Sofia Ira Ktena

Ira Ktena, Olivia Wiles, Isabela Albuquerque et al. · deepmind

A ubiquitous challenge in machine learning is the problem of domain generalisation. This can exacerbate bias against groups or labels that are underrepresented in the datasets used for model development. Model bias can lead to unintended harms, especially in safety-critical applications like healthcare. Furthermore, the challenge is compounded by the difficulty of obtaining labelled data due to high cost or lack of readily available domain expertise. In our work, we show that learning realistic augmentations automatically from data is possible in a label-efficient manner using generative models. In particular, we leverage the higher abundance of unlabelled data to capture the underlying data distribution of different conditions and subgroups for an imaging modality. By conditioning generative models on appropriate labels, we can steer the distribution of synthetic examples according to specific requirements. We demonstrate that these learned augmentations can surpass heuristic ones by making models more robust and statistically fair in- and out-of-distribution. To evaluate the generality of our approach, we study 3 distinct medical imaging contexts of varying difficulty: (i) histopathology images from a publicly available generalisation benchmark, (ii) chest X-rays from publicly available clinical datasets, and (iii) dermatology images characterised by complex shifts and imaging conditions. Complementing real training samples with synthetic ones improves the robustness of models in all three medical tasks and increases fairness by improving the accuracy of diagnosis within underrepresented groups. This approach leads to stark improvements OOD across modalities: 7.7% prediction accuracy improvement in histopathology, 5.2% in chest radiology with 44.6% lower fairness gap and a striking 63.5% improvement in high-risk sensitivity for dermatology with a 7.5x reduction in fairness gap.

Sahra Ghalebikesabi, Leonard Berrada, Sven Gowal et al. · deepmind

The ability to generate privacy-preserving synthetic versions of sensitive image datasets could unlock numerous ML applications currently constrained by data availability. Due to their astonishing image generation quality, diffusion models are a prime candidate for generating high-quality synthetic data. However, recent studies have found that, by default, the outputs of some diffusion models do not preserve training data privacy. By privately fine-tuning ImageNet pre-trained diffusion models with more than 80M parameters, we obtain SOTA results on CIFAR-10 and Camelyon17 in terms of both FID and the accuracy of downstream classifiers trained on synthetic data. We decrease the SOTA FID on CIFAR-10 from 26.2 to 9.8, and increase the accuracy from 51.0% to 88.0%. On synthetic data from Camelyon17, we achieve a downstream accuracy of 91.1% which is close to the SOTA of 96.5% when training on the real data. We leverage the ability of generative models to create infinite amounts of data to maximise the downstream prediction performance, and further show how to use synthetic data for hyperparameter tuning. Our results demonstrate that diffusion models fine-tuned with differential privacy can produce useful and provably private synthetic data, even in applications with significant distribution shift between the pre-training and fine-tuning distributions.

Tao Tu, Shekoofeh Azizi, Danny Driess et al.

Medicine is inherently multimodal, with rich data modalities spanning text, imaging, genomics, and more. Generalist biomedical artificial intelligence (AI) systems that flexibly encode, integrate, and interpret this data at scale can potentially enable impactful applications ranging from scientific discovery to care delivery. To enable the development of these models, we first curate MultiMedBench, a new multimodal biomedical benchmark. MultiMedBench encompasses 14 diverse tasks such as medical question answering, mammography and dermatology image interpretation, radiology report generation and summarization, and genomic variant calling. We then introduce Med-PaLM Multimodal (Med-PaLM M), our proof of concept for a generalist biomedical AI system. Med-PaLM M is a large multimodal generative model that flexibly encodes and interprets biomedical data including clinical language, imaging, and genomics with the same set of model weights. Med-PaLM M reaches performance competitive with or exceeding the state of the art on all MultiMedBench tasks, often surpassing specialist models by a wide margin. We also report examples of zero-shot generalization to novel medical concepts and tasks, positive transfer learning across tasks, and emergent zero-shot medical reasoning. To further probe the capabilities and limitations of Med-PaLM M, we conduct a radiologist evaluation of model-generated (and human) chest X-ray reports and observe encouraging performance across model scales. In a side-by-side ranking on 246 retrospective chest X-rays, clinicians express a pairwise preference for Med-PaLM M reports over those produced by radiologists in up to 40.50% of cases, suggesting potential clinical utility. While considerable work is needed to validate these models in real-world use cases, our results represent a milestone towards the development of generalist biomedical AI systems.

