Jonathan Passerat-Palmbach

Vasilis Siomos, Jonathan Passerat-Palmbach

Federated Learning (FL) has seen increasing interest in cases where entities want to collaboratively train models while maintaining privacy and governance over their data. In FL, clients with private and potentially heterogeneous data and compute resources come together to train a common model without raw data ever leaving their locale. Instead, the participants contribute by sharing local model updates, which, naturally, differ in quality. Quantitatively evaluating the worth of these contributions is termed the Contribution Evaluation (CE) problem. We review current CE approaches from the underlying mathematical framework to efficiently calculate a fair value for each client. Furthermore, we benchmark some of the most promising state-of-the-art approaches, along with a new one we introduce, on MNIST and CIFAR-10, to showcase their differences. Designing a fair and efficient CE method, while a small part of the overall FL system design, is tantamount to the mainstream adoption of FL.

Xinyuan Sun, Davide Crapis, Matt Stephenson et al.

Credible commitment devices have been a popular approach for robust multi-agent coordination. However, existing commitment mechanisms face limitations like privacy, integrity, and susceptibility to mediator or user strategic behavior. It is unclear if the cooperative AI techniques we study are robust to real-world incentives and attack vectors. However, decentralized commitment devices that utilize cryptography have been deployed in the wild, and numerous studies have shown their ability to coordinate algorithmic agents facing adversarial opponents with significant economic incentives, currently in the order of several million to billions of dollars. In this paper, we use examples in the decentralization and, in particular, Maximal Extractable Value (MEV) (arXiv:1904.05234) literature to illustrate the potential security issues in cooperative AI. We call for expanded research into decentralized commitments to advance cooperative AI capabilities for secure coordination in open environments and empirical testing frameworks to evaluate multi-agent coordination ability given real-world commitment constraints.

Vasilis Siomos, Sergio Naval-Marimont, Jonathan Passerat-Palmbach et al.

Federated Learning (FL) is a collaborative training paradigm that allows for privacy-preserving learning of cross-institutional models by eliminating the exchange of sensitive data and instead relying on the exchange of model parameters between the clients and a server. Despite individual studies on how client models are aggregated, and, more recently, on the benefits of ImageNet pre-training, there is a lack of understanding of the effect the architecture chosen for the federation has, and of how the aforementioned elements interconnect. To this end, we conduct the first joint ARchitecture-Initialization-Aggregation study and benchmark ARIAs across a range of medical image classification tasks. We find that, contrary to current practices, ARIA elements have to be chosen together to achieve the best possible performance. Our results also shed light on good choices for each element depending on the task, the effect of normalisation layers, and the utility of SSL pre-training, pointing to potential directions for designing FL-specific architectures and training pipelines.

Asia Belfiore, Jonathan Passerat-Palmbach, Dmitrii Usynin

The increased availability of genetic data has transformed genomics research, but raised many privacy concerns regarding its handling due to its sensitive nature. This work explores the use of language models (LMs) for the generation of synthetic genetic mutation profiles, leveraging differential privacy (DP) for the protection of sensitive genetic data. We empirically evaluate the privacy guarantees of our DP modes by introducing a novel Biologically-Informed Hybrid Membership Inference Attack (biHMIA), which combines traditional black box MIA with contextual genomics metrics for enhanced attack power. Our experiments show that both small and large transformer GPT-like models are viable synthetic variant generators for small-scale genomics, and that our hybrid attack leads, on average, to higher adversarial success compared to traditional metric-based MIAs.

Akis Linardos, Sarthak Pati, Ujjwal Baid et al.

