25 papers · ranked by Valyu relevance
Dilan Pathirana, Frank T. Bergmann, Domagoj Doresic, Polina Lakrisenko + 8 more
A central question in mathematical modeling of biological systems is determining which processes are relevant and how they can be described. There are often competing hypotheses, which yield different models. Model comparison requires parameter optimization and sampling methods. Yet, standards for the specification of…
Dilan Pathirana, Frank T. Bergmann, Domagoj Doresic, Polina Lakrisenko + 8 more
A central question in mathematical modeling of biological systems is determining which processes are most relevant and how they can be described. There are often competing hypotheses, which yield different models. Model comparison requires parameter optimization and sampling methods. Yet, standards for the…
Joram Soch, Carsten Allefeld
In cognitive neuroscience, functional magnetic resonance imaging (fMRI) data are widely analyzed using general linear models (GLMs). However, model quality of GLMs for fMRI is rarely assessed, in part due to the lack of formal measures for statistical model inference. We introduce a new SPM toolbox for model…
Nicolas Lartillot
There is still no consensus as to how to select models in Bayesian phylogenetics, and more generally in applied Bayesian statistics. Bayes factors are often presented as the method of choice, yet other approaches have been proposed, such as cross-validation or information criteria. Each of these paradigms raises…
Mohammad Ali Hajiani, Babak Seyfe
We propose a novel approach to select the best model of the data. Based on the exclusive properties of the nested models, we find the most parsimonious model containing the risk minimizer predictor. We prove the existence of probable approximately correct (PAC) bounds on the difference of the minimum empirical risk of…
Juho Piironen, Aki Vehtari
The goal of this paper is to compare several widely used Bayesian model selection methods in practical model selection problems, highlight their differences and give recommendations about the preferred approaches. We focus on the variable subset selection for regression and classification and perform several numerical…
Felipe Farias, Teresa B. Ludermir, Carmelo J. A. Bastos-Filho
The model selection procedure is usually a single-criterion decision making in which we select the model that maximizes a specific metric in a specific set, such as the Validation set performance. We claim this is very naive and can perform poor selections of over-fitted models due to the over-searching phenomenon…
Melissa Adrian, Jake A. Soloff, Rebecca Willett
Model selection is the process of choosing from a class of candidate models given data. For instance, methods such as the LASSO and sparse identification of nonlinear dynamics (SINDy) formulate model selection as finding a sparse solution to a linear system of equations determined by training data. However, absent…
Sanjay Basu, Jason Andrews
Sanjay Basu and colleagues explain how models are increasingly used to inform public health policy yet readers may struggle to evaluate the quality of models. All models require simplifying assumptions, and there are tradeoffs between creating models that are more “realistic” versus those that are grounded in more…
Xinnong Li, Mark Sale, Keith Nieforth, James Craig + 6 more
Forward addition/backward elimination (FABE) has been the standard for population pharmacokinetic model selection (PPK) since NONMEM® was introduced. We investigated five machine learning (ML) algorithms (Genetic algorithm [GA], Gaussian process [GP], random forest [RF], gradient boosted random tree [GBRT], and…
Daniel Silk, Paul D. W. Kirk, Chris P. Barnes, Tina Toni + 2 more
'Michael P. H. Stumpf' 'Burkhard Rost'] Experimental design attempts to maximise the information available for modelling tasks. An optimal experiment allows the inferred models or parameters to be chosen with the highest expected degree of confidence. If the true system is faithfully reproduced by one of the models…
Zihao Wen, David L. Dowe, Abhijit Mandal, Suneel Babu Chatla
Species distribution modeling is fundamental to biodiversity, evolution, conservation science, and the study of invasive species. Given environmental data and species distribution data, model selection techniques are frequently used to help identify relevant features. Existing studies aim to find the relevant features…
Eugenio Piasini, Shuze Liu, Pratik Chaudhari, Vijay Balasubramanian + 1 more
