Effectively representing heterogeneous tabular datasets for meta-learning purposes is still an open problem. Previous approaches rely on representations that are intended to be universal. This paper proposes two novel methods for tabular representation learning tailored to a specific meta-task - warm-starting Bayesian Hyperparameter Optimization. Both follow the specific requirement formulated by ourselves that enforces representations to capture the properties of landmarkers. The first approach involves deep metric learning, while the second one is based on landmarkers reconstruction. We evaluate the proposed encoders in two ways. Next to the gain in the target meta-task, we also use the degree of fulfillment of the proposed requirement as the evaluation metric. Experiments demonstrate that while the proposed encoders can effectively learn representations aligned with landmarkers, they may not directly translate to significant performance gains in the meta-task of HPO warm-starting.
Hyperparameter optimization (HPO) aims to identify an optimal hyperparameter configuration (HPC) such that the resulting model generalizes well to unseen data. As the expected generalization error cannot be optimized directly, it is estimated with a resampling strategy, such as holdout or cross-validation. This approach implicitly assumes that minimizing the validation error leads to improved generalization. However, since validation error estimates are inherently stochastic and depend on the resampling strategy, a natural question arises: Can excessive optimization of the validation error lead to overfitting at the HPO level, akin to overfitting in model training based on empirical risk minimization? In this paper, we investigate this phenomenon, which we term overtuning, a form of overfitting specific to HPO. Despite its practical relevance, overtuning has received limited attention in the HPO and AutoML literature. We provide a formal definition of overtuning and distinguish it from related concepts such as meta-overfitting. We then conduct a large-scale reanalysis of HPO benchmark data to assess the prevalence and severity of overtuning. Our results show that overtuning is more common than previously assumed, typically mild but occasionally severe. In approximately 10% of cases, overtuning leads to the selection of a seemingly optimal HPC with worse generalization error than the default or first configuration tried. We further analyze how factors such as performance metric, resampling strategy, dataset size, learning algorithm, and HPO method affect overtuning and discuss mitigation strategies. Our results highlight the need to raise awareness of overtuning, particularly in the small-data regime, indicating that further mitigation strategies should be studied.
As DBS technology advances toward directional leads and optimization-based current steering, this study aims to improve the selection of electrode contact configurations using the recently developed L1-norm regularized L1-norm fitting (L1L1) method. The focus is in particular on L1L1's capability to incorporate a priori lead field uncertainty, offering a potential advantage over conventional approaches that do not account for such variability. Our optimization framework incorporates uncertainty by constraining the solution space based on lead field attenuation. This reflects physiological expectations about the VTA and serves to avoid overfitting. By applying this method to 8- and 40-contact electrode configurations, we optimize current distributions within a discretized finite element (FE) model, focusing on the lead field's characteristics. The model accounts for uncertainty through these explicit constraints, enhancing the feasibility, focality, and robustness of the resulting solutions. The L1L1 method was validated through a series of numerical experiments using both noiseless and noisy lead fields, where the noise level was selected to reflect attenuation within VTA. It successfully fits and regularizes the current distribution across target structures, with hyperparameter optimization extracting either bipolar or multipolar electrode configurations. These configurations aim to maximize focused current density or prioritize a high gain field ratio in a discretized FE model. Compared to traditional methods, the L1L1 approach showed competitive performance in concentrating stimulation within the target region while minimizing unintended current spread, particularly under noisy conditions. By incorporating uncertainty directly into the optimization process, we obtain a noise-robust framework for current steering, allowing for variations in lead field models and simulation parameters.
In 2009, our group pioneered a novel method CBTOPE for predicting conformational B-cell epitopes in a protein from its amino acid sequence, which received extensive citations from the scientific community. In a recent study, Cia et al. (2023) evaluated the performance of conformational B-cell epitope prediction methods on a well-curated dataset, revealing that most approaches, including CBTOPE, exhibited poor performance. One plausible cause of this diminished performance is that available methods were trained on datasets that are both limited in size and outdated in content. In this study, we present an enhanced version of CBTOPE, trained, tested, and evaluated using the well-curated dataset from Cai et al. (2023). Initially, we developed machine learning-based models using binary profiles, achieving a maximum AUC of 0.58 on the validation dataset. The performance of our method improved significantly from an AUC of 0.58 to 0.63 when incorporating evolutionary information in the form of a Position-Specific Scoring Matrix (PSSM) profile. Furthermore, the performance increased from an AUC of 0.63 to 0.64 when we integrated both the PSSM profile and relative solvent accessibility (RSA). All models were trained, tested, and optimized on the training dataset using five-fold cross-validation. The final performance of our models was assessed using a validation or independent dataset that was not used during hyperparameter optimization. To facilitate scientific community working in the field of subunit vaccine, we develop a standalone software and web server CBTOPE2 (https://webs.iiitd.edu.in/raghava/cbtope2/).
