer could be cross-linked to form a gel using a novel Green Chemistry gelation method: the microwave-induced in-liquid-plasma (MILP) method that requires neither a cross-linking agent nor an initiator as are required in the conventional chemical…
Steffen Klamt, Radhakrishnan Mahadevan, Axel von Kamp
Background The concept of minimal cut sets (MCS) has become an important mathematical framework for analyzing and (re)designing metabolic networks. However, the calculation of MCS in genome-scale metabolic models is a complex computational problem. The development of duality-based algorithms in the last years allowed…
Authors not listed
Organometallic catalysis lies at the heart of numerous industrial processes that produce bulk and fine chemicals. The search for transition states and screening for organic ligands are vital in designing highly active organometallic catalysts with efficient reaction kinetics. However, identifying accurate transition…
Authors not listed
The rapid advancement in machine-learned interatomic potentials (MLIPs) and the proliferation of uni- versal MLIPs (uMLIPs) have significantly broadened their application scope. Community benchmarks and leaderboard rankings are frequently updated, providing statistical insights into overall progress. However, the…
Sean A. Bergin, Fang Zhao, Adam P. Ryan, Carolin A. Müller + 8 more
Flippases and floppases are two classes of proteins that have opposing functions in the maintenance of lipid asymmetry of the plasma membrane. Flippases translocate lipids from the exoplasmic leaflet to the cytosolic leaflet, and floppases act in the opposite direction. Phosphatidylcholine (PC) is a major component of…
Paige Banks, Emma M. Funkhouser, Angie M. Macias, Brian Lovett + 8 more
Millipedes have long been known to produce a diverse array of chemical defense agents that deter predation. These compounds, or their precursors, are stored in high concentration within glands (ozadenes) and are released upon disturbance. The subterclass Colobognatha contains four orders of millipedes, all of which are…
Luca Brugnoli, Maxime Ducamp, François-Xavier Coudert
Molecular dynamics simulations of zeolites are commonly employed for the characterization of their framework dynamics and response to the application of temperature and pressure. While classical interatomic potentials are commonly used for this task, they offer a description of the interactions in the system with…
Amy Yuet Ting Lau, Xuanjin Cheng, Chi Keung Cheng, Wenyan Nong + 4 more
Coprinopsis cinerea is a model mushroom particularly suited to study fungal fruiting body development and the evolution of multicellularity in fungi. While microRNAs (miRNAs) are extensively studied in animals and plants for their essential roles in post-transcriptional regulation of gene expression, miRNAs in fungi…
Qiang Hu, Hung-Jen Wu
Frequent monitoring of glycan patterns is a critical step for studying glycan-mediated cellular processes. However, the current glycan analysis tools are resource-intensive and less suitable for routine use in standard laboratories. We developed a novel glycan detection platform by integrating surface-enhanced Raman…
Yikai Fan, Jiazheng Han, Haitong Wang, Liangkang Nan + 14 more
Mid-infrared spectra (MIRS) can effectively reflect the chemical bonds in milk, which has been widely used in dairy herd improvement. However, the relationship between MIRS and animal evolution remains largely unclear. This study firstly found great differences in MIRS and the components of milk by analyzing MIRS…