Ryutaro Tanno, David G. T. Barrett, Andrew Sellergren et al.

Radiology reports are an instrumental part of modern medicine, informing key clinical decisions such as diagnosis and treatment. The worldwide shortage of radiologists, however, restricts access to expert care and imposes heavy workloads, contributing to avoidable errors and delays in report delivery. While recent progress in automated report generation with vision-language models offer clear potential in ameliorating the situation, the path to real-world adoption has been stymied by the challenge of evaluating the clinical quality of AI-generated reports. In this study, we build a state-of-the-art report generation system for chest radiographs, $\textit{Flamingo-CXR}$, by fine-tuning a well-known vision-language foundation model on radiology data. To evaluate the quality of the AI-generated reports, a group of 16 certified radiologists provide detailed evaluations of AI-generated and human written reports for chest X-rays from an intensive care setting in the United States and an inpatient setting in India. At least one radiologist (out of two per case) preferred the AI report to the ground truth report in over 60$\%$ of cases for both datasets. Amongst the subset of AI-generated reports that contain errors, the most frequently cited reasons were related to the location and finding, whereas for human written reports, most mistakes were related to severity and finding. This disparity suggested potential complementarity between our AI system and human experts, prompting us to develop an assistive scenario in which Flamingo-CXR generates a first-draft report, which is subsequently revised by a clinician. This is the first demonstration of clinician-AI collaboration for report writing, and the resultant reports are assessed to be equivalent or preferred by at least one radiologist to reports written by experts alone in 80$\%$ of in-patient cases and 60$\%$ of intensive care cases.

Jannik Kossen, Cătălina Cangea, Eszter Vértes et al. · cambridge

We introduce a challenging decision-making task that we call active acquisition for multimodal temporal data (A2MT). In many real-world scenarios, input features are not readily available at test time and must instead be acquired at significant cost. With A2MT, we aim to learn agents that actively select which modalities of an input to acquire, trading off acquisition cost and predictive performance. A2MT extends a previous task called active feature acquisition to temporal decision making about high-dimensional inputs. We propose a method based on the Perceiver IO architecture to address A2MT in practice. Our agents are able to solve a novel synthetic scenario requiring practically relevant cross-modal reasoning skills. On two large-scale, real-world datasets, Kinetics-700 and AudioSet, our agents successfully learn cost-reactive acquisition behavior. However, an ablation reveals they are unable to learn adaptive acquisition strategies, emphasizing the difficulty of the task even for state-of-the-art models. Applications of A2MT may be impactful in domains like medicine, robotics, or finance, where modalities differ in acquisition cost and informativeness.

Ameya Velingker, Ali Kemal Sinop, Ira Ktena et al.

Graph Neural Networks (GNNs) have emerged as a powerful technique for learning on relational data. Owing to the relatively limited number of message passing steps they perform -- and hence a smaller receptive field -- there has been significant interest in improving their expressivity by incorporating structural aspects of the underlying graph. In this paper, we explore the use of affinity measures as features in graph neural networks, in particular measures arising from random walks, including effective resistance, hitting and commute times. We propose message passing networks based on these features and evaluate their performance on a variety of node and graph property prediction tasks. Our architecture has lower computational complexity, while our features are invariant to the permutations of the underlying graph. The measures we compute allow the network to exploit the connectivity properties of the graph, thereby allowing us to outperform relevant benchmarks for a wide variety of tasks, often with significantly fewer message passing steps. On one of the largest publicly available graph regression datasets, OGB-LSC-PCQM4Mv1, we obtain the best known single-model validation MAE at the time of writing.

Yana Hasson, Pauline Luc, Liliane Momeni et al.

In recent years, there has been a proliferation of spatiotemporal foundation models in different scientific disciplines. While promising, these models are often domain-specific and are only assessed within the particular applications for which they are designed. Given that many tasks can be represented as video modeling problems, video foundation models (ViFMs) hold considerable promise as general-purpose domain-agnostic approaches. However, it is not known whether the knowledge acquired on large-scale but potentially out-of-domain data can be effectively transferred across diverse scientific disciplines, and if a single, pretrained ViFM can be competitive with domain-specific baselines. To address this, we introduce SciVid, a comprehensive benchmark comprising five *Sci*entific *Vid*eo tasks, across medical computer vision, animal behavior, and weather forecasting. We adapt six leading ViFMs to SciVid using simple trainable readout modules, establishing strong baselines and demonstrating the potential for effective transfer learning. Specifically, we show that state-of-the-art results can be obtained in several applications by leveraging the general-purpose representations from ViFM backbones. Furthermore, our results reveal the limitations of existing ViFMs, and highlight opportunities for the development of generalizable models for high-impact scientific applications. We release our code at https://github.com/google-deepmind/scivid to facilitate further research in the development of ViFMs.

