Learning dynamical models from data is not only fundamental but also holds great promise for advancing principle discovery, time-series prediction, and controller design. Among various approaches, Gaussian Process State-Space Models (GPSSMs) have recently gained significant attention due to their combination of flexibility and interpretability. However, for online learning, the field lacks an efficient method suitable for scenarios where prior information regarding data distribution and model function is limited. To address this issue, this paper proposes a recursive GPSSM method with adaptive capabilities for both operating domains and Gaussian process (GP) hyperparameters. Specifically, we first utilize first-order linearization to derive a Bayesian update equation for the joint distribution between the system state and the GP model, enabling closed-form and domain-independent learning. Second, an online selection algorithm for inducing points is developed based on informative criteria to achieve lightweight learning. Third, to support online hyperparameter optimization, we recover historical measurement information from the current filtering distribution. Comprehensive evaluations on both synthetic and real-world datasets demonstrate the superior accuracy, computational efficiency, and adaptability of our method compared to state-of-the-art online GPSSM techniques.
Building effective machine learning (ML) workflows to address complex tasks is a primary focus of the Automatic ML (AutoML) community and a critical step toward achieving artificial general intelligence (AGI). Recently, the integration of Large Language Models (LLMs) into ML workflows has shown great potential for automating and enhancing various stages of the ML pipeline. This survey provides a comprehensive and up-to-date review of recent advancements in using LLMs to construct and optimize ML workflows, focusing on key components encompassing data and feature engineering, model selection and hyperparameter optimization, and workflow evaluation. We discuss both the advantages and limitations of LLM-driven approaches, emphasizing their capacity to streamline and enhance ML workflow modeling process through language understanding, reasoning, interaction, and generation. Finally, we highlight open challenges and propose future research directions to advance the effective application of LLMs in ML workflows.
Protein engineering is important for biomedical applications, but conventional approaches are often inefficient and resource-intensive. While deep learning (DL) models have shown promise, their training or implementation into protein engineering remains challenging for biologists without specialized computational expertise. To address this gap, we propose AutoProteinEngine (AutoPE), an agent framework that leverages large language models (LLMs) for multimodal automated machine learning (AutoML) for protein engineering. AutoPE innovatively allows biologists without DL backgrounds to interact with DL models using natural language, lowering the entry barrier for protein engineering tasks. Our AutoPE uniquely integrates LLMs with AutoML to handle model selection for both protein sequence and graph modalities, automatic hyperparameter optimization, and automated data retrieval from protein databases. We evaluated AutoPE through two real-world protein engineering tasks, demonstrating substantial performance improvements compared to traditional zero-shot and manual fine-tuning approaches. By bridging the gap between DL and biologists' domain expertise, AutoPE empowers researchers to leverage DL without extensive programming knowledge. Our code is available at https://github.com/tsynbio/AutoPE.
Multi-objective Bayesian optimization has been widely adopted in scientific experiment design, including drug discovery and hyperparameter optimization. In practice, regulatory or safety concerns often impose additional thresholds on certain attributes of the experimental outcomes. Previous work has primarily focused on constrained single-objective optimization tasks or active search under constraints. The existing constrained multi-objective algorithms address the issue with heuristics and approximations, posing challenges to the analysis of the sample efficiency. We propose a novel constrained multi-objective Bayesian optimization algorithm COMBOO that balances active learning of the level-set defined on multiple unknowns with multi-objective optimization within the feasible region. We provide both theoretical analysis and empirical evidence, demonstrating the efficacy of our approach on various synthetic benchmarks and real-world applications.