We present the design and results of the MICCAI Federated Tumor Segmentation (FeTS) Challenge 2024, which focuses on federated learning (FL) for glioma sub-region segmentation in multi-parametric MRI and evaluates new weight aggregation methods aimed at improving robustness and efficiency. Six participating teams were evaluated using a standardized FL setup and a multi-institutional dataset derived from the BraTS glioma benchmark, consisting of 1,251 training cases, 219 validation cases, and 570 hidden test cases with segmentations for enhancing tumor (ET), tumor core (TC), and whole tumor (WT). Teams were ranked using a cumulative scoring system that considered both segmentation performance, measured by Dice Similarity Coefficient (DSC) and the 95th percentile Hausdorff Distance (HD95), and communication efficiency assessed through the convergence score. A PID-controller-based method achieved the top overall ranking, obtaining mean DSC values of 0.733, 0.761, and 0.751 for ET, TC, and WT, respectively, with corresponding HD95 values of 33.922 mm, 33.623 mm, and 32.309 mm, while also demonstrating the highest communication efficiency with a convergence score of 0.764. These findings advance the state of federated learning for medical imaging, surpassing top-performing methods from previous challenge iterations and highlighting PID controllers as effective mechanisms for stabilizing and optimizing weight aggregation in FL. The challenge code is available at https://github.com/FeTS-AI/Challenge.

Vasilis Siomos, Jonathan Passerat-Palmbach, Giacomo Tarroni

Federated learning is a decentralized training approach that keeps data under stakeholder control while achieving superior performance over isolated training. While inter-institutional feature discrepancies pose a challenge in all federated settings, medical imaging is particularly affected due to diverse imaging devices and population variances, which can diminish the global model's effectiveness. Existing aggregation methods generally fail to adapt across varied circumstances. To address this, we propose FedCLAM, which integrates \textit{client-adaptive momentum} terms derived from each client's loss reduction during local training, as well as a \textit{personalized dampening factor} to curb overfitting. We further introduce a novel \textit{intensity alignment} loss that matches predicted and ground-truth foreground distributions to handle heterogeneous image intensity profiles across institutions and devices. Extensive evaluations on two datasets show that FedCLAM surpasses eight cutting-edge methods in medical segmentation tasks, underscoring its efficacy. The code is available at https://github.com/siomvas/FedCLAM.

Bianca-Mihaela Ganescu, Jonathan Passerat-Palmbach

Generative AI, exemplified by models like transformers, has opened up new possibilities in various domains but also raised concerns about fairness, transparency and reliability, especially in fields like medicine and law. This paper emphasizes the urgency of ensuring fairness and quality in these domains through generative AI. It explores using cryptographic techniques, particularly Zero-Knowledge Proofs (ZKPs), to address concerns regarding performance fairness and accuracy while protecting model privacy. Applying ZKPs to Machine Learning models, known as ZKML (Zero-Knowledge Machine Learning), enables independent validation of AI-generated content without revealing sensitive model information, promoting transparency and trust. ZKML enhances AI fairness by providing cryptographic audit trails for model predictions and ensuring uniform performance across users. We introduce snarkGPT, a practical ZKML implementation for transformers, to empower users to verify output accuracy and quality while preserving model privacy. We present a series of empirical results studying snarkGPT's scalability and performance to assess the feasibility and challenges of adopting a ZKML-powered approach to capture quality and performance fairness problems in generative AI models.

Olivia Ma, Jonathan Passerat-Palmbach, Dmitrii Usynin

Fine-tuning large language models (LLMs) for specific tasks introduces privacy risks, as models may inadvertently memorise and leak sensitive training data. While Differential Privacy (DP) offers a solution to mitigate these risks, it introduces significant computational and performance trade-offs, particularly with standard fine-tuning approaches. Previous work has primarily focused on full-parameter updates, which are computationally intensive and may not fully leverage DPs potential in large models. In this work, we address these shortcomings by investigating Parameter-Efficient Fine-Tuning (PEFT) methods under DP constraints. We show that PEFT methods achieve comparable performance to standard fine-tuning while requiring fewer parameters and significantly reducing privacy leakage. Furthermore, we incorporate a data poisoning experiment involving intentional mislabelling to assess model memorisation and directly measure privacy risks. Our findings indicate that PEFT methods not only provide a promising alternative but also serve as a complementary approach for privacy-preserving, resource-efficient fine-tuning of LLMs.