David Restrepo, Ira Ktena, Maria Vakalopoulou et al.

Clinical decision-making relies on the integrated analysis of medical images and the associated clinical reports. While Vision-Language Models (VLMs) can offer a unified framework for such tasks, they can exhibit strong biases toward one modality, frequently overlooking critical visual cues in favor of textual information. In this work, we introduce Selective Modality Shifting (SMS), a perturbation-based approach to quantify a model's reliance on each modality in binary classification tasks. By systematically swapping images or text between samples with opposing labels, we expose modality-specific biases. We assess six open-source VLMs-four generalist models and two fine-tuned for medical data-on two medical imaging datasets with distinct modalities: MIMIC-CXR (chest X-ray) and FairVLMed (scanning laser ophthalmoscopy). By assessing model performance and the calibration of every model in both unperturbed and perturbed settings, we reveal a marked dependency on text input, which persists despite the presence of complementary visual information. We also perform a qualitative attention-based analysis which further confirms that image content is often overshadowed by text details. Our findings highlight the importance of designing and evaluating multimodal medical models that genuinely integrate visual and textual cues, rather than relying on single-modality signals.

Pinelopi Papalampidi, Olivia Wiles, Ira Ktena et al.

Classifier-free guidance (CFG) is a cornerstone of text-to-image diffusion models, yet its effectiveness is limited by the use of static guidance scales. This "one-size-fits-all" approach fails to adapt to the diverse requirements of different prompts; moreover, prior solutions like gradient-based correction or fixed heuristic schedules introduce additional complexities and fail to generalize. In this work, we challeng this static paradigm by introducing a framework for dynamic CFG scheduling. Our method leverages online feedback from a suite of general-purpose and specialized small-scale latent-space evaluations, such as CLIP for alignment, a discriminator for fidelity and a human preference reward model, to assess generation quality at each step of the reverse diffusion process. Based on this feedback, we perform a greedy search to select the optimal CFG scale for each timestep, creating a unique guidance schedule tailored to every prompt and sample. We demonstrate the effectiveness of our approach on both small-scale models and the state-of-the-art Imagen 3, showing significant improvements in text alignment, visual quality, text rendering and numerical reasoning. Notably, when compared against the default Imagen 3 baseline, our method achieves up to 53.8% human preference win-rate for overall preference, a figure that increases up to to 55.5% on prompts targeting specific capabilities like text rendering. Our work establishes that the optimal guidance schedule is inherently dynamic and prompt-dependent, and provides an efficient and generalizable framework to achieve it.

Virginia Aglietti, Ira Ktena, Jessica Schrouff et al.

The sample efficiency of Bayesian optimization algorithms depends on carefully crafted acquisition functions (AFs) guiding the sequential collection of function evaluations. The best-performing AF can vary significantly across optimization problems, often requiring ad-hoc and problem-specific choices. This work tackles the challenge of designing novel AFs that perform well across a variety of experimental settings. Based on FunSearch, a recent work using Large Language Models (LLMs) for discovery in mathematical sciences, we propose FunBO, an LLM-based method that can be used to learn new AFs written in computer code by leveraging access to a limited number of evaluations for a set of objective functions. We provide the analytic expression of all discovered AFs and evaluate them on various global optimization benchmarks and hyperparameter optimization tasks. We show how FunBO identifies AFs that generalize well in and out of the training distribution of functions, thus outperforming established general-purpose AFs and achieving competitive performance against AFs that are customized to specific function types and are learned via transfer-learning algorithms.

Lin Yang, Shawn Xu, Andrew Sellergren et al.