This study introduces SLLMBO, an innovative framework leveraging large language models (LLMs) for hyperparameter optimization (HPO), incorporating dynamic search space adaptability, enhanced parameter space exploitation, and a novel LLM-tree-structured parzen estimator (LLM-TPE) sampler. By addressing limitations in recent fully LLM-based methods and traditional bayesian optimization (BO), SLLMBO achieves more robust optimization. This comprehensive benchmarking evaluates multiple LLMs, including GPT-3.5-Turbo, GPT-4o, Claude-Sonnet-3.5, and Gemini-1.5-Flash, extending prior work and establishing SLLMBO as the first framework to benchmark a diverse set of LLMs for HPO. By integrating LLMs' established strengths in parameter initialization with the exploitation abilities demonstrated in this study, alongside TPE's exploration capabilities, the LLM-TPE sampler achieves a balanced exploration-exploitation trade-off, reduces API costs, and mitigates premature early stoppings for more effective parameter searches. Across 14 tabular tasks in classification and regression, the LLM-TPE sampler outperformed fully LLM-based methods and achieved superior results over BO methods in 9 tasks. Testing early stopping in budget-constrained scenarios demonstrated competitive performance, indicating that LLM-based methods generally benefit from extended iterations for optimal results. This work lays the foundation for future research exploring open-source LLMs, reproducibility of LLM results in HPO, and benchmarking SLLMBO on complex datasets, such as image classification, segmentation, and machine translation.
Large-scale industrial recommendation models predict the most relevant items from catalogs containing millions or billions of options. To train these models efficiently, a small set of irrelevant items (negative samples) is selected from the vast catalog for each relevant item (positive example), helping the model distinguish between relevant and irrelevant items. Choosing the right negative sampling method is a common challenge. We address this by implementing and comparing various negative sampling methods - random, popularity-based, in-batch, mixed, adaptive, and adaptive with mixed variants - on modern sequential recommendation models. Our experiments, including hyperparameter optimization and 20x repeats on three benchmark datasets with varying popularity biases, show how the choice of method and dataset characteristics impact key model performance metrics. We also reveal that average performance metrics often hide imbalances across popularity bands (head, mid, tail). We find that commonly used random negative sampling reinforces popularity bias and performs best for head items. Popularity-based methods (in-batch and global popularity negative sampling) can offer balanced performance at the cost of lower overall model performance results. Our study serves as a practical guide to the trade-offs in selecting a negative sampling method for large-scale sequential recommendation models. Code, datasets, experimental results and hyperparameters are available at: https://github.com/apple/ml-negative-sampling.
Bayesian Optimization is ubiquitous in the field of experimental design and blackbox optimization for improving search efficiency, but has been traditionally restricted to regression models which are only applicable to fixed search spaces and tabular input features. We propose Embed-then-Regress, a paradigm for applying in-context regression over string inputs, through the use of string embedding capabilities of pretrained language models. By expressing all inputs as strings, we are able to perform general-purpose regression for Bayesian Optimization over various domains including synthetic, combinatorial, and hyperparameter optimization, obtaining comparable results to state-of-the-art Gaussian Process-based algorithms. Code can be found at https://github.com/google-research/optformer/tree/main/optformer/embed_then_regress.
Hyperparameter optimization is an essential component in many data science pipelines and typically entails exhaustive time and resource-consuming computations in order to explore the combinatorial search space. Similar to this problem, other key operations in data science pipelines exhibit the exact same properties. Important examples are: neural architecture search, where the goal is to identify the best design choices for a neural network, and query cardinality estimation, where given different predicate values for a SQL query the goal is to estimate the size of the output. In this paper, we abstract away those essential components of data science pipelines and we model them as instances of tensor completion, where each variable of the search space corresponds to one mode of the tensor, and the goal is to identify all missing entries of the tensor, corresponding to all combinations of variable values, starting from a very small sample of observed entries. In order to do so, we first conduct a thorough experimental evaluation of existing state-of-the-art tensor completion techniques and introduce domain-inspired adaptations (such as smoothness across the discretized variable space) and an ensemble technique which is able to achieve state-of-the-art performance. We extensively evaluate existing and proposed methods in a number of datasets generated corresponding to (a) hyperparameter optimization for non-neural network models, (b) neural architecture search, and (c) variants of query cardinality estimation, demonstrating the effectiveness of tensor completion as a tool for automating data science pipelines. Furthermore, we release our generated datasets and code in order to provide benchmarks for future work on this topic.
