Nontawat Charoenphakdee

Shuhan Zheng, Nontawat Charoenphakdee

Missing value imputation in machine learning is the task of estimating the missing values in the dataset accurately using available information. In this task, several deep generative modeling methods have been proposed and demonstrated their usefulness, e.g., generative adversarial imputation networks. Recently, diffusion models have gained popularity because of their effectiveness in the generative modeling task in images, texts, audio, etc. To our knowledge, less attention has been paid to the investigation of the effectiveness of diffusion models for missing value imputation in tabular data. Based on recent development of diffusion models for time-series data imputation, we propose a diffusion model approach called "Conditional Score-based Diffusion Models for Tabular data" (TabCSDI). To effectively handle categorical variables and numerical variables simultaneously, we investigate three techniques: one-hot encoding, analog bits encoding, and feature tokenization. Experimental results on benchmark datasets demonstrated the effectiveness of TabCSDI compared with well-known existing methods, and also emphasized the importance of the categorical embedding techniques.

Kenta Oono, Nontawat Charoenphakdee, Kotatsu Bito et al.

Virtual Human Generative Model (VHGM) is a generative model that approximates the joint probability over more than 2000 human healthcare-related attributes. This paper presents the core algorithm, VHGM-MAE, a masked autoencoder (MAE) tailored for handling high-dimensional, sparse healthcare data. VHGM-MAE tackles four key technical challenges: (1) heterogeneity of healthcare data types, (2) probability distribution modeling, (3) systematic missingness in the training dataset arising from multiple data sources, and (4) the high-dimensional, small-$n$-large-$p$ problem. To address these challenges, VHGM-MAE employs a likelihood-based approach to model distributions with heterogeneous types, a transformer-based MAE to capture complex dependencies among observed and missing attributes, and a novel training scheme that effectively leverages available samples with diverse missingness patterns to mitigate the small-n-large-p problem. Experimental results demonstrate that VHGM-MAE outperforms existing methods in both missing value imputation and synthetic data generation.

Wenwen Li, Yuki Orimo, Nontawat Charoenphakdee

Developing machine learning interatomic potentials (MLIPs) for complex materials systems remains challenging because it requires expertise in atomistic simulations, machine learning, and workflow design, as well as iterative active learning procedures. Existing automated pipelines typically assume a fixed sequence of stages or depend on domain experts, which limits their adaptability to heterogeneous materials systems where the optimal curriculum is not known in advance. To lower the barrier to developing MLIPs for non-experts, we propose Lang2MLIP, a multi-agent framework that takes natural-language input and formulates end-to-end MLIP development as a sequential decision-making problem solved by large language models (LLMs). At each step, a decision-making agent observes the current dataset, model, evaluation results, and execution log, and then automatically selects an appropriate action to improve the model. This removes the need for a predefined pipeline and enables the agent to self-correct by revisiting earlier subsystems when new failures arise. We evaluate this approach on a solid electrolyte interphase (SEI) system with multiple components and interfaces. These results suggest that LLM-based multi-agent systems are a promising direction for automating MLIP development and making it more accessible to non-experts.

Shih-Peng Huang, Nontawat Charoenphakdee, Yuta Tsuboi et al.

Ensemble method is considered the gold standard for uncertainty quantification (UQ) in machine learning interatomic potentials (MLIPs). However, their high computational cost can limit its practicality. Alternative techniques, such as Monte Carlo dropout and deep kernel learning, have been proposed to improve computational efficiency; however, some of these methods cannot be applied to already trained models and may affect the prediction accuracy. In this paper, we propose a simple and efficient post-hoc framework for UQ that leverages the descriptor of a trained graph neural network potential to estimate residual errors. We refer to this method as post-hoc descriptor-based residual uncertainty modeling (P-DRUM). P-DRUM models the discrepancy between MLIP predictions and ground truth values, allowing these residuals to act as proxies for prediction uncertainty. We explore multiple variants of P-DRUM and benchmark them against established UQ methods, evaluating both their effectiveness and limitations.

