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Hyperopt: A Python library for optimizing the hyperparameters of machine learning algorithms

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... This study has also adopted the Python Hyperopt library [72] to deduce optimal hyperparameters, shown in Table 3 for BILSTM, LSTMCNN, DNN, MARS, MLP, KRR and GPR benchmark models. In this way, users can select their models or optimize their parameters simultaneously in Python programming environment. ...
... In this way, users can select their models or optimize their parameters simultaneously in Python programming environment. In fact, Hyperopt operates as a black box system in which the users can provide an evaluation function and parameter space to attain the best values based on the inputs [72]. When selecting an optimization algorithm through the Hyperopt, the distribution over the choice ('Adagrad', 'Adam', 'SGD', and 'RMSprop') is used. ...
... TPE, as named by Bergstra et al. [18], is the technique of using Bayesian optimization heuristics for guiding and speeding up the hyperparameter configuration optimization process. Its innovative approach involves the creation of a binary tree-like model that adeptly maps out the probability distributions for various hyperparameters. ...
... Its innovative approach involves the creation of a binary tree-like model that adeptly maps out the probability distributions for various hyperparameters. This model is particularly adept at navigating the complex landscapes often encountered in high-dimensional spaces, where objective functions can be costly to evaluate, thereby streamlining the optimization trajectory towards optimal solutions with efficiency and precision [18]. Mathematically, TPE optimizes by iteratively selecting hyperparameters based on the following principle: θ * = arg min θ P (Objective better than current best | θ) P (Objective worse than current best | θ) ...
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In this paper, we explore the optimization of hyperparameters for the Soft Actor-Critic (SAC) and Proximal Policy Optimization (PPO) algorithms using the Tree-structured Parzen Estimator (TPE) in the context of robotic arm control with seven Degrees of Freedom (DOF). Our results demonstrate a significant enhancement in algorithm performance, TPE improves the success rate of SAC by 10.48 percentage points and PPO by 34.28 percentage points, where models trained for 50K episodes. Furthermore, TPE enables PPO to converge to a reward within 95% of the maximum reward 76% faster than without TPE, which translates to about 40K fewer episodes of training required for optimal performance. Also, this improvement for SAC is 80% faster than without TPE. This study underscores the impact of advanced hyperparameter optimization on the efficiency and success of deep reinforcement learning algorithms in complex robotic tasks.
... The researcher starts with pipeline A in Fig. 1: 1 conversion of raw data from a sequencer into count matrices, 2 frequency threshold filtering for quality control, 3 data normalization, 4 principal component analysis for dimensionality reduction, and 5 correlation analysis to calculate gene co-expression scores. 6 Then, they create graph embedding A that preserves relations between co-expressed genes [32]. By analyzing the difference in the embedding between the "healthy" and the "exposed to a disease" conditions, the domain expert is able to identify key genes that might be associated with that particular disease. ...
... AutoML. Related AutoML solutions [6,21,23,26,27,39,46,47] consider the problem at hand an optimization task by iteratively generating and evaluating pipelines. To evaluate the generated candidate, these solutions require defining an objective loss function. ...
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When designing data science (DS) pipelines, end-users can get overwhelmed by the large and growing set of available data preprocessing and modeling techniques. Intelligent discovery assistants (IDAs) and automated machine learning (AutoML) solutions aim to facilitate end-users by (semi-)automating the process. However, they are expensive to compute and yield limited applicability for a wide range of real-world use cases and application domains. This is due to (a) their need to execute thousands of pipelines to get the optimal one, (b) their limited support of DS tasks, e.g., supervised classification or regression only, and a small, static set of available data preprocessing and ML algorithms; and (c) their restriction to quantifiable evaluation processes and metrics, e.g., tenfold cross-validation using the ROC AUC score for classification. To overcome these limitations, we propose a human-in-the-loop approach for the assisteddesignofdatasciencepipelines using previously executed pipelines. Based on a user query, i.e., data and a DS task, our framework outputs a ranked list of pipeline candidates from which the user can choose to execute or modify in real time. To recommend pipelines, it first identifies relevant datasets and pipelines utilizing efficient similarity search. It then ranks the candidate pipelines using multi-objective sorting and takes user interactions into account to improve suggestions over time. In our experimental evaluation, the proposed framework significantly outperforms the state-of-the-art IDA tool and achieves similar predictive performance with state-of-the-art long-running AutoML solutions while being real-time, generic to any evaluation processes and DS tasks, and extensible to new operators.