George-Liviu Pereteanu, Amir Alansary, Jonathan Passerat-Palmbach

This work presents a novel protocol for fast secure inference of neural networks applied to computer vision applications. It focuses on improving the overall performance of the online execution by deploying a subset of the model weights in plaintext on the client's machine, in the fashion of SplitNNs. We evaluate our protocol on benchmark neural networks trained on the CIFAR-10 dataset using SEAL via TenSEAL and discuss runtime and security performances. Empirical security evaluation using Membership Inference and Model Extraction attacks showed that the protocol was more resilient under the same attacks than a similar approach also based on SplitNN. When compared to related work, we demonstrate improvements of 2.5x-10x for the inference time and 14x-290x in communication costs.

Dmitrii Usynin, Alexander Ziller, Daniel Rueckert et al.

The utilisation of large and diverse datasets for machine learning (ML) at scale is required to promote scientific insight into many meaningful problems. However, due to data governance regulations such as GDPR as well as ethical concerns, the aggregation of personal and sensitive data is problematic, which prompted the development of alternative strategies such as distributed ML (DML). Techniques such as Federated Learning (FL) allow the data owner to maintain data governance and perform model training locally without having to share their data. FL and related techniques are often described as privacy-preserving. We explain why this term is not appropriate and outline the risks associated with over-reliance on protocols that were not designed with formal definitions of privacy in mind. We further provide recommendations and examples on how such algorithms can be augmented to provide guarantees of governance, security, privacy and verifiability for a general ML audience without prior exposure to formal privacy techniques.

Stefán Páll Sturluson, Samuel Trew, Luis Muñoz-González et al.

The robustness of federated learning (FL) is vital for the distributed training of an accurate global model that is shared among large number of clients. The collaborative learning framework by typically aggregating model updates is vulnerable to model poisoning attacks from adversarial clients. Since the shared information between the global server and participants are only limited to model parameters, it is challenging to detect bad model updates. Moreover, real-world datasets are usually heterogeneous and not independent and identically distributed (Non-IID) among participants, which makes the design of such robust FL pipeline more difficult. In this work, we propose a novel robust aggregation method, Federated Robust Adaptive Distillation (FedRAD), to detect adversaries and robustly aggregate local models based on properties of the median statistic, and then performing an adapted version of ensemble Knowledge Distillation. We run extensive experiments to evaluate the proposed method against recently published works. The results show that FedRAD outperforms all other aggregators in the presence of adversaries, as well as in heterogeneous data distributions.

Ashly Lau, Jonathan Passerat-Palmbach

Differential privacy provides strong privacy guarantees for machine learning applications. Much recent work has been focused on developing differentially private models, however there has been a gap in other stages of the machine learning pipeline, in particular during the preprocessing phase. Our contributions are twofold: we adapt a privacy violation detection framework based on statistical methods to empirically measure privacy levels of machine learning pipelines, and apply the newly created framework to show that resampling techniques used when dealing with imbalanced datasets cause the resultant model to leak more privacy. These results highlight the need for developing private preprocessing techniques.

Alexander Ziller, Jonathan Passerat-Palmbach, Théo Ryffel et al.

The utilisation of artificial intelligence in medicine and healthcare has led to successful clinical applications in several domains. The conflict between data usage and privacy protection requirements in such systems must be resolved for optimal results as well as ethical and legal compliance. This calls for innovative solutions such as privacy-preserving machine learning (PPML). We present PriMIA (Privacy-preserving Medical Image Analysis), a software framework designed for PPML in medical imaging. In a real-life case study we demonstrate significantly better classification performance of a securely aggregated federated learning model compared to human experts on unseen datasets. Furthermore, we show an inference-as-a-service scenario for end-to-end encrypted diagnosis, where neither the data nor the model are revealed. Lastly, we empirically evaluate the framework's security against a gradient-based model inversion attack and demonstrate that no usable information can be recovered from the model.

