PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modelling and machine learning

Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for allowing researchers to make optimal use of their research effort. The tools presented here are useful for collating existing public cryoEM datasets and/or creating new synthetic cryoEM datasets to aid the development of novel data processing and interpretation algorithms. In recent years, structural biology has seen the development of a multitude of machine-learning based algorithms for aiding numerous steps in the processing and reconstruction of experimental datasets and the use of these approaches has become widespread. Developing such techniques in structural biology requires access to large datasets which can be cumbersome to curate and unwieldy to make use of. In this paper we present a suite of Python software packages which we collectively refer to as PERC (profet, EMPIARreader and CAKED). These are designed to reduce the burden which data curation places upon structural biology research. The protein structure fetcher (profet) package allows users to conveniently download and cleave sequences or structures from the Protein Data Bank or Alphafold databases. EMPIARreader allows lazy loading of Electron Microscopy Public Image Archive datasets in a machine-learning compatible structure. The Class Aggregator for Key Electron-microscopy Data (CAKED) package is designed to seamlessly facilitate the training of machine learning models on electron microscopy data, including electron-cryo-microscopy-specific data augmentation and labelling. These packages may be utilised independently or as building blocks in workflows. All are available in open source repositories and designed to be easily extensible to facilitate more advanced workflows if required.

TAPAS: a Toolbox for Adversarial Privacy Auditing of Synthetic Data

Personal data collected at scale promises to improve decision-making and accelerate innovation. However, sharing and using such data raises serious privacy concerns. A promising solution is to produce synthetic data, artificial records to share instead of real data. Since synthetic records are not linked to real persons, this intuitively prevents classical re-identification attacks. However, this is insufficient to protect privacy. We here present TAPAS, a toolbox of attacks to evaluate synthetic data privacy under a wide range of scenarios. These attacks include generalizations of prior works and novel attacks. We also introduce a general framework for reasoning about privacy threats to synthetic data and showcase TAPAS on several examples.