... This will stop the process if the present loss is lower than 90% of the mean value of the last 10 losses. In contrast to the trial-and-error method, we used grid search [29] to decrease the range of hyper-parameters, and then used the Python Hyperopt library [30] to find the best values. The Hyperopt library provides a parallel solution for model selection and parameter optimization in Python. ...
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Data analytics helps basketball teams to create tactics. However, manual data collection and analytics are costly and ineffective. Therefore, we applied a deep bidirectional long short-term memory (BLSTM) and mixture density network (MDN) approach. This model is not only capable of predicting a basketball trajectory based on real data, but it also can generate new trajectory samples. It is an excellent application to help coaches and players decide when and where to shoot. Its structure is particularly suitable for dealing with time series problems. BLSTM receives forward and backward information at the same time, while stacking multiple BLSTMs further increases the learning ability of the model. Combined with BLSTMs, MDN is used to generate a multi-modal distribution of outputs. Thus, the proposed model can, in principle, represent arbitrary conditional probability distributions of output variables. We tested our model with two experiments on three-pointer datasets from NBA SportVu data. In the hit-or-miss classification experiment, the proposed model outperformed other models in terms of the convergence speed and accuracy. In the trajectory generation experiment, eight model-generated trajectories at a given time closely matched real trajectories.
... Using LightGBM to analyze non-indigenous populations or datasets from other regions is a possible direction for future research. Additionally, several automated hyperparameter optimization frameworks have been proposed, including SMAC [57], Hyperopt [58,59], Spearmint [60], Google Vizier [61], AutoTune [62], Ray Tune [63], and Optuna. Among these, Optuna is one of the more recent approaches, which is why this study adopts it. ...
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Effectively and equitably allocating medical resources, particularly for minority groups, is a critical issue that warrants further investigation in rural hospitals. Machine learning techniques have gained significant traction and demonstrated strong performance across various fields in recent years. The determination of hyperparameters significantly influences the performance of machine learning models. Thus, this study employs Optuna, a framework specifically designed for optimizing the hyperparameters of machine learning models. Building on prior research, machine learning models with Optuna (MLOPTA) are introduced to forecast diseases of indigenous patients. The numerical results reveal that the designed MLOPTA system can accurately capture the occurrences of specified diseases. Therefore, the MLOPTA system offers a promising approach for disease forecasting. The disease forecasting results can serve as crucial references for allocating hospital resources.
... smaller sets of hyper-parameters over large ranges). In such situations it is advisable to instead use a method such as outlined in , or consider a commercial hyperparameter optimizer such as Optuna (Akiba et al., 2019), Ray Tune (Lai et al., 2018) or HyperOpt (Bergstra et al., 2013). ...
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Purpose Increasing reliance on autonomous systems requires confidence in the accuracies produced from computer vision classification algorithms. Computer vision (CV) for video classification provides phenomenal abilities, but it often suffers from “flickering” of results. Flickering occurs when the CV algorithm switches between declared classes over successive frames. Such behavior causes a loss of trust and confidence in their operations. Design/methodology/approach This “flickering” behavior often results from CV algorithms treating successive observations as independent, which ignores the dependence inherent in most videos. Bayesian neural networks are a potential remedy to this issue using Bayesian priors. This research compares a traditional video classification neural network to its Bayesian equivalent based on performance and capabilities. Additionally, this work introduces the concept of smoothing to reduce the opportunities for “flickering.” Findings The augmentation of Bayesian layers to CNNs matched with an exponentially decaying weighted average for classifications demonstrates promising benefits in reducing flickering. In the best case the proposed Bayesian CNN model reduces flickering by 67% while maintaining both overall accuracy and class level accuracy. Research limitations/implications The training of the Bayesian CNN is more computationally demanding and the requirement to classify frames multiple times reduces resulting framerate. However, for some high surety mission applications this is a tradeoff the decision analyst may be willing to make. Originality/value Our research expands on previous efforts by first using a variable number of frames to produce the moving average as well as by using an exponentially decaying moving average in conjunction with Bayesian augmentation.
... Hyperopt [45] with a random grid search algorithm. ...