Here in this work, we present a novel Quadratic Binary Optimization (QBO) model for quantized neural network training, enabling the use of arbitrary activation and loss functions through spline interpolation. We introduce Forward Interval Propagation (FIP), a method designed to tackle the challenges of non-linearity and the multi-layer composite structure in neural networks by discretizing activation functions into linear subintervals. This approach preserves the universal approximation properties of neural networks while allowing complex nonlinear functions to be optimized using quantum computers, thus broadening their applicability in artificial intelligence. We provide theoretical upper bounds on the approximation error and the number of Ising spins required, by deriving the sample complexity of the empirical risk minimization problem, from an optimization perspective. A significant challenge in solving the associated Quadratic Constrained Binary Optimization (QCBO) model on a large scale is the presence of numerous constraints. When employing the penalty method to handle these constraints, tuning a large number of penalty coefficients becomes a critical hyperparameter optimization problem, increasing computational complexity and potentially affecting solution quality. To address this, we employ the Quantum Conditional Gradient Descent (QCGD) algorithm, which leverages quantum computing to directly solve the QCBO problem. We prove the convergence of QCGD under a quantum oracle with randomness and bounded variance in objective value, as well as under limited precision constraints in the coefficient matrix. Additionally, we provide an upper bound on the Time-To-Solution for the QCBO solving process. Experimental results using a coherent Ising machine (CIM) demonstrate a 94.95% accuracy on the Fashion MNIST classification task, with only 1.1-bit precision.
Bilevel optimization, in which one optimization problem is nested inside another, underlies many machine learning applications with a hierarchical structure -- such as meta-learning and hyperparameter optimization. Such applications often involve sensitive training data, raising pressing concerns about individual privacy. Motivated by this, we study differentially private bilevel optimization. We first focus on settings where the outer-level objective is \textit{convex}, and provide novel upper and lower bounds on the excess risk for both pure and approximate differential privacy, covering both empirical and population-level loss. These bounds are nearly tight and essentially match the optimal rates for standard single-level differentially private ERM and stochastic convex optimization (SCO), up to additional terms that capture the intrinsic complexity of the nested bilevel structure. The bounds are achieved in polynomial time via efficient implementations of the exponential and regularized exponential mechanisms. A key technical contribution is a new method and analysis of log-concave sampling under inexact function evaluations, which may be of independent interest. In the \textit{non-convex} setting, we develop novel algorithms with state-of-the-art rates for privately finding approximate stationary points. Notably, our bounds do not depend on the dimension of the inner problem.
Diffusion bridges are a promising class of deep-learning methods for sampling from unnormalized distributions. Recent works show that the Log Variance (LV) loss consistently outperforms the reverse Kullback-Leibler (rKL) loss when using the reparametrization trick to compute rKL-gradients. While the on-policy LV loss yields identical gradients to the rKL loss when combined with the log-derivative trick for diffusion samplers with non-learnable forward processes, this equivalence does not hold for diffusion bridges or when diffusion coefficients are learned. Based on this insight we argue that for diffusion bridges the LV loss does not represent an optimization objective that can be motivated like the rKL loss via the data processing inequality. Our analysis shows that employing the rKL loss with the log-derivative trick (rKL-LD) does not only avoid these conceptual problems but also consistently outperforms the LV loss. Experimental results with different types of diffusion bridges on challenging benchmarks show that samplers trained with the rKL-LD loss achieve better performance. From a practical perspective we find that rKL-LD requires significantly less hyperparameter optimization and yields more stable training behavior.