Knowledge graph (KG) completion aims to identify additional facts that can be inferred from the existing facts in the KG. Recent developments in this field have explored this task in the inductive setting, where at test time one sees entities that were not present during training; the most performant models in the inductive setting have employed path encoding modules in addition to standard subgraph encoding modules. This work similarly focuses on KG completion in the inductive setting, without the explicit use of path encodings, which can be time-consuming and introduces several hyperparameters that require costly hyperparameter optimization. Our approach uses a Transformer-based subgraph encoding module only; we introduce connection-biased attention and entity role embeddings into the subgraph encoding module to eliminate the need for an expensive and time-consuming path encoding module. Evaluations on standard inductive KG completion benchmark datasets demonstrate that our \textbf{C}onnection-\textbf{B}iased \textbf{Li}nk \textbf{P}rediction (CBLiP) model has superior performance to models that do not use path information. Compared to models that utilize path information, CBLiP shows competitive or superior performance while being faster. Additionally, to show that the effectiveness of connection-biased attention and entity role embeddings also holds in the transductive setting, we compare CBLiP's performance on the relation prediction task in the transductive setting.
Hyperparameters are a critical factor in reliably training well-performing reinforcement learning (RL) agents. Unfortunately, developing and evaluating automated approaches for tuning such hyperparameters is both costly and time-consuming. As a result, such approaches are often only evaluated on a single domain or algorithm, making comparisons difficult and limiting insights into their generalizability. We propose ARLBench, a benchmark for hyperparameter optimization (HPO) in RL that allows comparisons of diverse HPO approaches while being highly efficient in evaluation. To enable research into HPO in RL, even in settings with low compute resources, we select a representative subset of HPO tasks spanning a variety of algorithm and environment combinations. This selection allows for generating a performance profile of an automated RL (AutoRL) method using only a fraction of the compute previously necessary, enabling a broader range of researchers to work on HPO in RL. With the extensive and large-scale dataset on hyperparameter landscapes that our selection is based on, ARLBench is an efficient, flexible, and future-oriented foundation for research on AutoRL. Both the benchmark and the dataset are available at https://github.com/automl/arlbench.
In the AutoML domain, test accuracy is heralded as the quintessential metric for evaluating model efficacy, underpinning a wide array of applications from neural architecture search to hyperparameter optimization. However, the reliability of test accuracy as the primary performance metric has been called into question, notably through research highlighting how label noise can obscure the true ranking of state-of-the-art models. We venture beyond, along another perspective where the existence of hard samples within datasets casts further doubt on the generalization capabilities inferred from test accuracy alone. Our investigation reveals that the distribution of hard samples between training and test sets affects the difficulty levels of those sets, thereby influencing the perceived generalization capability of models. We unveil two distinct generalization pathways-toward easy and hard samples-highlighting the complexity of achieving balanced model evaluation. Finally, we propose a benchmarking procedure for comparing hard sample identification methods, facilitating the advancement of more nuanced approaches in this area. Our primary goal is not to propose a definitive solution but to highlight the limitations of relying primarily on test accuracy as an evaluation metric, even when working with balanced datasets, by introducing the in-class data imbalance problem. By doing so, we aim to stimulate a critical discussion within the research community and open new avenues for research that consider a broader spectrum of model evaluation criteria. The anonymous code is available at https://github.com/PawPuk/CurvBIM blueunder the GPL-3.0 license.
Inference-time techniques are emerging as highly effective tools to enhance large language model (LLM) capabilities. However, best practices for developing systems that combine these techniques remain underdeveloped due to our limited understanding of the utility of individual inference-time techniques and the interactions between them. Additionally, efficiently and automatically searching the space of model choices, inference-time techniques, and their compositions is challenging due to the large design space. To address these challenges, we introduce Archon, a modular framework for selecting, combining, and stacking layers of inference-time techniques to construct optimized LLM systems for target benchmarks. Rather than relying on a single LLM called once, we leverage a diverse set of LLMs and inference-time techniques, creating LLM systems greater than the sum of their parts. Archon defines an extensible design space, encompassing techniques such as generation ensembling, repeated sampling, ranking, fusion, critiquing, verification, and unit testing. It transforms the problem of building LLM systems into a hyperparameter optimization objective. Given the available LLMs, inference-time techniques, and compute budget, Archon utilizes hyperparameter search techniques to discover optimized architectures for target benchmark(s). We evaluate Archon architectures across a range of instruction-following, reasoning, and coding benchmarks, including MT-Bench, Arena-Hard-Auto, AlpacaEval 2.0, MixEval, MixEval Hard, MATH, and CodeContests. Archon architectures outperform frontier models, such as GPT-4o and Claude 3.5 Sonnet, on these benchmarks, achieving an average accuracy increase of 15.1 percentage points by using all available LLMs. We make our code and datasets available publicly on Github: https://github.com/ScalingIntelligence/Archon.