Harry Cai, Daniel Rueckert, Jonathan Passerat-Palmbach

Federated Learning harnesses data from multiple sources to build a single model. While the initial model might belong solely to the actor bringing it to the network for training, determining the ownership of the trained model resulting from Federated Learning remains an open question. In this paper we explore how Blockchains (in particular Ethereum) can be used to determine the evolving ownership of a model trained with Federated Learning. Firstly, we use the step-by-step evaluation metric to assess the relative contributivities of participants in a Federated Learning process. Next, we introduce 2CP, a framework comprising two novel protocols for Blockchained Federated Learning, which both reward contributors with shares in the final model based on their relative contributivity. The Crowdsource Protocol allows an actor to bring a model forward for training, and use their own data to evaluate the contributions made to it. Potential trainers are guaranteed a fair share of the resulting model, even in a trustless setting. The Consortium Protocol gives trainers the same guarantee even when no party owns the initial model and no evaluator is available. We conduct experiments with the MNIST dataset that reveal sound contributivity scores resulting from both Protocols by rewarding larger datasets with greater shares in the model. Our experiments also showed the necessity to pair 2CP with a robust model aggregation mechanism to discard low quality inputs coming from model poisoning attacks.

Veneta Haralampieva, Daniel Rueckert, Jonathan Passerat-Palmbach

This work provides a comprehensive review of existing frameworks based on secure computing techniques in the context of private image classification. The in-depth analysis of these approaches is followed by careful examination of their performance costs, in particular runtime and communication overhead. To further illustrate the practical considerations when using different privacy-preserving technologies, experiments were conducted using four state-of-the-art libraries implementing secure computing at the heart of the data science stack: PySyft and CrypTen supporting private inference via Secure Multi-Party Computation, TF-Trusted utilising Trusted Execution Environments and HE- Transformer relying on Homomorphic encryption. Our work aims to evaluate the suitability of these frameworks from a usability, runtime requirements and accuracy point of view. In order to better understand the gap between state-of-the-art protocols and what is currently available in practice for a data scientist, we designed three neural network architecture to obtain secure predictions via each of the four aforementioned frameworks. Two networks were evaluated on the MNIST dataset and one on the Malaria Cell image dataset. We observed satisfying performances for TF-Trusted and CrypTen and noted that all frameworks perfectly preserved the accuracy of the corresponding plaintext model.

Matei Grama, Maria Musat, Luis Muñoz-González et al.

Federated learning (FL) has enabled training models collaboratively from multiple data owning parties without sharing their data. Given the privacy regulations of patient's healthcare data, learning-based systems in healthcare can greatly benefit from privacy-preserving FL approaches. However, typical model aggregation methods in FL are sensitive to local model updates, which may lead to failure in learning a robust and accurate global model. In this work, we implement and evaluate different robust aggregation methods in FL applied to healthcare data. Furthermore, we show that such methods can detect and discard faulty or malicious local clients during training. We run two sets of experiments using two real-world healthcare datasets for training medical diagnosis classification tasks. Each dataset is used to simulate the performance of three different robust FL aggregation strategies when facing different poisoning attacks. The results show that privacy preserving methods can be successfully applied alongside Byzantine-robust aggregation techniques. We observed in particular how using differential privacy (DP) did not significantly impact the final learning convergence of the different aggregation strategies.

Jonathan Passerat-Palmbach, Tyler Farnan, Robert Miller et al.

We propose a novel architecture for federated learning within healthcare consortia. At the heart of the solution is a unique integration of privacy preserving technologies, built upon native enterprise blockchain components available in the Ethereum ecosystem. We show how the specific characteristics and challenges of healthcare consortia informed our design choices, notably the conception of a new Secure Aggregation protocol assembled with a protected hardware component and an encryption toolkit native to Ethereum. Our architecture also brings in a privacy preserving audit trail that logs events in the network without revealing identities.

Theo Ryffel, Andrew Trask, Morten Dahl et al.