Takashi Ishida, Ikko Yamane, Nontawat Charoenphakdee et al.

There is a fundamental limitation in the prediction performance that a machine learning model can achieve due to the inevitable uncertainty of the prediction target. In classification problems, this can be characterized by the Bayes error, which is the best achievable error with any classifier. The Bayes error can be used as a criterion to evaluate classifiers with state-of-the-art performance and can be used to detect test set overfitting. We propose a simple and direct Bayes error estimator, where we just take the mean of the labels that show \emph{uncertainty} of the class assignments. Our flexible approach enables us to perform Bayes error estimation even for weakly supervised data. In contrast to others, our method is model-free and even instance-free. Moreover, it has no hyperparameters and gives a more accurate estimate of the Bayes error than several baselines empirically. Experiments using our method suggest that recently proposed deep networks such as the Vision Transformer may have reached, or is about to reach, the Bayes error for benchmark datasets. Finally, we discuss how we can study the inherent difficulty of the acceptance/rejection decision for scientific articles, by estimating the Bayes error of the ICLR papers from 2017 to 2023.

Nuttapong Chairatanakul, Noppayut Sriwatanasakdi, Nontawat Charoenphakdee et al.

In cross-lingual text classification, it is required that task-specific training data in high-resource source languages are available, where the task is identical to that of a low-resource target language. However, collecting such training data can be infeasible because of the labeling cost, task characteristics, and privacy concerns. This paper proposes an alternative solution that uses only task-independent word embeddings of high-resource languages and bilingual dictionaries. First, we construct a dictionary-based heterogeneous graph (DHG) from bilingual dictionaries. This opens the possibility to use graph neural networks for cross-lingual transfer. The remaining challenge is the heterogeneity of DHG because multiple languages are considered. To address this challenge, we propose dictionary-based heterogeneous graph neural network (DHGNet) that effectively handles the heterogeneity of DHG by two-step aggregations, which are word-level and language-level aggregations. Experimental results demonstrate that our method outperforms pretrained models even though it does not access to large corpora. Furthermore, it can perform well even though dictionaries contain many incorrect translations. Its robustness allows the usage of a wider range of dictionaries such as an automatically constructed dictionary and crowdsourced dictionary, which are convenient for real-world applications.

Nontawat Charoenphakdee, Jongyeong Lee, Masashi Sugiyama

When minimizing the empirical risk in binary classification, it is a common practice to replace the zero-one loss with a surrogate loss to make the learning objective feasible to optimize. Examples of well-known surrogate losses for binary classification include the logistic loss, hinge loss, and sigmoid loss. It is known that the choice of a surrogate loss can highly influence the performance of the trained classifier and therefore it should be carefully chosen. Recently, surrogate losses that satisfy a certain symmetric condition (aka., symmetric losses) have demonstrated their usefulness in learning from corrupted labels. In this article, we provide an overview of symmetric losses and their applications. First, we review how a symmetric loss can yield robust classification from corrupted labels in balanced error rate (BER) minimization and area under the receiver operating characteristic curve (AUC) maximization. Then, we demonstrate how the robust AUC maximization method can benefit natural language processing in the problem where we want to learn only from relevant keywords and unlabeled documents. Finally, we conclude this article by discussing future directions, including potential applications of symmetric losses for reliable machine learning and the design of non-symmetric losses that can benefit from the symmetric condition.

Nontawat Charoenphakdee, Jayakorn Vongkulbhisal, Nuttapong Chairatanakul et al.