Occam’s razor is the principle that, all else being equal, simpler explanations should be preferred over more complex ones^1^. This principle is thought to play a role in human perception and decision-making^2^, but the nature of our presumed preference for simplicity is not understood. Here we use preregistered…
Joseph Beyene, Eshetu G Atenafu, Jemila S Hamid, Teresa To + 1 more
'Lillian Sung'] Background Multiple regression models are used in a wide range of scientific disciplines and automated model selection procedures are frequently used to identify independent predictors. However, determination of relative importance of potential predictors and validating the fitted models for their…
Keita Yoshii, Hiroshi Nishiura, Kaoru Inoue, Takayuki Yamaguchi + 1 more
'Akihiko Hirose'] Background To employ the benchmark dose (BMD) method in toxicological risk assessment, it is critical to understand how the BMD lower bound for reference dose calculation is selected following statistical fitting procedures of multiple mathematical models. The purpose of this study was to compare the…
Moayad Alnammi, Shengchao Liu, Spencer S Ericksen, Gene E Ananiev + 6 more
Traditional small molecule drug discovery is a time consuming and costly endeavor. High-throughput chemical screening can only assess a tiny fraction of drug-like chemical space. The strong predictive power of modern machine learning methods for virtual chemical screening enables training models on known active and…
James R. H. Cooke, Luc P. J. Selen, Robert J. van Beers, W. Pieter Medendorp
Comparing models facilitates testing different hypotheses regarding the computational basis of perception and action. Effective model comparison requires stimuli for which models make different predictions. Typically, experiments use a predetermined set of stimuli or sample stimuli randomly. Both methods have…
Christine Yuen, Piotr Fryźlewicz
We propose Combined Selection and Uncertainty Visualizer (CSUV), which estimates the set of true covariates in high-dimensional linear regression and visualizes selection uncertainties by exploiting the (dis)agreement among different base selectors. Our proposed method selects covariates that get selected the most…
Authors not listed
Background: Janus Kinase 2 (JAK2) is a key kinase in cellular signal transduction. Its abnormal activation is closely related to various myeloproliferative neoplasms and inflammatory diseases. Developing selective JAK2 inhibitors is an important direction in drug discovery. Accurate prediction of compound inhibitory…
Kan Hatakeyama-Sato, Seigo Watanabe, Naoki Yamane, Yasuhiko Igarashi + 1 more
Materials informatics and cheminformatics struggle with data scarcity, hindering the extraction of significant relationships between structures and properties. The "Ugly Duckling" theorem, suggesting the difficulty of data processing without assumptions or prior knowledge, exacerbates this problem. Current…
Authors not listed
Solubility is critical in drug discovery and development, as it significantly influences a medication's bioavailability and therapeutic efficacy. Understanding solubility at the early stages of drug discovery is essential for minimizing resource consumption and enhancing the likelihood of clinical success via…
Xuan-Truc Dinh Tran, Tieu-Long Phan, Van-Thinh To, Ngoc-Vi Nguyen Tran + 4 more
3D pharmacophore models describe the ligand’s chemical interactions in their bioactive conformation. They offer a simple but sophisticated approach to decipher the chemically encoded ligand information, making them a valuable tool in Drug Design. Our research summarized the key studies for applying 3D pharmacophore…
Authors not listed
Machine learning holds significant promise for accelerating biomarker discovery in clinical proteomics, yet its real-world impact remains limited by widespread methodological pitfalls and unrealistic expectations. In this perspective, we critically examine the integration of machine learning into clinical proteomics…
Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev, Henry Brodaty + 1 more
'Henry Brodaty' 'Arcot Sowmya' ''] Background Feature selection is often used to identify the important features in a dataset but can produce unstable results when applied to high-dimensional data. The stability of feature selection can be improved with the use of feature selection ensembles, which aggregate the…
Paul Francoeur, Daniel Penaherrera, David Koes
The immense size of chemical space, the relative scarcity of high quality data, and the cost of running experiments to accurately measure molecular properties makes active learning (AL) an attractive approach to efficiently explore the space and train high-quality models for molecular property prediction. While AL is…