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.
The increasing integration of machine learning across various domains has underscored the necessity for accessible systems that non-experts can utilize effectively. To address this need, the field of automated machine learning (AutoML) has developed tools to simplify the construction and optimization of ML pipelines. However, existing AutoML solutions often lack efficiency in creating online pipelines and ease of use for Human-Computer Interaction (HCI) applications. Therefore, in this paper, we introduce AdaptoML-UX, an adaptive framework that incorporates automated feature engineering, machine learning, and incremental learning to assist non-AI experts in developing robust, user-centered ML models. Our toolkit demonstrates the capability to adapt efficiently to diverse problem domains and datasets, particularly in HCI, thereby reducing the necessity for manual experimentation and conserving time and resources. Furthermore, it supports model personalization through incremental learning, customizing models to individual user behaviors. HCI researchers can employ AdaptoML-UX (\url{https://github.com/MichaelSargious/AdaptoML_UX}) without requiring specialized expertise, as it automates the selection of algorithms, feature engineering, and hyperparameter tuning based on the unique characteristics of the data.
Automated Machine Learning (AutoML) approaches encompass traditional methods that optimize fixed pipelines for model selection and ensembling, as well as newer LLM-based frameworks that autonomously build pipelines. While LLM-based agents have shown promise in automating machine learning tasks, they often generate low-diversity and suboptimal code, even after multiple iterations. To overcome these limitations, we introduce Tree-Search Enhanced LLM Agents (SELA), an innovative agent-based system that leverages Monte Carlo Tree Search (MCTS) to optimize the AutoML process. By representing pipeline configurations as trees, our framework enables agents to conduct experiments intelligently and iteratively refine their strategies, facilitating a more effective exploration of the machine learning solution space. This novel approach allows SELA to discover optimal pathways based on experimental feedback, improving the overall quality of the solutions. In an extensive evaluation across 20 machine learning datasets, we compare the performance of traditional and agent-based AutoML methods, demonstrating that SELA achieves a win rate of 65% to 80% against each baseline across all datasets. These results underscore the significant potential of agent-based strategies in AutoML, offering a fresh perspective on tackling complex machine learning challenges.
Automated Machine Learning (AutoML) has simplified complex ML processes such as data pre-processing, model selection, and hyper-parameter searching. However, traditional AutoML frameworks focus solely on discriminative tasks, often falling short in tackling AutoML for generative models. Additionally, these frameworks lack interpretability and user engagement during the training process, primarily due to the absence of human-centered design. It leads to a lack of transparency in final decision-making and limited user control, potentially reducing trust and adoption of AutoML methods. To address these limitations, we introduce UniAutoML, a human-centered AutoML framework that leverages Large Language Models (LLMs) to unify AutoML for both discriminative (e.g., Transformers and CNNs for classification or regression tasks) and generative tasks (e.g., fine-tuning diffusion models or LLMs). The human-centered design of UniAutoML innovatively features a conversational user interface (CUI) that facilitates natural language interactions, providing users with real-time guidance, feedback, and progress updates for better interpretability. This design enhances transparency and user control throughout the AutoML training process, allowing users to seamlessly break down or modify the model being trained. To mitigate potential risks associated with LLM generated content, UniAutoML incorporates a safety guardline that filters inputs and censors outputs. We evaluated UniAutoML's performance and usability through experiments on eight diverse datasets and user studies involving 25 participants, demonstrating that UniAutoML not only enhances performance but also improves user control and trust. Our human-centered design bridges the gap between AutoML capabilities and user understanding, making ML more accessible to a broader audience.
This paper introduces Mamba4Cast, a zero-shot foundation model for time series forecasting. Based on the Mamba architecture and inspired by Prior-data Fitted Networks (PFNs), Mamba4Cast generalizes robustly across diverse time series tasks without the need for dataset specific fine-tuning. Mamba4Cast's key innovation lies in its ability to achieve strong zero-shot performance on real-world datasets while having much lower inference times than time series foundation models based on the transformer architecture. Trained solely on synthetic data, the model generates forecasts for entire horizons in a single pass, outpacing traditional auto-regressive approaches. Our experiments show that Mamba4Cast performs competitively against other state-of-the-art foundation models in various data sets while scaling significantly better with the prediction length. The source code can be accessed at https://github.com/automl/Mamba4Cast.
