Synthetic data has emerged as a powerful resource in life sciences, offering solutions for data scarcity, privacy protection and accessibility constraints. By creating artificial datasets that mirror the characteristics of real data, allows researchers to develop and validate computational methods in controlled environments. Despite its promise, the adoption of synthetic data in Life Sciences hinges on rigorous evaluation metrics designed to assess their fidelity and reliability. To explore the current landscape of synthetic data evaluation metrics in several Life Sciences domains, the ELIXIR Machine Learning Focus Group performed a systematic review of the scientific literature following the PRISMA guidelines. Six critical domains were examined to identify current practices for assessing synthetic data. Findings reveal that, while generation methods are rapidly evolving, systematic evaluation is often overlooked, limiting researchers ability to compare, validate, and trust synthetic datasets across different domains. This systematic review underscores the urgent need for robust, standardized evaluation approaches that not only bolster confidence in synthetic data but also guide its effective and responsible implementation. By laying the groundwork for establishing domain-specific yet interoperable standards, this scoping review paves the way for future initiatives aimed at enhancing the role of synthetic data in scientific discovery, clinical practice and beyond.
Evaluating synthetic tabular data is challenging, since they can differ from the real data in so many ways. There exist numerous metrics of synthetic data quality, ranging from statistical distances to predictive performance, often providing conflicting results. Moreover, they fail to explain or pinpoint the specific weaknesses in the synthetic data. To address this, we apply explainable AI (XAI) techniques to a binary detection classifier trained to distinguish real from synthetic data. While the classifier identifies distributional differences, XAI concepts such as feature importance and feature effects, analyzed through methods like permutation feature importance, partial dependence plots, Shapley values and counterfactual explanations, reveal why synthetic data are distinguishable, highlighting inconsistencies, unrealistic dependencies, or missing patterns. This interpretability increases transparency in synthetic data evaluation and provides deeper insights beyond conventional metrics, helping diagnose and improve synthetic data quality. We apply our approach to two tabular datasets and generative models, showing that it uncovers issues overlooked by standard evaluation techniques.
Causal discovery, or identifying causal relationships from observational data, is a notoriously challenging task, with numerous methods proposed to tackle it. Despite this, in-the-wild evaluation of these methods is still lacking, as works frequently rely on synthetic data evaluation and sparse real-world examples under critical theoretical assumptions. Real-world causal structures, however, are often complex, making it hard to decide on a proper causal discovery strategy. To bridge this gap, we introduce CausalRivers, the largest in-the-wild causal discovery benchmarking kit for time-series data to date. CausalRivers features an extensive dataset on river discharge that covers the eastern German territory (666 measurement stations) and the state of Bavaria (494 measurement stations). It spans the years 2019 to 2023 with a 15-minute temporal resolution. Further, we provide additional data from a flood around the Elbe River, as an event with a pronounced distributional shift. Leveraging multiple sources of information and time-series meta-data, we constructed two distinct causal ground truth graphs (Bavaria and eastern Germany). These graphs can be sampled to generate thousands of subgraphs to benchmark causal discovery across diverse and challenging settings. To demonstrate the utility of CausalRivers, we evaluate several causal discovery approaches through a set of experiments to identify areas for improvement. CausalRivers has the potential to facilitate robust evaluations and comparisons of causal discovery methods. Besides this primary purpose, we also expect that this dataset will be relevant for connected areas of research, such as time-series forecasting and anomaly detection. Based on this, we hope to push benchmark-driven method development that fosters advanced techniques for causal discovery, as is the case for many other areas of machine learning.
The phenomenon of "black swans" has posed a fundamental challenge to performance of classical machine learning models. The perceived rise in frequency of outlier conditions, especially in post-pandemic environment, has necessitated exploration of synthetic data as a complement to real data in model training. This article provides a general overview and experimental investigation of the zGAN model architecture developed for the purpose of generating synthetic tabular data with outlier characteristics. The model is put to test in binary classification environments and shows promising results on realistic synthetic data generation, as well as uplift capabilities vis-\`a-vis model performance. A distinctive feature of zGAN is its enhanced correlation capability between features in the generated data, replicating correlations of features in real training data. Furthermore, crucial is the ability of zGAN to generate outliers based on covariance of real data or synthetically generated covariances. This approach to outlier generation enables modeling of complex economic events and augmentation of outliers for tasks such as training predictive models and detecting, processing or removing outliers. Experiments and comparative analyses as part of this study were conducted on both private (credit risk in financial services) and public datasets.
Generative models have been found effective for data synthesis due to their ability to capture complex underlying data distributions. The quality of generated data from these models is commonly evaluated by visual inspection for image datasets or downstream analytical tasks for tabular datasets. These evaluation methods neither measure the implicit data distribution nor consider the data privacy issues, and it remains an open question of how to compare and rank different generative models. Medical data can be sensitive, so it is of great importance to draw privacy concerns of patients while maintaining the data utility of the synthetic dataset. Beyond the utility evaluation, this work outlines two metrics called Similarity and Uniqueness for sample-wise assessment of synthetic datasets. We demonstrate the proposed notions with several state-of-the-art generative models to synthesise Cystic Fibrosis (CF) patients' electronic health records (EHRs), observing that the proposed metrics are suitable for synthetic data evaluation and generative model comparison.
The switch from a Model-Centric to a Data-Centric mindset is putting emphasis on data and its quality rather than algorithms, bringing forward new challenges. In particular, the sensitive nature of the information in highly regulated scenarios needs to be accounted for. Specific approaches to address the privacy issue have been developed, as Privacy Enhancing Technologies. However, they frequently cause loss of information, putting forward a crucial trade-off among data quality and privacy. A clever way to bypass such a conundrum relies on Synthetic Data: data obtained from a generative process, learning the real data properties. Both Academia and Industry realized the importance of evaluating synthetic data quality: without all-round reliable metrics, the innovative data generation task has no proper objective function to maximize. Despite that, the topic remains under-explored. For this reason, we systematically catalog the important traits of synthetic data quality and privacy, and devise a specific methodology to test them. The result is DAISYnt (aDoption of Artificial Intelligence SYnthesis): a comprehensive suite of advanced tests, which sets a de facto standard for synthetic data evaluation. As a practical use-case, a variety of generative algorithms have been trained on real-world Credit Bureau Data. The best model has been assessed, using DAISYnt on the different synthetic replicas. Further potential uses, among others, entail auditing and fine-tuning of generative models or ensuring high quality of a given synthetic dataset. From a prescriptive viewpoint, eventually, DAISYnt may pave the way to synthetic data adoption in highly regulated domains, ranging from Finance to Healthcare, through Insurance and Education.
Non-negative tensor factorization models enable predictive analysis on count data. Among them, Bayesian Poisson-Gamma models can derive full posterior distributions of latent factors and are less sensitive to sparse count data. However, current inference methods for these Bayesian models adopt restricted update rules for the posterior parameters. They also fail to share the update information to better cope with the data sparsity. Moreover, these models are not endowed with a component that handles the imbalance in count data values. In this paper, we propose a novel variational auto-encoder framework called VAE-BPTF which addresses the above issues. It uses multi-layer perceptron networks to encode and share complex update information. The encoded information is then reweighted per data instance to penalize common data values before aggregated to compute the posterior parameters for the latent factors. Under synthetic data evaluation, VAE-BPTF tended to recover the right number of latent factors and posterior parameter values. It also outperformed current models in both reconstruction errors and latent factor (semantic) coherence across five real-world datasets. Furthermore, the latent factors inferred by VAE-BPTF are perceived to be meaningful and coherent under a qualitative analysis.