The rapid evolution of mobile networks from 5G to 6G has necessitated the development of autonomous network management systems, such as Zero-Touch Networks (ZTNs). However, the increased complexity and automation of these networks have also escalated cybersecurity risks. Existing Intrusion Detection Systems (IDSs) leveraging traditional Machine Learning (ML) techniques have shown effectiveness in mitigating these risks, but they often require extensive manual effort and expert knowledge. To address these challenges, this paper proposes an Automated Machine Learning (AutoML)-based autonomous IDS framework towards achieving autonomous cybersecurity for next-generation networks. To achieve autonomous intrusion detection, the proposed AutoML framework automates all critical procedures of the data analytics pipeline, including data pre-processing, feature engineering, model selection, hyperparameter tuning, and model ensemble. Specifically, it utilizes a Tabular Variational Auto-Encoder (TVAE) method for automated data balancing, tree-based ML models for automated feature selection and base model learning, Bayesian Optimization (BO) for hyperparameter optimization, and a novel Optimized Confidence-based Stacking Ensemble (OCSE) method for automated model ensemble. The proposed AutoML-based IDS was evaluated on two public benchmark network security datasets, CICIDS2017 and 5G-NIDD, and demonstrated improved performance compared to state-of-the-art cybersecurity methods. This research marks a significant step towards fully autonomous cybersecurity in next-generation networks, potentially revolutionizing network security applications.
Machine Learning (ML) has gained popularity in actuarial research and insurance industrial applications. However, the performance of most ML tasks heavily depends on data preprocessing, model selection, and hyperparameter optimization, which are considered to be intensive in terms of domain knowledge, experience, and manual labor. Automated Machine Learning (AutoML) aims to automatically complete the full life-cycle of ML tasks and provides state-of-the-art ML models without human intervention or supervision. This paper introduces an AutoML workflow that allows users without domain knowledge or prior experience to achieve robust and effortless ML deployment by writing only a few lines of code. This proposed AutoML is specifically tailored for the insurance application, with features like the balancing step in data preprocessing, ensemble pipelines, and customized loss functions. These features are designed to address the unique challenges of the insurance domain, including the imbalanced nature of common insurance datasets. The full code and documentation are available on the GitHub repository. (https://github.com/PanyiDong/InsurAutoML)
Hyperparameter optimization is a crucial problem in Evolutionary Computation. In fact, the values of the hyperparameters directly impact the trajectory taken by the optimization process, and their choice requires extensive reasoning by human operators. Although a variety of self-adaptive Evolutionary Algorithms have been proposed in the literature, no definitive solution has been found. In this work, we perform a preliminary investigation to automate the reasoning process that leads to the choice of hyperparameter values. We employ two open-source Large Language Models (LLMs), namely Llama2-70b and Mixtral, to analyze the optimization logs online and provide novel real-time hyperparameter recommendations. We study our approach in the context of step-size adaptation for (1+1)-ES. The results suggest that LLMs can be an effective method for optimizing hyperparameters in Evolution Strategies, encouraging further research in this direction.
The importance of tuning hyperparameters in Machine Learning (ML) and Deep Learning (DL) is established through empirical research and applications, evident from the increase in new hyperparameter optimization (HPO) algorithms and benchmarks steadily added by the community. However, current benchmarking practices using averaged performance across many datasets may obscure key differences between HPO methods, especially for pairwise comparisons. In this work, we apply Linear Mixed-Effect Models-based (LMEMs) significance testing for post-hoc analysis of HPO benchmarking runs. LMEMs allow flexible and expressive modeling on the entire experiment data, including information such as benchmark meta-features, offering deeper insights than current analysis practices. We demonstrate this through a case study on the PriorBand paper's experiment data to find insights not reported in the original work.
