相关论文: Creation and analysis of biochemical constraint-ba…

We introduce COBRA (Cosmology with Optimally factorized Bases of Radial Approximants), a novel framework for rapid computation of large-scale structure observables. COBRA separates scale dependence from cosmological parameters in the linear…

A new method for combining several initial estimators of the regression function is introduced. Instead of building a linear or convex optimized combination over a collection of basic estimators $r_1,\dots,r_M$, we use them as a collective…

COBRAPRO is a new open-source physics-based battery modeling software with the capability to conduct closed-loop parameter optimization using experimental data. Physics-based battery models require systematic parameter calibration to…

Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux…

We propose a new supervised learning algorithm, for classification and regression problems where two or more preliminary predictors are available. We introduce \texttt{KernelCobra}, a non-linear learning strategy for combining an arbitrary…

Chronic obesity management requires continuous monitoring of energy balance behaviors, yet traditional self-reported methods suffer from significant underreporting and recall bias, and difficulty in integration with modern digital health…

The optimization problems in realistic world present significant challenges onto optimization algorithms, such as the expensive evaluation issue and complex constraint conditions. COBRA optimizer (including its up-to-date variants) is a…

The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…

Recently Goswami et al. \cite{goswami2022concordance} introduced two novel implementations of combined regression strategy to find the conditional survival function. The paper uses regression-based weak learners and provides an alternative…

Data analytics often involves hypothetical reasoning: repeatedly modifying the data and observing the induced effect on the computation result of a data-centric application. Recent work has proposed to leverage ideas from data provenance…

Accurately measuring protein-RNA binding affinity is crucial in many biological processes and drug design. Previous computational methods for protein-RNA binding affinity prediction rely on either sequence or structure features, unable to…

Clustering is inherently ill-posed: there often exist multiple valid clusterings of a single dataset, and without any additional information a clustering system has no way of knowing which clustering it should produce. This motivates the…

The paper explores a different variation of combined regression strategy to calculate the conditional survival function. We use regression based weak learners to create the proposed ensemble technique. The proposed combined regression…

There are a wide range of applications that involve multi-modal data, such as cross-modal retrieval, visual question-answering, and image captioning. Such applications are primarily dependent on aligned distributions of the different…

Motivation: Automatically testing changes to code is an essential feature of continuous integration. For open-source code, without licensed dependencies, a variety of continuous integration services exist. The COnstraint-Based…

Constrained optimization of high-dimensional numerical problems plays an important role in many scientific and industrial applications. Function evaluations in many industrial applications are severely limited and no analytical information…

Constraint-based clustering algorithms exploit background knowledge to construct clusterings that are aligned with the interests of a particular user. This background knowledge is often obtained by allowing the clustering system to pose…

Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account. Results: We…

A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation results. We manually drew a comprehensive map, ReconMap 2.0,…

Developing new molecular compounds is crucial to address pressing challenges, from health to environmental sustainability. However, exploring the molecular space to discover new molecules is difficult due to the vastness of the space. Here…