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In this study, we introduce Modular State-based Stackelberg Games (Mod-SbSG), a novel game structure developed for distributed self-learning in modular manufacturing systems. Mod-SbSG enhances cooperative decision-making among self-learning agents within production systems by integrating State-based Potential Games (SbPG) with Stackelberg games. This hierarchical structure assigns more important modules of the manufacturing system a first-mover advantage, while less important modules respond optimally to the leaders' decisions. This decision-making process differs from typical multi-agent learning algorithms in manufacturing systems, where decisions are made simultaneously. We provide convergence guarantees for the novel game structure and design learning algorithms to account for the hierarchical game structure. We further analyse the effects of single-leader/multiple-follower and multiple-leader/multiple-follower scenarios within a Mod-SbSG. To assess its effectiveness, we implement and test Mod-SbSG in an industrial control setting using two laboratory-scale testbeds featuring sequential and serial-parallel processes. The proposed approach delivers promising results compared to the vanilla SbPG, which reduces overflow by 97.1%, and in some cases, prevents overflow entirely. Additionally, it decreases power consumption by 5-13% while satisfying the production demand, which significantly improves potential (global objective) values.
... Figure 2 illustrates the process of nCV and Bayesian optimization. The hyperparameters are determined prior to the training process and are primarily employed to regulate the performance of the selected models [69]. Table 2 presents a comprehensive overview of the hyperparameters used in all chosen algorithms, as well as the enhanced hyperparameters. ...
Article
The interfacial bond strength between the normal strength concrete (NSC) substrate and ultra-high-performance concrete (UHPC) overlays exhibits crucial significance for the longevity and structural integrity of existing or damaged structures. The effectiveness of better repair and retrofitting of NSC is contingent upon the ability of the UHPC-NSC interface to establish a resilient bond with each other under diverse conditions. So, continuous monitoring and assessing the interfacial bond strength with higher prediction accuracy becomes essential for preserving the integrity of NSC structures. Despite numerous empirical formulations, accurately capturing the factors affecting bond strength has remained elusive. In this study, split tensile and slant shear strength of the UHPC-NSC interface are predicted using five data-driven ensemble machine learning algorithms: gradient boosting regressor, adaboost, LightGBM, Xgboost, and Catboost. Notably, gradient boosting regression and Catboost consistently outperformed other models, demonstrating high R2 as 0.963 and 0.827 and low RMSE as 0.351 and 3.137 in testing sets. Nested cross-validation and Bayesian optimization techniques are incorporated for hyperparameter tuning to enhance model robustness. Additionally, the study incorporated Shapley additive explanations plots to reveal the complex relationships between the variables across both local and global scopes, consequently enhancing their viability and interpretability. The results obtained from the SHAP plots unveiled the substantial influence of surface treatment and other factors on bond strength. Further, the study introduced a reverse design approach to elucidate the factors influencing bond strength, guiding future concrete rehabilitation design schemes with a comprehensive understanding of the relationship between input and target features.
... This iterative process continued until the predefined stopping criterion was reached. For the TPE method, we relied on the stochasticity inherent in draws from the models, ensuring diverse candidate suggestions from one iteration to the next while incorporating new recommendations from BO [54]. To obtain a balance between time consumption and precision of the performance metric results, we set the BO stopping criterion to 1e-5. ...
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Purpose More accurate prediction of phenotype traits can increase the success of genomic selection in both plant and animal breeding studies and provide more reliable disease risk prediction in humans. Traditional approaches typically use regression models based on linear assumptions between the genetic markers and the traits of interest. Non-linear models have been considered as an alternative tool for modeling genomic interactions (i.e. non-additive effects) and other subtle non-linear patterns between markers and phenotype. Deep learning has become a state-of-the-art non-linear prediction method for sound, image and language data. However, genomic data is better represented in a tabular format. The existing literature on deep learning for tabular data proposes a wide range of novel architectures and reports successful results on various datasets. Tabular deep learning applications in genome-wide prediction (GWP) are still rare. In this work, we perform an overview of the main families of recent deep learning architectures for tabular data and apply them to multi-trait regression and multi-class classification for GWP on real gene datasets. Methods The study involves an extensive overview of recent deep learning architectures for tabular data learning: NODE, TabNet, TabR, TabTransformer, FT-Transformer, AutoInt, GANDALF, SAINT and LassoNet. These architectures are applied to multi-trait GWP. Comprehensive benchmarks of various tabular deep learning methods are conducted to identify best practices and determine their effectiveness compared to traditional methods. Results Extensive experimental results on several genomic datasets (three for multi-trait regression and two for multi-class classification) highlight LassoNet as a standout performer, surpassing both other tabular deep learning models and the highly efficient tree based LightGBM method in terms of both best prediction accuracy and computing efficiency. Conclusion Through series of evaluations on real-world genomic datasets, the study identifies LassoNet as a standout performer, surpassing decision tree methods like LightGBM and other tabular deep learning architectures in terms of both predictive accuracy and computing efficiency. Moreover, the inherent variable selection property of LassoNet provides a systematic way to find important genetic markers that contribute to phenotype expression.