The focal loss has demonstrated its effectiveness in many real-world applications such as object detection and image classification, but its theoretical understanding has been limited so far. In this paper, we first prove that the focal loss is classification-calibrated, i.e., its minimizer surely yields the Bayes-optimal classifier and thus the use of the focal loss in classification can be theoretically justified. However, we also prove a negative fact that the focal loss is not strictly proper, i.e., the confidence score of the classifier obtained by focal loss minimization does not match the true class-posterior probability and thus it is not reliable as a class-posterior probability estimator. To mitigate this problem, we next prove that a particular closed-form transformation of the confidence score allows us to recover the true class-posterior probability. Through experiments on benchmark datasets, we demonstrate that our proposed transformation significantly improves the accuracy of class-posterior probability estimation.

Nontawat Charoenphakdee, Zhenghang Cui, Yivan Zhang et al.

The goal of classification with rejection is to avoid risky misclassification in error-critical applications such as medical diagnosis and product inspection. In this paper, based on the relationship between classification with rejection and cost-sensitive classification, we propose a novel method of classification with rejection by learning an ensemble of cost-sensitive classifiers, which satisfies all the following properties: (i) it can avoid estimating class-posterior probabilities, resulting in improved classification accuracy, (ii) it allows a flexible choice of losses including non-convex ones, (iii) it does not require complicated modifications when using different losses, (iv) it is applicable to both binary and multiclass cases, and (v) it is theoretically justifiable for any classification-calibrated loss. Experimental results demonstrate the usefulness of our proposed approach in clean-labeled, noisy-labeled, and positive-unlabeled classification.

Voot Tangkaratt, Nontawat Charoenphakdee, Masashi Sugiyama

Robust learning from noisy demonstrations is a practical but highly challenging problem in imitation learning. In this paper, we first theoretically show that robust imitation learning can be achieved by optimizing a classification risk with a symmetric loss. Based on this theoretical finding, we then propose a new imitation learning method that optimizes the classification risk by effectively combining pseudo-labeling with co-training. Unlike existing methods, our method does not require additional labels or strict assumptions about noise distributions. Experimental results on continuous-control benchmarks show that our method is more robust compared to state-of-the-art methods.

Yivan Zhang, Nontawat Charoenphakdee, Zhenguo Wu et al.

We study the problem of learning from aggregate observations where supervision signals are given to sets of instances instead of individual instances, while the goal is still to predict labels of unseen individuals. A well-known example is multiple instance learning (MIL). In this paper, we extend MIL beyond binary classification to other problems such as multiclass classification and regression. We present a general probabilistic framework that accommodates a variety of aggregate observations, e.g., pairwise similarity/triplet comparison for classification and mean/difference/rank observation for regression. Simple maximum likelihood solutions can be applied to various differentiable models such as deep neural networks and gradient boosting machines. Moreover, we develop the concept of consistency up to an equivalence relation to characterize our estimator and show that it has nice convergence properties under mild assumptions. Experiments on three problem settings -- classification via triplet comparison and regression via mean/rank observation indicate the effectiveness of the proposed method.

Hideaki Imamura, Nontawat Charoenphakdee, Futoshi Futami et al.

The Gaussian process bandit is a problem in which we want to find a maximizer of a black-box function with the minimum number of function evaluations. If the black-box function varies with time, then time-varying Bayesian optimization is a promising framework. However, a drawback with current methods is in the assumption that the evaluation time for every observation is constant, which can be unrealistic for many practical applications, e.g., recommender systems and environmental monitoring. As a result, the performance of current methods can be degraded when this assumption is violated. To cope with this problem, we propose a novel time-varying Bayesian optimization algorithm that can effectively handle the non-constant evaluation time. Furthermore, we theoretically establish a regret bound of our algorithm. Our bound elucidates that a pattern of the evaluation time sequence can hugely affect the difficulty of the problem. We also provide experimental results to validate the practical effectiveness of the proposed method.