Automated Machine Learning (AutoML) offers a promising approach to streamline the training of machine learning models. However, existing AutoML frameworks are often limited to unimodal scenarios and require extensive manual configuration. Recent advancements in Large Language Models (LLMs) have showcased their exceptional abilities in reasoning, interaction, and code generation, presenting an opportunity to develop a more automated and user-friendly framework. To this end, we introduce AutoM3L, an innovative Automated Multimodal Machine Learning framework that leverages LLMs as controllers to automatically construct multimodal training pipelines. AutoM3L comprehends data modalities and selects appropriate models based on user requirements, providing automation and interactivity. By eliminating the need for manual feature engineering and hyperparameter optimization, our framework simplifies user engagement and enables customization through directives, addressing the limitations of previous rule-based AutoML approaches. We evaluate the performance of AutoM3L on six diverse multimodal datasets spanning classification, regression, and retrieval tasks, as well as a comprehensive set of unimodal datasets. The results demonstrate that AutoM3L achieves competitive or superior performance compared to traditional rule-based AutoML methods. Furthermore, a user study highlights the user-friendliness and usability of our framework, compared to the rule-based AutoML methods.
Tuning parameters of a non-differentiable or black-box compute is challenging. Existing methods rely mostly on random sampling or grid sampling from the parameter space. Further, with all the current methods, it is not possible to supply any input specific parameters to the black-box. To the best of our knowledge, for the first time, we are able to learn input-specific parameters for a black box in this work. As a test application, we choose a popular image denoising method BM3D as our black-box compute. Then, we use a differentiable surrogate model (a neural network) to approximate the black-box behaviour. Next, another neural network is used in an end-to-end fashion to learn input instance-specific parameters for the black-box. Motivated by prior advances in surrogate-based optimization, we applied our method to the Smartphone Image Denoising Dataset (SIDD) and the Color Berkeley Segmentation Dataset (CBSD68) for image denoising. The results are compelling, demonstrating a significant increase in PSNR and a notable improvement in SSIM nearing 0.93. Experimental results underscore the effectiveness of our approach in achieving substantial improvements in both model performance and optimization efficiency. For code and implementation details, please refer to our GitHub repository: https://github.com/arnisha-k/instance-specific-param
Gradient-based attacks are a primary tool to evaluate robustness of machine-learning models. However, many attacks tend to provide overly-optimistic evaluations as they use fixed loss functions, optimizers, step-size schedulers, and default hyperparameters. In this work, we tackle these limitations by proposing a parametric variation of the well-known fast minimum-norm attack algorithm, whose loss, optimizer, step-size scheduler, and hyperparameters can be dynamically adjusted. We re-evaluate 12 robust models, showing that our attack finds smaller adversarial perturbations without requiring any additional tuning. This also enables reporting adversarial robustness as a function of the perturbation budget, providing a more complete evaluation than that offered by fixed-budget attacks, while remaining efficient. We release our open-source code at https://github.com/pralab/HO-FMN.
Objective: Brain metastases (BMs) are common in cancer patients and determining the primary tumor site is crucial for effective treatment. This study aims to predict the primary tumor site from BM MRI data using radiomic features and advanced machine learning algorithms. Methods: We utilized a comprehensive dataset from Ocana-Tienda et al. (2023) comprising MRI and clinical data from 75 patients with BMs. Radiomic features were extracted from post-contrast T1-weighted MRI sequences. Feature selection was performed using the GINI index, and data normalization was applied to ensure consistent scaling. We developed and evaluated Random Forest and XGBoost classifiers, both with and without hyperparameter optimization using the FOX (Fox optimizer) algorithm. Model interpretability was enhanced using SHAP (SHapley Additive exPlanations) values. Results: The baseline Random Forest model achieved an accuracy of 0.85, which improved to 0.93 with FOX optimization. The XGBoost model showed an initial accuracy of 0.96, increasing to 0.99 after optimization. SHAP analysis revealed the most influential radiomic features contributing to the models' predictions. The FOX-optimized XGBoost model exhibited the best performance with a precision, recall, and F1-score of 0.99. Conclusion: This study demonstrates the effectiveness of using radiomic features and machine learning to predict primary tumor sites from BM MRI data. The FOX optimization algorithm significantly enhanced model performance, and SHAP provided valuable insights into feature importance. These findings highlight the potential of integrating radiomics and machine learning into clinical practice for improved diagnostic accuracy and personalized treatment planning.