... We partitioned the data into a training set of roughly 20% of observations and a test set of the remaining 80%. We used the hyperopt Python package [41] for identifying optimal hyperparameters subsequently used for fitting the final model. We evaluate our model on a set of four Period II-III test sets, each consisting of samples taken from each month in the April 2021 -July 2021 time frame. ...
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We develop a simulation framework for studying misinformation spread within online social networks that blends agent-based modeling and natural language processing techniques. While many other agent-based simulations exist in this space, questions over their fidelity and generalization to existing networks in part hinder their ability to drive policy-relevant decision making. To partially address these concerns, we create a ’digital clone’ of a known misinformation sharing network by downloading social media histories for over ten thousand of its users. We parse these histories to both extract the structure of the network and model the nuanced ways in which information is shared and spread among its members. Unlike many other agent-based methods in this space, information sharing between users in our framework is sensitive to topic of discussion, user preferences, and online community dynamics. To evaluate the fidelity of our method, we seed our cloned network with a set of posts recorded in the base network and compare propagation dynamics between the two, observing reasonable agreement across the twin networks over a variety of metrics. Lastly, we explore how the cloned network may serve as a flexible, low-cost testbed for misinformation countermeasure evaluation and red teaming analysis. We hope the tools explored here augment existing efforts in the space and unlock new opportunities for misinformation countermeasure evaluation, a field that may become increasingly important to consider with the anticipated rise of misinformation campaigns fueled by generative artificial intelligence.
... Additionally, we discretize the state space into 40. Furthermore, all parameters related to the algorithms and learning approaches pass automated tuning using Hyperopt [41]. Then, the simulation model of the BGLP is publicly accessible through both the MLPro [42] and MLPro-MPPS [43] frameworks. ...
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In this paper, we introduce novel gradient-based optimization methods for state-based potential games (SbPGs) within self-learning distributed production systems. SbPGs are recognised for their efficacy in enabling self-optimizing distributed multi-agent systems and offer a proven convergence guarantee, which facilitates collaborative player efforts towards global objectives. Our study strives to replace conventional ad-hoc random exploration-based learning in SbPGs with contemporary gradient-based approaches, which aim for faster convergence and smoother exploration dynamics, thereby shortening training duration while upholding the efficacy of SbPGs. Moreover, we propose three distinct variants for estimating the objective function of gradient-based learning, each developed to suit the unique characteristics of the systems under consideration. To validate our methodology, we apply it to a laboratory testbed, namely Bulk Good Laboratory Plant, which represents a smart and flexible distributed multi-agent production system. The incorporation of gradient-based learning in SbPGs reduces training times and achieves more optimal policies than its baseline.
... Additionally, there is little knowledge regarding how cleaning one type of error impacts how effectively other data errors can be cleaned example, Krishnan and Wu (2019)'s approach can minimize the number of outliers in a dataset or the number of integrity constraints violated. Technically, ML hyperparameter optimizers, such as Python Hyperopt (Bergstra et al. 2013), could be used to configure the data pipelines. However, as Krishnan and Wu (2019) pointed out, these optimizers do not leverage the incremental nature of data cleaning. ...