Many clinical tasks require an understanding of specialized data, such as medical images and genomics, which is not typically found in general-purpose large multimodal models. Building upon Gemini's multimodal models, we develop several models within the new Med-Gemini family that inherit core capabilities of Gemini and are optimized for medical use via fine-tuning with 2D and 3D radiology, histopathology, ophthalmology, dermatology and genomic data. Med-Gemini-2D sets a new standard for AI-based chest X-ray (CXR) report generation based on expert evaluation, exceeding previous best results across two separate datasets by an absolute margin of 1% and 12%, where 57% and 96% of AI reports on normal cases, and 43% and 65% on abnormal cases, are evaluated as "equivalent or better" than the original radiologists' reports. We demonstrate the first ever large multimodal model-based report generation for 3D computed tomography (CT) volumes using Med-Gemini-3D, with 53% of AI reports considered clinically acceptable, although additional research is needed to meet expert radiologist reporting quality. Beyond report generation, Med-Gemini-2D surpasses the previous best performance in CXR visual question answering (VQA) and performs well in CXR classification and radiology VQA, exceeding SoTA or baselines on 17 of 20 tasks. In histopathology, ophthalmology, and dermatology image classification, Med-Gemini-2D surpasses baselines across 18 out of 20 tasks and approaches task-specific model performance. Beyond imaging, Med-Gemini-Polygenic outperforms the standard linear polygenic risk score-based approach for disease risk prediction and generalizes to genetically correlated diseases for which it has never been trained. Although further development and evaluation are necessary in the safety-critical medical domain, our results highlight the potential of Med-Gemini across a wide range of medical tasks.

Virginia Aglietti, Alan Malek, Ira Ktena et al.

We propose constrained causal Bayesian optimization (cCBO), an approach for finding interventions in a known causal graph that optimize a target variable under some constraints. cCBO first reduces the search space by exploiting the graph structure and, if available, an observational dataset; and then solves the restricted optimization problem by modelling target and constraint quantities using Gaussian processes and by sequentially selecting interventions via a constrained expected improvement acquisition function. We propose different surrogate models that enable to integrate observational and interventional data while capturing correlation among effects with increasing levels of sophistication. We evaluate cCBO on artificial and real-world causal graphs showing successful trade off between fast convergence and percentage of feasible interventions.

Olivia Wiles, Sven Gowal, Florian Stimberg et al.

Robustness to distribution shifts is critical for deploying machine learning models in the real world. Despite this necessity, there has been little work in defining the underlying mechanisms that cause these shifts and evaluating the robustness of algorithms across multiple, different distribution shifts. To this end, we introduce a framework that enables fine-grained analysis of various distribution shifts. We provide a holistic analysis of current state-of-the-art methods by evaluating 19 distinct methods grouped into five categories across both synthetic and real-world datasets. Overall, we train more than 85K models. Our experimental framework can be easily extended to include new methods, shifts, and datasets. We find, unlike previous work~\citep{Gulrajani20}, that progress has been made over a standard ERM baseline; in particular, pretraining and augmentations (learned or heuristic) offer large gains in many cases. However, the best methods are not consistent over different datasets and shifts.

Nicolas Sonnerat, Pengming Wang, Ira Ktena et al.

Large Neighborhood Search (LNS) is a combinatorial optimization heuristic that starts with an assignment of values for the variables to be optimized, and iteratively improves it by searching a large neighborhood around the current assignment. In this paper we consider a learning-based LNS approach for mixed integer programs (MIPs). We train a Neural Diving model to represent a probability distribution over assignments, which, together with an off-the-shelf MIP solver, generates an initial assignment. Formulating the subsequent search steps as a Markov Decision Process, we train a Neural Neighborhood Selection policy to select a search neighborhood at each step, which is searched using a MIP solver to find the next assignment. The policy network is trained using imitation learning. We propose a target policy for imitation that, given enough compute resources, is guaranteed to select the neighborhood containing the optimal next assignment amongst all possible choices for the neighborhood of a specified size. Our approach matches or outperforms all the baselines on five real-world MIP datasets with large-scale instances from diverse applications, including two production applications at Google. It achieves $2\times$ to $37.8\times$ better average primal gap than the best baseline on three of the datasets at large running times.

Vinod Nair, Sergey Bartunov, Felix Gimeno et al.

