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Jim Achterberg

Publications and source records attributed to Jim Achterberg.

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XGenBoost: Synthesizing Small and Large Tabular Datasets with XGBoost

Tree ensembles such as XGBoost are often preferred for discriminative tasks in mixed-type tabular data, due to their inductive biases, minimal hyperparameter tuning, and training efficiency. We argue that these qualities, when leveraged correctly, can make for better generative models as well. As such, we present XGenBoost, a pair of generative models based on XGBoost: i) a Denoising Diffusion Implicit Model (DDIM) with XGBoost as score-estimator suited for smaller datasets, and ii) a hierarchical autoregressive model whose conditionals are learned via XGBoost classifiers, suited for large-scale tabular synthesis. The architectures follow from the natural constraints imposed by tree-based learners, e.g., in the diffusion model, combining Gaussian and multinomial diffusion to leverage native categorical splits and avoid one-hot encoding while accurately modelling mixed data types. In the autoregressive model, we use a fixed-order factorization, a hierarchical classifier to impose ordinal inductive biases when modelling numerical features, and de-quantization based on empirical quantile functions to model the non-continuous nature of most real-world tabular datasets. Through two benchmarks, one containing smaller and the other larger datasets, we show that our proposed architectures outperform previous neural- and tree-based generative models for mixed-type tabular synthesis at lower training cost.

cs.LG

OpenExtract: Automated Data Extraction for Systematic Reviews in Health

This study presents OpenExtract, an open-source pipeline for automated data extraction in large-scale systematic literature reviews. The pipeline queries large language models (LLMs) to predict data entries based on relevant sections of scientific articles. To test the efficacy of OpenExtract, we apply it to a systematic literature review in digital health and compare its outputs with those of human researchers. OpenExtract achieves precision and recall scores of > 0.8 in this task, indicating that it can be effective at extracting data automatically and efficiently. OpenExtract: https://github.com/JimAchterbergLUMC/OpenExtract.

cs.IR

The Data Sharing Paradox of Synthetic Data in Healthcare

Synthetic data offers a promising solution to privacy concerns in healthcare by generating useful datasets in a privacy-aware manner. However, although synthetic data is typically developed with the intention of sharing said data, ambiguous reidentification risk assessments often prevent synthetic data from seeing the light of day. One of the main causes is that privacy metrics for synthetic data, which inform on reidentification risks, are not well-aligned with practical requirements and regulations regarding data sharing in healthcare. This article discusses the paradoxical situation where synthetic data is designed for data sharing but is often still restricted. We also discuss how the field should move forward to mitigate this issue.

cs.DB

A Novel Taxonomy for Navigating and Classifying Synthetic Data in Healthcare Applications

Data-driven technologies have improved the efficiency, reliability and effectiveness of healthcare services, but come with an increasing demand for data, which is challenging due to privacy-related constraints on sharing data in healthcare contexts. Synthetic data has recently gained popularity as potential solution, but in the flurry of current research it can be hard to oversee its potential. This paper proposes a novel taxonomy of synthetic data in healthcare to navigate the landscape in terms of three main varieties. Data Proportion comprises different ratios of synthetic data in a dataset and associated pros and cons. Data Modality refers to the different data formats amenable to synthesis and format-specific challenges. Data Transformation concerns improving specific aspects of a dataset like its utility or privacy with synthetic data. Our taxonomy aims to help researchers in the healthcare domain interested in synthetic data to grasp what types of datasets, data modalities, and transformations are possible with synthetic data, and where the challenges and overlaps between the varieties lie.

cs.CY