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Machine Learning (ML) is integrated into a growing number of systems for various applications. Because the performance of an ML model is highly dependent on the quality of the data it has been trained on, there is a growing interest in approaches to detect and repair data errors (i.e., data cleaning). Researchers are also exploring how ML can be used for data cleaning; hence creating a dual relationship between ML and data cleaning. To the best of our knowledge, there is no study that comprehensively reviews this relationship. This paper’s objectives are twofold. First, it aims to summarize the latest approaches for data cleaning for ML and ML for data cleaning. Second, it provides future work recommendations. We conduct a systematic literature review of the papers published between 2016 and 2022 inclusively. We identify different types of data cleaning activities with and for ML: feature cleaning, label cleaning, entity matching, outlier detection, imputation, and holistic data cleaning. We summarize the content of 101 papers covering various data cleaning activities and provide 24 future work recommendations. Our review highlights many promising data cleaning techniques that can be further extended. We believe that our review of the literature will help the community develop better approaches to clean data.
... We take one configuration performing quite well for each model on each physical system and compare their performance with and without the NBgE. For each case, the hyperparameters of the encoder, the epochs, the learning rate and the linear decreasing rate 2 are tuned with the help of Tune and HyperOpt [3,19]. In each case, we take 80% of the samples for training (with 10% for validation) and 20% for testing. ...
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In the trend of hybrid Artificial Intelligence (AI) techniques, Physic Informed Machine Learning has seen a growing interest. It operates mainly by imposing a data, learning or inductive bias with simulation data, Partial Differential Equations or equivariance and invariance properties. While these models have shown great success on tasks involving one physical domain such as fluid dynamics, existing methods still struggle on tasks with complex multi-physical and multi-domain phenomena. To address this challenge, we propose to leverage Bond Graphs, a multi-physics modeling approach together with Graph Neural Network. We thus propose Neural Bond Graph Encoder (NBgE), a model agnostic physical-informed encoder tailored for multi-physics systems. It provides an unified framework for any multi-physics informed AI with a graph encoder readable for any deep learning model. Our experiments on two challenging multi-domain physical systems - a Direct Current Motor and the Respiratory system - demonstrate the effectiveness of our approach on a multi-variate time series forecasting task.
... [43] making use of the deep learning frameworks, Keras to build the neural network architecture and Optuna to tune the architecture [44,45]. Hyperopt [46] was used to optimize training steps and select the optimal parameters for the best fit of given data without over/under fitting. The program was executed on UAB high-performance computing cluster (Cheaha) to enable efficient training and evaluation of the neural network. ...
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Accurate diagnosis for the 400 million people with rare diseases is critical for healthcare decisions, prognosis, understanding disease mechanisms, and identification of treatments. Despite advances in genome sequencing, barriers such as high interpretation costs, diagnostic expertise, throughput associated delays, and uncertain variant classifications persist, with demand exceeding capacity. Many variant classification methods focus narrowly on specific consequences, leading to the use of complex integrative pipelines that often overlook transcript variability and lack prediction transparency. To overcome these limitations, we introduce DITTO. This transparent, transcript-aware machine-learning method demonstrates superior overall performance in accuracy, recall, and precision when compared to existing tools. DITTO is publicly available at https://github.com/uab-cgds-worthey/DITTO
... Therefore, in this paper, the Bayesian optimization (BO) method is used to tune the ML model's hyperparameters (Frazier, 2018). The BO method is a global algorithm based on probability distribution, requiring fewer resources and boasting faster execution speeds (Bergstra et al., 2013). ...
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Geotechnical engineering data are usually small-sample and high-dimensional, which brings a lot of challenges in predictive modeling. This paper uses a typical high-dimensional and small-sample swell pressure (Ps) dataset to explore the possibility of using multi-algorithm hybrid ensemble and dimensionality reduction methods to mitigate the uncertainty of soil parameter prediction. Based on six machine learning (ML) algorithms, the base learner pool is constructed, and four ensemble methods, Stacking (SG), Blending (BG), Voting regression (VR), and Feature weight linear stacking (FWL), are used for the multi-algorithm ensemble. Furthermore, the importance of permutation is used for feature dimensionality reduction to mitigate the impact of weakly correlated variables on predictive modeling. The results show that the proposed methods are superior to traditional prediction models and base ML models, where FWL is more suitable for modeling with small-sample datasets, and dimensionality reduction can simplify the data structure and reduce the adverse impact of the small-sample effect, which points the way to feature selection for predictive modeling. Based on the ensemble methods, the feature importance of the five primary factors affecting Ps is the maximum dry density (31.145%), clay fraction (15.876%), swell percent (15.289%), plasticity index (14%), and optimum moisture content (13.69%), the influence of input parameters on Ps is also investigated, in line with the findings of the existing literature.
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