A variety of pruning methods have been introduced for over-parameterized Recurrent Neural Networks to improve efficiency in terms of power consumption and storage utilization. These advances motivate a new paradigm, termed `hyperpruning', which seeks to identify the most suitable pruning strategy for a given network architecture and application. Unlike conventional hyperparameter search, where the optimal configuration's accuracy remains uncertain, in the context of network pruning, the accuracy of the dense model sets the target for the accuracy of the pruned one. The goal, therefore, is to discover pruned variants that match or even surpass this established accuracy. However, exhaustive search over pruning configurations is computationally expensive and lacks early performance guarantees. To address this challenge, we propose a novel Lyapunov Spectrum (LS)-based distance metric that enables early comparison between pruned and dense networks, allowing accurate prediction of post-training performance. By integrating this LS-based distance with standard hyperparameter optimization algorithms, we introduce an efficient hyperpruning framework, termed LS-based Hyperpruning (LSH). LSH reduces search time by an order of magnitude compared to conventional approaches relying on full training. Experiments on stacked LSTM and RHN architectures using the Penn Treebank dataset, and on AWD-LSTM-MoS using WikiText-2, demonstrate that under fixed training budgets and target pruning ratios, LSH consistently identifies superior pruned models. Remarkably, these pruned variants not only outperform those selected by loss-based baseline but also exceed the performance of their dense counterpart.
The development of modern Artificial Intelligence (AI) models, particularly diffusion-based models employed in computer vision and image generation tasks, is undergoing a paradigmatic shift in development methodologies. Traditionally dominated by a "Model Centric" approach, in which performance gains were primarily pursued through increasingly complex model architectures and hyperparameter optimization, the field is now recognizing a more nuanced "Data-Centric" approach. This emergent framework foregrounds the quality, structure, and relevance of training data as the principal driver of model performance. To operationalize this paradigm shift, we introduce the DataSeeds.AI sample dataset (the "DSD"), initially comprised of approximately 10,610 high-quality human peer-ranked photography images accompanied by extensive multi-tier annotations. The DSD is a foundational computer vision dataset designed to usher in a new standard for commercial image datasets. Representing a small fraction of DataSeed.AI's 100 million-plus image catalog, the DSD provides a scalable foundation necessary for robust commercial and multimodal AI development. Through this in-depth exploratory analysis, we document the quantitative improvements generated by the DSD on specific models against known benchmarks and make the code and the trained models used in our evaluation publicly available.
When training autoregressive models to forecast dynamical systems, a critical question arises: how far into the future should the model be trained to predict? Too short a horizon may miss long-term trends, while too long a horizon can impede convergence due to accumulating prediction errors. In this work, we formalize this trade-off by analyzing how the geometry of the loss landscape depends on the training horizon. We prove that for chaotic systems, the loss landscape's roughness grows exponentially with the training horizon, while for limit cycles, it grows linearly, making long-horizon training inherently challenging. However, we also show that models trained on long horizons generalize well to short-term forecasts, whereas those trained on short horizons suffer exponentially (resp. linearly) worse long-term predictions in chaotic (resp. periodic) systems. We validate our theory through numerical experiments and discuss practical implications for selecting training horizons. Our results provide a principled foundation for hyperparameter optimization in autoregressive forecasting models.
As machine learning models are increasingly embedded into society through high-stakes decision-making, selecting the right algorithm for a given task, audience, and sector presents a critical challenge, particularly in the context of fairness. Traditional assessments of model fairness have often framed fairness as an objective mathematical property, treating model selection as an optimization problem under idealized informational conditions. This overlooks model multiplicity as a consideration--that multiple models can deliver similar performance while exhibiting different fairness characteristics. Legal scholars have engaged this challenge through the concept of Less Discriminatory Algorithms (LDAs), which frames model selection as a civil rights obligation. In real-world deployment, this normative challenge is bounded by constraints on fairness experimentation, e.g., regulatory standards, institutional priorities, and resource capacity. Against these considerations, the paper revisits Lee and Floridi (2021)'s relational fairness approach using updated 2021 Home Mortgage Disclosure Act (HMDA) data, and proposes an expansion of the scope of the LDA search process. We argue that extending the LDA search horizontally, considering fairness across model families themselves, provides a lightweight complement, or alternative, to within-model hyperparameter optimization, when operationalizing fairness in non-experimental, resource constrained settings. Fairness metrics alone offer useful, but insufficient signals to accurately evaluate candidate LDAs. Rather, by using a horizontal LDA search approach with the relational trade-off framework, we demonstrate a responsible minimum viable LDA search on real-world lending outcomes. Organizations can modify this approach to systematically compare, evaluate, and select LDAs that optimize fairness and accuracy in a sector-based contextualized manner.