We detail a new framework for privacy preserving deep learning and discuss its assets. The framework puts a premium on ownership and secure processing of data and introduces a valuable representation based on chains of commands and tensors. This abstraction allows one to implement complex privacy preserving constructs such as Federated Learning, Secure Multiparty Computation, and Differential Privacy while still exposing a familiar deep learning API to the end-user. We report early results on the Boston Housing and Pima Indian Diabetes datasets. While the privacy features apart from Differential Privacy do not impact the prediction accuracy, the current implementation of the framework introduces a significant overhead in performance, which will be addressed at a later stage of the development. We believe this work is an important milestone introducing the first reliable, general framework for privacy preserving deep learning.

Amir Alansary, Loic Le Folgoc, Ghislain Vaillant et al.

We propose a fully automatic method to find standardized view planes in 3D image acquisitions. Standard view images are important in clinical practice as they provide a means to perform biometric measurements from similar anatomical regions. These views are often constrained to the native orientation of a 3D image acquisition. Navigating through target anatomy to find the required view plane is tedious and operator-dependent. For this task, we employ a multi-scale reinforcement learning (RL) agent framework and extensively evaluate several Deep Q-Network (DQN) based strategies. RL enables a natural learning paradigm by interaction with the environment, which can be used to mimic experienced operators. We evaluate our results using the distance between the anatomical landmarks and detected planes, and the angles between their normal vector and target. The proposed algorithm is assessed on the mid-sagittal and anterior-posterior commissure planes of brain MRI, and the 4-chamber long-axis plane commonly used in cardiac MRI, achieving accuracy of 1.53mm, 1.98mm and 4.84mm, respectively.

Giacomo Tarroni, Ozan Oktay, Wenjia Bai et al.

The effectiveness of a cardiovascular magnetic resonance (CMR) scan depends on the ability of the operator to correctly tune the acquisition parameters to the subject being scanned and on the potential occurrence of imaging artefacts such as cardiac and respiratory motion. In the clinical practice, a quality control step is performed by visual assessment of the acquired images: however, this procedure is strongly operator-dependent, cumbersome and sometimes incompatible with the time constraints in clinical settings and large-scale studies. We propose a fast, fully-automated, learning-based quality control pipeline for CMR images, specifically for short-axis image stacks. Our pipeline performs three important quality checks: 1) heart coverage estimation, 2) inter-slice motion detection, 3) image contrast estimation in the cardiac region. The pipeline uses a hybrid decision forest method - integrating both regression and structured classification models - to extract landmarks as well as probabilistic segmentation maps from both long- and short-axis images as a basis to perform the quality checks. The technique was tested on up to 3000 cases from the UK Biobank as well as on 100 cases from the UK Digital Heart Project, and validated against manual annotations and visual inspections performed by expert interpreters. The results show the capability of the proposed pipeline to correctly detect incomplete or corrupted scans (e.g. on UK Biobank, sensitivity and specificity respectively 88% and 99% for heart coverage estimation, 85% and 95% for motion detection), allowing their exclusion from the analysed dataset or the triggering of a new acquisition.

Martin Rajchl, Lisa M. Koch, Christian Ledig et al.

To efficiently establish training databases for machine learning methods, collaborative and crowdsourcing platforms have been investigated to collectively tackle the annotation effort. However, when this concept is ported to the medical imaging domain, reading expertise will have a direct impact on the annotation accuracy. In this study, we examine the impact of expertise and the amount of available annotations on the accuracy outcome of a liver segmentation problem in an abdominal computed tomography (CT) image database. In controlled experiments, we study this impact for different types of weak annotations. To address the decrease in accuracy associated with lower expertise, we propose a method for outlier correction making use of a weakly labelled atlas. Using this approach, we demonstrate that weak annotations subject to high error rates can achieve a similarly high accuracy as state-of-the-art multi-atlas segmentation approaches relying on a large amount of expert manual segmentations. Annotations of this nature can realistically be obtained from a non-expert crowd and can potentially enable crowdsourcing of weak annotation tasks for medical image analysis.