Optimization of the formation step in lithium-ion battery manufacturing is challenging due to limited physical understanding of solid electrolyte interphase formation and the long testing time (~100 days) for cells to reach the end of life. We propose a systematic feature design framework that requires minimal domain knowledge for accurate cycle life prediction during formation. Two simple Q(V) features designed from our framework, extracted from formation data without any additional diagnostic cycles, achieved a median of 9.20% error for cycle life prediction, outperforming thousands of autoML models using pre-defined features. We attribute the strong performance of our designed features to their physical origins - the voltage ranges identified by our framework capture the effects of formation temperature and microscopic particle resistance heterogeneity. By designing highly interpretable features, our approach can accelerate formation research, leveraging the interplay between data-driven feature design and mechanistic understanding.
Despite its significant promise and continuous technical advances, real-world applications of artificial intelligence (AI) remain limited. We attribute this to the "domain expert-AI-conundrum": while domain experts, such as clinician scientists, should be able to build predictive models such as risk scores, they face substantial barriers in accessing state-of-the-art (SOTA) tools. While automated machine learning (AutoML) has been proposed as a partner in clinical predictive modeling, many additional requirements need to be fulfilled to make machine learning accessible for clinician scientists. To address this gap, we introduce CliMB, a no-code AI-enabled partner designed to empower clinician scientists to create predictive models using natural language. CliMB guides clinician scientists through the entire medical data science pipeline, thus empowering them to create predictive models from real-world data in just one conversation. CliMB also creates structured reports and interpretable visuals. In evaluations involving clinician scientists and systematic comparisons against a baseline GPT-4, CliMB consistently demonstrated superior performance in key areas such as planning, error prevention, code execution, and model performance. Moreover, in blinded assessments involving 45 clinicians from diverse specialties and career stages, more than 80% preferred CliMB over GPT-4. Overall, by providing a no-code interface with clear guidance and access to SOTA methods in the fields of data-centric AI, AutoML, and interpretable ML, CliMB empowers clinician scientists to build robust predictive models. The proof-of-concept version of CliMB is available as open-source software on GitHub: https://github.com/vanderschaarlab/climb.
Automated machine learning (AutoML) accelerates AI development by automating tasks in the development pipeline, such as optimal model search and hyperparameter tuning. Existing AutoML systems often require technical expertise to set up complex tools, which is in general time-consuming and requires a large amount of human effort. Therefore, recent works have started exploiting large language models (LLM) to lessen such burden and increase the usability of AutoML frameworks via a natural language interface, allowing non-expert users to build their data-driven solutions. These methods, however, are usually designed only for a particular process in the AI development pipeline and do not efficiently use the inherent capacity of the LLMs. This paper proposes AutoML-Agent, a novel multi-agent framework tailored for full-pipeline AutoML, i.e., from data retrieval to model deployment. AutoML-Agent takes user's task descriptions, facilitates collaboration between specialized LLM agents, and delivers deployment-ready models. Unlike existing work, instead of devising a single plan, we introduce a retrieval-augmented planning strategy to enhance exploration to search for more optimal plans. We also decompose each plan into sub-tasks (e.g., data preprocessing and neural network design) each of which is solved by a specialized agent we build via prompting executing in parallel, making the search process more efficient. Moreover, we propose a multi-stage verification to verify executed results and guide the code generation LLM in implementing successful solutions. Extensive experiments on seven downstream tasks using fourteen datasets show that AutoML-Agent achieves a higher success rate in automating the full AutoML process, yielding systems with good performance throughout the diverse domains.
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.
A successful Machine Learning (ML) model implementation requires three main components: training dataset, suitable model architecture and training procedure. Given dataset and task, finding an appropriate model might be challenging. AutoML, a branch of ML, focuses on automatic architecture search -- a meta method that aims at moving human from ML system design process. The success of ML and the development of quantum computing (QC) in recent years led to a birth of new fascinating field called Quantum Machine Learning (QML) that, amongst others, incorporates quantum computers into ML models. In this paper we present AQMLator, an Auto Quantum Machine Learning platform that aims to automatically propose and train the quantum layers of an ML model with minimal input from the user. This way, data scientists can bypass the entry barrier for QC and use QML. AQMLator uses standard ML libraries, making it easy to introduce into existing ML pipelines.
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.
The majority of automated machine learning (AutoML) solutions are developed in Python, however a large percentage of data scientists are associated with the R language. Unfortunately, there are limited R solutions available. Moreover high entry level means they are not accessible to everyone, due to required knowledge about machine learning (ML). To fill this gap, we present the forester package, which offers ease of use regardless of the user's proficiency in the area of machine learning. The forester is an open-source AutoML package implemented in R designed for training high-quality tree-based models on tabular data. It fully supports binary and multiclass classification, regression, and partially survival analysis tasks. With just a few functions, the user is capable of detecting issues regarding the data quality, preparing the preprocessing pipeline, training and tuning tree-based models, evaluating the results, and creating the report for further analysis.