Integrating Large Language Models (LLMs) with Knowledge Graphs (KGs) results in complex systems with numerous hyperparameters that directly affect performance. While such systems are increasingly common in retrieval-augmented generation, the role of systematic hyperparameter optimization remains underexplored. In this paper, we study this problem in the context of Cognee, a modular framework for end-to-end KG construction and retrieval. Using three multi-hop QA benchmarks (HotPotQA, TwoWikiMultiHop, and MuSiQue) we optimize parameters related to chunking, graph construction, retrieval, and prompting. Each configuration is scored using established metrics (exact match, F1, and DeepEval's LLM-based correctness metric). Our results demonstrate that meaningful gains can be achieved through targeted tuning. While the gains are consistent, they are not uniform, with performance varying across datasets and metrics. This variability highlights both the value of tuning and the limitations of standard evaluation measures. While demonstrating the immediate potential of hyperparameter tuning, we argue that future progress will depend not only on architectural advances but also on clearer frameworks for optimization and evaluation in complex, modular systems.
Bayesian optimization (BO) offers an efficient pipeline for optimizing black-box functions with the help of a Gaussian process prior and an acquisition function (AF). Recently, in the context of single-objective BO, learning-based AFs witnessed promising empirical results given its favorable non-myopic nature. Despite this, the direct extension of these approaches to multi-objective Bayesian optimization (MOBO) suffer from the \textit{hypervolume identifiability issue}, which results from the non-Markovian nature of MOBO problems. To tackle this, inspired by the non-Markovian RL literature and the success of Transformers in language modeling, we present a generalized deep Q-learning framework and propose \textit{BOFormer}, which substantiates this framework for MOBO via sequence modeling. Through extensive evaluation, we demonstrate that BOFormer constantly outperforms the benchmark rule-based and learning-based algorithms in various synthetic MOBO and real-world multi-objective hyperparameter optimization problems. We have made the source code publicly available to encourage further research in this direction.
Hyperparameter optimization (HPO) is a critical yet challenging aspect of machine learning model development, significantly impacting model performance and generalization. Traditional HPO methods often struggle with high dimensionality, complex interdependencies, and computational expense. This paper introduces OptiMindTune, a novel multi-agent framework designed to intelligently and efficiently optimize hyperparameters. OptiMindTune leverages the collaborative intelligence of three specialized AI agents -- a Recommender Agent, an Evaluator Agent, and a Decision Agent -- each powered by Google's Gemini models. These agents address distinct facets of the HPO problem, from model selection and hyperparameter suggestion to robust evaluation and strategic decision-making. By fostering dynamic interactions and knowledge sharing, OptiMindTune aims to converge to optimal hyperparameter configurations more rapidly and robustly than existing single-agent or monolithic approaches. Our framework integrates principles from advanced large language models, and adaptive search to achieve scalable and intelligent AutoML. We posit that this multi-agent paradigm offers a promising avenue for tackling the increasing complexity of modern machine learning model tuning.
Determining the 3D pose of a patient from a limited set of 2D X-ray images is a critical task in interventional settings. While preoperative volumetric imaging (e.g., CT and MRI) provides precise 3D localization and visualization of anatomical targets, these modalities cannot be acquired during procedures, where fast 2D imaging (X-ray) is used instead. To integrate volumetric guidance into intraoperative procedures, we present PolyPose, a simple and robust method for deformable 2D/3D registration. PolyPose parameterizes complex 3D deformation fields as a composition of rigid transforms, leveraging the biological constraint that individual bones do not bend in typical motion. Unlike existing methods that either assume no inter-joint movement or fail outright in this under-determined setting, our polyrigid formulation enforces anatomically plausible priors that respect the piecewise rigid nature of human movement. This approach eliminates the need for expensive deformation regularizers that require patient- and procedure-specific hyperparameter optimization. Across extensive experiments on diverse datasets from orthopedic surgery and radiotherapy, we show that this strong inductive bias enables PolyPose to successfully align the patient's preoperative volume to as few as two X-ray images, thereby providing crucial 3D guidance in challenging sparse-view and limited-angle settings where current registration methods fail.
Medical Image Segmentation (MIS) includes diverse tasks, from bone to organ segmentation, each with its own challenges in finding the best segmentation model. The state-of-the-art AutoML-related MIS-framework nnU-Net automates many aspects of model configuration but remains constrained by fixed hyperparameters and heuristic design choices. As a full-AutoML framework for MIS, we propose Auto-nnU-Net, a novel nnU-Net variant enabling hyperparameter optimization (HPO), neural architecture search (NAS), and hierarchical NAS (HNAS). Additionally, we propose Regularized PriorBand to balance model accuracy with the computational resources required for training, addressing the resource constraints often faced in real-world medical settings that limit the feasibility of extensive training procedures. We evaluate our approach across diverse MIS datasets from the well-established Medical Segmentation Decathlon, analyzing the impact of AutoML techniques on segmentation performance, computational efficiency, and model design choices. The results demonstrate that our AutoML approach substantially improves the segmentation performance of nnU-Net on 6 out of 10 datasets and is on par on the other datasets while maintaining practical resource requirements. Our code is available at https://github.com/LUH-AI/AutonnUNet.