Yivan Zhang, Nontawat Charoenphakdee, Masashi Sugiyama

Weakly-supervised learning is a paradigm for alleviating the scarcity of labeled data by leveraging lower-quality but larger-scale supervision signals. While existing work mainly focuses on utilizing a certain type of weak supervision, we present a probabilistic framework, learning from indirect observations, for learning from a wide range of weak supervision in real-world problems, e.g., noisy labels, complementary labels and coarse-grained labels. We propose a general method based on the maximum likelihood principle, which has desirable theoretical properties and can be straightforwardly implemented for deep neural networks. Concretely, a discriminative model for the true target is used for modeling the indirect observation, which is a random variable entirely depending on the true target stochastically or deterministically. Then, maximizing the likelihood given indirect observations leads to an estimator of the true target implicitly. Comprehensive experiments for two novel problem settings --- learning from multiclass label proportions and learning from coarse-grained labels, illustrate practical usefulness of our method and demonstrate how to integrate various sources of weak supervision.

Nontawat Charoenphakdee, Jongyeong Lee, Yiping Jin et al.

We consider a document classification problem where document labels are absent but only relevant keywords of a target class and unlabeled documents are given. Although heuristic methods based on pseudo-labeling have been considered, theoretical understanding of this problem has still been limited. Moreover, previous methods cannot easily incorporate well-developed techniques in supervised text classification. In this paper, we propose a theoretically guaranteed learning framework that is simple to implement and has flexible choices of models, e.g., linear models or neural networks. We demonstrate how to optimize the area under the receiver operating characteristic curve (AUC) effectively and also discuss how to adjust it to optimize other well-known evaluation metrics such as the accuracy and F1-measure. Finally, we show the effectiveness of our framework using benchmark datasets.

Zhenghang Cui, Nontawat Charoenphakdee, Issei Sato et al.

Learning from triplet comparison data has been extensively studied in the context of metric learning, where we want to learn a distance metric between two instances, and ordinal embedding, where we want to learn an embedding in an Euclidean space of the given instances that preserves the comparison order as well as possible. Unlike fully-labeled data, triplet comparison data can be collected in a more accurate and human-friendly way. Although learning from triplet comparison data has been considered in many applications, an important fundamental question of whether we can learn a classifier only from triplet comparison data has remained unanswered. In this paper, we give a positive answer to this important question by proposing an unbiased estimator for the classification risk under the empirical risk minimization framework. Since the proposed method is based on the empirical risk minimization framework, it inherently has the advantage that any surrogate loss function and any model, including neural networks, can be easily applied. Furthermore, we theoretically establish an estimation error bound for the proposed empirical risk minimizer. Finally, we provide experimental results to show that our method empirically works well and outperforms various baseline methods.

Taira Tsuchiya, Nontawat Charoenphakdee, Issei Sato et al.

Ordinal regression is aimed at predicting an ordinal class label. In this paper, we consider its semi-supervised formulation, in which we have unlabeled data along with ordinal-labeled data to train an ordinal regressor. There are several metrics to evaluate the performance of ordinal regression, such as the mean absolute error, mean zero-one error, and mean squared error. However, the existing studies do not take the evaluation metric into account, have a restriction on the model choice, and have no theoretical guarantee. To overcome these problems, we propose a novel generic framework for semi-supervised ordinal regression based on the empirical risk minimization principle that is applicable to optimizing all of the metrics mentioned above. Besides, our framework has flexible choices of models, surrogate losses, and optimization algorithms without the common geometric assumption on unlabeled data such as the cluster assumption or manifold assumption. We further provide an estimation error bound to show that our risk estimator is consistent. Finally, we conduct experiments to show the usefulness of our framework.

Chenri Ni, Nontawat Charoenphakdee, Junya Honda et al.

We investigate the problem of multiclass classification with rejection, where a classifier can choose not to make a prediction to avoid critical misclassification. First, we consider an approach based on simultaneous training of a classifier and a rejector, which achieves the state-of-the-art performance in the binary case. We analyze this approach for the multiclass case and derive a general condition for calibration to the Bayes-optimal solution, which suggests that calibration is hard to achieve by general loss functions unlike the binary case. Next, we consider another traditional approach based on confidence scores, in which the existing work focuses on a specific class of losses. We propose rejection criteria for more general losses for this approach and guarantee calibration to the Bayes-optimal solution. Finally, we conduct experiments to validate the relevance of our theoretical findings.

