26 papers · ranked by Valyu relevance
Takuya Akiba, Shotaro Sano, Toshihiko Yanase, Takeru Ohta + 1 more
'Masanori Koyama'] The purpose of this study is to introduce new design-criteria for next-generation hyperparameter optimization software. The criteria we propose include (1) define-by-run API that allows users to construct the parameter search space dynamically, (2) efficient implementation of both searching and…
Johnathan M. Bardsley, Tiangang Cui, Youssef Marzouk, Zheng Wang
Optimization-based samplers such as randomize-then-optimize (RTO) [2] provide an efficient and parallellizable approach to solving large-scale Bayesian inverse problems. These methods solve randomly perturbed optimization problems to draw samples from an approximate posterior distribution. "Correcting" these samples…
David Eriksson, Matthias Poloczek
The global optimization of a high-dimensional black-box function under black-box constraints is a pervasive task in machine learning, control, and engineering. These problems are challenging since the feasible set is typically non-convex and hard to find, in addition to the curses of dimensionality and the…
Jonathan Lorraine
Gradient-based optimization has been critical to the success of machine learning, updating a single set of parameters to minimize a single loss. A growing number of applications rely on a generalization of this, where we have a bilevel or nested optimization of which subsets of parameters update on different objectives…
Roumaissa Ghlib, Rania Bouhadouza, Faicel Hnaien
Designing compact and efficient quantum circuits that are compatible with Noisy Intermediate-Scale Quantum (NISQ) hardware remains a central challenge in quantum computing. Most existing optimization approaches rely on fidelity-based fitness functions that require computing the full unitary matrix of the circuit.…
Mingrui Zhang
We first propose 1-SFW, the first projection-free method that requires only one sample per iteration to update the optimization variable and yet achieves the best known complexity bounds for convex, non-convex, and monotone DR-submodular settings. Then we move forward to the distributed setting, and develop Quantized…
Masahiro Nomura
In recent years, leveraging parallel and distributed computational resources has become essential to solve problems of high computational cost. Bayesian optimization (BO) has shown attractive results in those expensive-to-evaluate problems such as hyperparameter optimization of machine learning algorithms. While many…
Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer + 1 more
'Jan Hasenauer' 'Jorg Stelling'] Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the…
J Kyle Medley, Shaik Asifullah, Joseph Hellerstein, Herbert M Sauro
Mechanistic kinetic models of biological pathways are an important tool for understanding biological systems. Constructing kinetic models requires fitting the parameters to experimental data. However, parameter fitting on these models is a non–convex, non–linear optimization problem. Many algorithms have been proposed…
Vikas Sindhwani, Haim Avron
We propose a framework for massive-scale training of kernel-based statistical models, based on combining distributed convex optimization with randomization techniques. Our approach is based on a block-splitting variant of the Alternating Directions Method of Multipliers, carefully reconfigured to handle very large…
Chaoming Wang, Xingsi Dong, Jiedong Jiang, Zilong Ji + 2 more
Whole-brain simulation stands as one of the most ambitious endeavors of our time, yet it remains constrained by significant technical challenges. A critical obstacle in this pursuit is the absence of a scalable online learning framework capable of supporting the efficient training of complex, diverse, and large-scale…
Abbas Kazemipour, Behtash Babadi, Min Wu, Kaspar Podgorski + 1 more
We consider the problem of optimizing general convex objective functions with nonnegativity constraints. Using the Karush-Kuhn-Tucker (KKT) conditions for the nonnegativity constraints we will derive fast multiplicative update rules for several problems of interest in signal processing, including non-negative…
Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer
Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small-and medium-scale biological processes. While the same should in principle hold for large-and genome-scale processes, the computational methods for the analysis of…
Hyeonuk Sim, Jongeun Lee
While convolutional neural networks (CNNs) continue to renew state-of-the-art performance across many fields of machine learning, their hardware implementations tend to be very costly and inflexible. Neuromorphic hardware, on the other hand, targets higher efficiency but their inference accuracy lags far behind that of…
Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer + 1 more
Mechanistic models of biochemical reaction networks facilitate the quantitative understanding of biological processes and the integration of heterogeneous datasets. However, some biological processes require the consideration of comprehensive reaction networks and therefore large-scale models. Parameter estimation for…
Yijie Wang, Xiaoning Qian
With increasingly “big” data available in biomedical research, deriving accurate and reproducible biology knowledge from such big data imposes enormous computational challenges. In this paper, motivated by recently developed stochastic block coordinate algorithms, we propose a highly scalable randomized block…
Authors not listed
This work establishes theoretical foundations for hierarchical quantum-classical algorithm design, where complex problems are decomposed across multiple spatial, temporal, or organizational scales with quantum and classical computation assigned to appropriate levels. We develop a mathematical framework that…
Mary Pitman, David Hahn, Gary Tresadern, David Mobley
Drug discovery is accelerated with computational methods such as alchemical simulations to estimate ligand affinities. In particular, relative binding free energy (RBFE) simulations are beneficial for lead optimization. To use RBFE simulations to compare prospective ligands in silico, researchers first plan the…
Rakbin Sung, Seongmi Woo, Dongmin Shin, Junil Kim + 2 more
The expression values of genes can be tracked through RNA sequencing. The process of bulk RNA sequencing involves the calculation of the mean expression value of a given gene across multiple cells. This results in low resolution for expression dynamics from each individual cell. Single-cell RNA sequencing (scRNA-seq)…
Robert Arbon, Yanchen Zhu, Antonia S. J. S. Mey
Markov state models (MSM) are a popular statistical method for analyzing the conformational dynamics of proteins, including protein folding. With all statistical and machine learning (ML) models choices must be made about the modeling pipeline that cannot be directly learned from the data. These choices, or…
Riley Hickman, Priyansh Parakh, Austin Cheng, Qianxiang Ai + 3 more
Experiment planning algorithms are a required component of autonomous platforms for scientific discovery. Selecting a suitable optimization algorithm for a novel application is an important yet difficult choice a researcher has to make based on past empirical performance on similar tasks. To facilitate the evaluation…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? Physics-based simulations and wet-lab experiments often have symmetries (degeneracies) that allow reducing problem dimensionality or search space, but constraining these degeneracies is often unsupported or difficult to implement in many…
Andre KY Low, Flore Mekki-Berrada, Aleksandr Ostudin, Jiaxun Xie + 7 more
The development of automated high-throughput experimental platforms has enabled fast sampling of high-dimensional decision spaces. To reach target properties efficiently, these platforms are increasingly paired with intelligent experimental design. When solving optimization problems, Bayesian-based optimizers are often…
Yuanchao Zhang, Deanne M. Taylor
In single-cell RNA-seq (scRNA-seq) experiments, the number of individual cells has increased exponentially due to significant improvements on single-cell isolation and massively parallel sequencing technologies. However, computational methods have not scaled to the same order, presenting analytical challenges to the…
Shengyong Chen, Yujun Zheng, Carlo Cattani, Wanliang Wang
This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM…
Riley Hickman, Matteo Aldeghi, Alán Aspuru-Guzik
Model-based optimization strategies, such as Bayesian optimization (BO), have been deployed across the natural sciences in design and discovery campaigns due to their sample efficiency and flexibility. The combination of such strategies with automated laboratory equipment and/or high-performance computing in a…