In this paper we propose for the first time the hyperparameter optimization (HPO) algorithm POCAII. POCAII differs from the Hyperband and Successive Halving literature by explicitly separating the search and evaluation phases and utilizing principled approaches to exploration and exploitation principles during both phases. Such distinction results in a highly flexible scheme for managing a hyperparameter optimization budget by focusing on search (i.e., generating competing configurations) towards the start of the HPO process while increasing the evaluation effort as the HPO comes to an end. POCAII was compared to state of the art approaches SMAC, BOHB and DEHB. Our algorithm shows superior performance in low-budget hyperparameter optimization regimes. Since many practitioners do not have exhaustive resources to assign to HPO, it has wide applications to real-world problems. Moreover, the empirical evidence showed how POCAII demonstrates higher robustness and lower variance in the results. This is again very important when considering realistic scenarios with extremely expensive models to train.
Parkinson's disease (PD) poses a growing global health challenge, with Bangladesh experiencing a notable rise in PD-related mortality. Early detection of PD remains particularly challenging in resource-constrained settings, where voice-based analysis has emerged as a promising non-invasive and cost-effective alternative. However, existing studies predominantly focus on English or other major languages; notably, no voice dataset for PD exists for Bengali - posing a significant barrier to culturally inclusive and accessible healthcare solutions. Moreover, most prior studies employed only a narrow set of acoustic features, with limited or no hyperparameter tuning and feature selection strategies, and little attention to model explainability. This restricts the development of a robust and generalizable machine learning model. To address this gap, we present BenSparX, the first Bengali conversational speech dataset for PD detection, along with a robust and explainable machine learning framework tailored for early diagnosis. The proposed framework incorporates diverse acoustic feature categories, systematic feature selection methods, and state-of-the-art machine learning algorithms with extensive hyperparameter optimization. Furthermore, to enhance interpretability and trust in model predictions, the framework incorporates SHAP (SHapley Additive exPlanations) analysis to quantify the contribution of individual acoustic features toward PD detection. Our framework achieves state-of-the-art performance, yielding an accuracy of 95.77%, F1 score of 95.57%, and AUC-ROC of 0.982. We further externally validated our approach by applying the framework to existing PD datasets in other languages, where it consistently outperforms state-of-the-art approaches. To facilitate further research and reproducibility, the dataset has been made publicly available at https://github.com/Riad071/BenSParX.
Suppressor variables can influence model predictions without being dependent on the target outcome and they pose a significant challenge for Explainable AI (XAI) methods. These variables may cause false-positive feature attributions, undermining the utility of explanations. Although effective remedies exist for linear models, their extension to non-linear models and to instance-based explanations has remained limited. We introduce PatternLocal, a novel XAI technique that addresses this gap. PatternLocal begins with a locally linear surrogate, e.g. LIME, KernelSHAP, or gradient-based methods, and transforms the resulting discriminative model weights into a generative representation, thereby suppressing the influence of suppressor variables while preserving local fidelity. In extensive hyperparameter optimization on the XAI-TRIS benchmark, PatternLocal consistently outperformed other XAI methods and reduced false-positive attributions when explaining non-linear tasks, thereby enabling more reliable and actionable insights.
This case study applies a phased hyperparameter optimization process to compare multitask natural language model variants that utilize multiphase learning rate scheduling and optimizer parameter grouping. We employ short, Bayesian optimization sessions that leverage multi-fidelity, hyperparameter space pruning, progressive halving, and a degree of human guidance. We utilize the Optuna TPE sampler and Hyperband pruner, as well as the Scikit-Learn Gaussian process minimization. Initially, we use efficient low-fidelity sprints to prune the hyperparameter space. Subsequent sprints progressively increase their model fidelity and employ hyperband pruning for efficiency. A second aspect of our approach is using a meta-learner to tune threshold values to resolve classification probabilities during inference. We demonstrate our method on a collection of variants of the 2021 Joint Entity and Relation Extraction model proposed by Eberts and Ulges.