Jongyeong Lee, Nontawat Charoenphakdee, Seiichi Kuroki et al.

Appropriately evaluating the discrepancy between domains is essential for the success of unsupervised domain adaptation. In this paper, we first point out that existing discrepancy measures are less informative when complex models such as deep neural networks are used, in addition to the facts that they can be computationally highly demanding and their range of applications is limited only to binary classification. We then propose a novel domain discrepancy measure, called the paired hypotheses discrepancy (PHD), to overcome these shortcomings. PHD is computationally efficient and applicable to multi-class classification. Through generalization error bound analysis, we theoretically show that PHD is effective even for complex models. Finally, we demonstrate the practical usefulness of PHD through experiments.

Yueh-Hua Wu, Nontawat Charoenphakdee, Han Bao et al.

Imitation learning (IL) aims to learn an optimal policy from demonstrations. However, such demonstrations are often imperfect since collecting optimal ones is costly. To effectively learn from imperfect demonstrations, we propose a novel approach that utilizes confidence scores, which describe the quality of demonstrations. More specifically, we propose two confidence-based IL methods, namely two-step importance weighting IL (2IWIL) and generative adversarial IL with imperfect demonstration and confidence (IC-GAIL). We show that confidence scores given only to a small portion of sub-optimal demonstrations significantly improve the performance of IL both theoretically and empirically.

Nontawat Charoenphakdee, Jongyeong Lee, Masashi Sugiyama

This paper aims to provide a better understanding of a symmetric loss. First, we emphasize that using a symmetric loss is advantageous in the balanced error rate (BER) minimization and area under the receiver operating characteristic curve (AUC) maximization from corrupted labels. Second, we prove general theoretical properties of symmetric losses, including a classification-calibration condition, excess risk bound, conditional risk minimizer, and AUC-consistency condition. Third, since all nonnegative symmetric losses are non-convex, we propose a convex barrier hinge loss that benefits significantly from the symmetric condition, although it is not symmetric everywhere. Finally, we conduct experiments to validate the relevance of the symmetric condition.

Nontawat Charoenphakdee, Masashi Sugiyama

Bottlenecks of binary classification from positive and unlabeled data (PU classification) are the requirements that given unlabeled patterns are drawn from the test marginal distribution, and the penalty of the false positive error is identical to the false negative error. However, such requirements are often not fulfilled in practice. In this paper, we generalize PU classification to the class prior shift and asymmetric error scenarios. Based on the analysis of the Bayes optimal classifier, we show that given a test class prior, PU classification under class prior shift is equivalent to PU classification with asymmetric error. Then, we propose two different frameworks to handle these problems, namely, a risk minimization framework and density ratio estimation framework. Finally, we demonstrate the effectiveness of the proposed frameworks and compare both frameworks through experiments using benchmark datasets.

Seiichi Kuroki, Nontawat Charoenphakdee, Han Bao et al.

Unsupervised domain adaptation is the problem setting where data generating distributions in the source and target domains are different, and labels in the target domain are unavailable. One important question in unsupervised domain adaptation is how to measure the difference between the source and target domains. A previously proposed discrepancy that does not use the source domain labels requires high computational cost to estimate and may lead to a loose generalization error bound in the target domain. To mitigate these problems, we propose a novel discrepancy called source-guided discrepancy (S-disc), which exploits labels in the source domain. As a consequence, S-disc can be computed efficiently with a finite sample convergence guarantee. In addition, we show that S-disc can provide a tighter generalization error bound than the one based on an existing discrepancy. Finally, we report experimental results that demonstrate the advantages of S-disc over the existing discrepancies.