Entity matching (EM) is the problem of determining whether two records refer to same real-world entity, which is crucial in data integration, e.g., for product catalogs or address databases. A major drawback of many EM approaches is their dependence on labelled examples. We thus focus on the challenging setting of zero-shot entity matching where no labelled examples are available for an unseen target dataset. Recently, large language models (LLMs) have shown promising results for zero-shot EM, but their low throughput and high deployment cost limit their applicability and scalability. We revisit the zero-shot EM problem with AnyMatch, a small language model fine-tuned in a transfer learning setup. We propose several novel data selection techniques to generate fine-tuning data for our model, e.g., by selecting difficult pairs to match via an AutoML filter, by generating additional attribute-level examples, and by controlling label imbalance in the data. We conduct an extensive evaluation of the prediction quality and deployment cost of our model, in a comparison to thirteen baselines on nine benchmark datasets. We find that AnyMatch provides competitive prediction quality despite its small parameter size: it achieves the second-highest F1 score overall, and outperforms several other approaches that employ models with hundreds of billions of parameters. Furthermore, our approach exhibits major cost benefits: the average prediction quality of AnyMatch is within 4.4% of the state-of-the-art method MatchGPT with the proprietary trillion-parameter model GPT-4, yet AnyMatch requires four orders of magnitude less parameters and incurs a 3,899 times lower inference cost (in dollars per 1,000 tokens).
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.
In practice, we are often faced with small-sized tabular data. However, current tabular benchmarks are not geared towards data-scarce applications, making it very difficult to derive meaningful conclusions from empirical comparisons. We introduce PMLBmini, a tabular benchmark suite of 44 binary classification datasets with sample sizes $\leq$ 500. We use our suite to thoroughly evaluate current automated machine learning (AutoML) frameworks, off-the-shelf tabular deep neural networks, as well as classical linear models in the low-data regime. Our analysis reveals that state-of-the-art AutoML and deep learning approaches often fail to appreciably outperform even a simple logistic regression baseline, but we also identify scenarios where AutoML and deep learning methods are indeed reasonable to apply. Our benchmark suite, available on https://github.com/RicardoKnauer/TabMini , allows researchers and practitioners to analyze their own methods and challenge their data efficiency.
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)
Large semantic knowledge bases are grounded in factual knowledge. However, recent approaches to dense text representations (i.e. embeddings) do not efficiently exploit these resources. Dense and robust representations of documents are essential for effectively solving downstream classification and retrieval tasks. This work demonstrates that injecting embedded information from knowledge bases can augment the performance of contemporary Large Language Model (LLM)-based representations for the task of text classification. Further, by considering automated machine learning (AutoML) with the fused representation space, we demonstrate it is possible to improve classification accuracy even if we use low-dimensional projections of the original representation space obtained via efficient matrix factorization. This result shows that significantly faster classifiers can be achieved with minimal or no loss in predictive performance, as demonstrated using five strong LLM baselines on six diverse real-life datasets. The code is freely available at \url{https://github.com/bkolosk1/bablfusion.git}.
Automated Machine Learning (AutoML) significantly simplifies the deployment of machine learning models by automating tasks from data preprocessing to model selection to ensembling. AutoML systems for tabular data often employ post hoc ensembling, where multiple models are combined to improve predictive accuracy. This typically results in longer inference times, a major limitation in practical deployments. Addressing this, we introduce a hardware-aware ensemble selection approach that integrates inference time into post hoc ensembling. By leveraging an existing framework for ensemble selection with quality diversity optimization, our method evaluates ensemble candidates for their predictive accuracy and hardware efficiency. This dual focus allows for a balanced consideration of accuracy and operational efficiency. Thus, our approach enables practitioners to choose from a Pareto front of accurate and efficient ensembles. Our evaluation using 83 classification datasets shows that our approach sustains competitive accuracy and can significantly improve ensembles' operational efficiency. The results of this study provide a foundation for extending these principles to additional hardware constraints, setting the stage for the development of more resource-efficient AutoML systems.
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.
In this paper, we present the Fast Optimizer Benchmark (FOB), a tool designed for evaluating deep learning optimizers during their development. The benchmark supports tasks from multiple domains such as computer vision, natural language processing, and graph learning. The focus is on convenient usage, featuring human-readable YAML configurations, SLURM integration, and plotting utilities. FOB can be used together with existing hyperparameter optimization (HPO) tools as it handles training and resuming of runs. The modular design enables integration into custom pipelines, using it simply as a collection of tasks. We showcase an optimizer comparison as a usage example of our tool. FOB can be found on GitHub: https://github.com/automl/FOB.