Sofia Ira Ktena, Sarah Parisot, Jonathan Passerat-Palmbach et al.

Graph theory has drawn a lot of attention in the field of Neuroscience during the last decade, mainly due to the abundance of tools that it provides to explore the interactions of elements in a complex network like the brain. The local and global organization of a brain network can shed light on mechanisms of complex cognitive functions, while disruptions within the network can be linked to neurodevelopmental disorders. In this effort, the construction of a representative brain network for each individual is critical for further analysis. Additionally, graph comparison is an essential step for inference and classification analyses on brain graphs. In this work we explore a method based on graph edit distance for evaluating graph similarity, when correspondences between network elements are unknown due to different underlying subdivisions of the brain. We test this method on 30 unrelated subjects as well as 40 twin pairs and show that this method can accurately reflect the higher similarity between two related networks compared to unrelated ones, while identifying node correspondences.

Sarah Parisot, Jonathan Passerat-Palmbach, Markus D. Schirmer et al.

Understanding brain connectivity in a network-theoretic context has shown much promise in recent years. This type of analysis identifies brain organisational principles, bringing a new perspective to neuroscience. At the same time, large public databases of connectomic data are now available. However, connectome analysis is still an emerging field and there is a crucial need for robust computational methods to fully unravelits potential. This workshop provides a platform to discuss the development of new analytic techniques; methods for evaluating and validating commonly used approaches; as well as the effects of variations in pre-processing steps.

Martin Rajchl, Matthew C. H. Lee, Franklin Schrans et al.

The availability of training data for supervision is a frequently encountered bottleneck of medical image analysis methods. While typically established by a clinical expert rater, the increase in acquired imaging data renders traditional pixel-wise segmentations less feasible. In this paper, we examine the use of a crowdsourcing platform for the distribution of super-pixel weak annotation tasks and collect such annotations from a crowd of non-expert raters. The crowd annotations are subsequently used for training a fully convolutional neural network to address the problem of fetal brain segmentation in T2-weighted MR images. Using this approach we report encouraging results compared to highly targeted, fully supervised methods and potentially address a frequent problem impeding image analysis research.

Martin Rajchl, Matthew C. H. Lee, Ozan Oktay et al.

In this paper, we propose DeepCut, a method to obtain pixelwise object segmentations given an image dataset labelled with bounding box annotations. It extends the approach of the well-known GrabCut method to include machine learning by training a neural network classifier from bounding box annotations. We formulate the problem as an energy minimisation problem over a densely-connected conditional random field and iteratively update the training targets to obtain pixelwise object segmentations. Additionally, we propose variants of the DeepCut method and compare those to a naive approach to CNN training under weak supervision. We test its applicability to solve brain and lung segmentation problems on a challenging fetal magnetic resonance dataset and obtain encouraging results in terms of accuracy.

Lisa M. Koch, Martin Rajchl, Wenjia Bai et al.

Multi-atlas segmentation is a widely used tool in medical image analysis, providing robust and accurate results by learning from annotated atlas datasets. However, the availability of fully annotated atlas images for training is limited due to the time required for the labelling task. Segmentation methods requiring only a proportion of each atlas image to be labelled could therefore reduce the workload on expert raters tasked with annotating atlas images. To address this issue, we first re-examine the labelling problem common in many existing approaches and formulate its solution in terms of a Markov Random Field energy minimisation problem on a graph connecting atlases and the target image. This provides a unifying framework for multi-atlas segmentation. We then show how modifications in the graph configuration of the proposed framework enable the use of partially annotated atlas images and investigate different partial annotation strategies. The proposed method was evaluated on two Magnetic Resonance Imaging (MRI) datasets for hippocampal and cardiac segmentation. Experiments were performed aimed at (1) recreating existing segmentation techniques with the proposed framework and (2) demonstrating the potential of employing sparsely annotated atlas data for multi-atlas segmentation.