Mixed Integer Programming (MIP) solvers rely on an array of sophisticated heuristics developed with decades of research to solve large-scale MIP instances encountered in practice. Machine learning offers to automatically construct better heuristics from data by exploiting shared structure among instances in the data. This paper applies learning to the two key sub-tasks of a MIP solver, generating a high-quality joint variable assignment, and bounding the gap in objective value between that assignment and an optimal one. Our approach constructs two corresponding neural network-based components, Neural Diving and Neural Branching, to use in a base MIP solver such as SCIP. Neural Diving learns a deep neural network to generate multiple partial assignments for its integer variables, and the resulting smaller MIPs for un-assigned variables are solved with SCIP to construct high quality joint assignments. Neural Branching learns a deep neural network to make variable selection decisions in branch-and-bound to bound the objective value gap with a small tree. This is done by imitating a new variant of Full Strong Branching we propose that scales to large instances using GPUs. We evaluate our approach on six diverse real-world datasets, including two Google production datasets and MIPLIB, by training separate neural networks on each. Most instances in all the datasets combined have $10^3-10^6$ variables and constraints after presolve, which is significantly larger than previous learning approaches. Comparing solvers with respect to primal-dual gap averaged over a held-out set of instances, the learning-augmented SCIP is 2x to 10x better on all datasets except one on which it is $10^5$x better, at large time limits. To the best of our knowledge, ours is the first learning approach to demonstrate such large improvements over SCIP on both large-scale real-world application datasets and MIPLIB.

Dalin Guo, Sofia Ira Ktena, Ferenc Huszar et al.

Recommender systems trained in a continuous learning fashion are plagued by the feedback loop problem, also known as algorithmic bias. This causes a newly trained model to act greedily and favor items that have already been engaged by users. This behavior is particularly harmful in personalised ads recommendations, as it can also cause new campaigns to remain unexplored. Exploration aims to address this limitation by providing new information about the environment, which encompasses user preference, and can lead to higher long-term reward. In this work, we formulate a display advertising recommender as a contextual bandit and implement exploration techniques that require sampling from the posterior distribution of click-through-rates in a computationally tractable manner. Traditional large-scale deep learning models do not provide uncertainty estimates by default. We approximate these uncertainty measurements of the predictions by employing a bootstrapped model with multiple heads and dropout units. We benchmark a number of different models in an offline simulation environment using a publicly available dataset of user-ads engagements. We test our proposed deep Bayesian bandits algorithm in the offline simulation and online AB setting with large-scale production traffic, where we demonstrate a positive gain of our exploration model.

Caojin Zhang, Yicun Liu, Yuanpu Xie et al.

Deep Neural Networks (DNNs) with sparse input features have been widely used in recommender systems in industry. These models have large memory requirements and need a huge amount of training data. The large model size usually entails a cost, in the range of millions of dollars, for storage and communication with the inference services. In this paper, we propose a hybrid hashing method to combine frequency hashing and double hashing techniques for model size reduction, without compromising performance. We evaluate the proposed models on two product surfaces. In both cases, experiment results demonstrated that we can reduce the model size by around 90 % while keeping the performance on par with the original baselines.

Luca Belli, Sofia Ira Ktena, Alykhan Tejani et al.

Recommender systems constitute the core engine of most social network platforms nowadays, aiming to maximize user satisfaction along with other key business objectives. Twitter is no exception. Despite the fact that Twitter data has been extensively used to understand socioeconomic and political phenomena and user behaviour, the implicit feedback provided by users on Tweets through their engagements on the Home Timeline has only been explored to a limited extent. At the same time, there is a lack of large-scale public social network datasets that would enable the scientific community to both benchmark and build more powerful and comprehensive models that tailor content to user interests. By releasing an original dataset of 160 million Tweets along with engagement information, Twitter aims to address exactly that. During this release, special attention is drawn on maintaining compliance with existing privacy laws. Apart from user privacy, this paper touches on the key challenges faced by researchers and professionals striving to predict user engagements. It further describes the key aspects of the RecSys 2020 Challenge that was organized by ACM RecSys in partnership with Twitter using this dataset.

Sofia Ira Ktena, Alykhan Tejani, Lucas Theis et al.

One of the challenges in display advertising is that the distribution of features and click through rate (CTR) can exhibit large shifts over time due to seasonality, changes to ad campaigns and other factors. The predominant strategy to keep up with these shifts is to train predictive models continuously, on fresh data, in order to prevent them from becoming stale. However, in many ad systems positive labels are only observed after a possibly long and random delay. These delayed labels pose a challenge to data freshness in continuous training: fresh data may not have complete label information at the time they are ingested by the training algorithm. Naive strategies which consider any data point a negative example until a positive label becomes available tend to underestimate CTR, resulting in inferior user experience and suboptimal performance for advertisers. The focus of this paper is to identify the best combination of loss functions and models that enable large-scale learning from a continuous stream of data in the presence of delayed labels. In this work, we compare 5 different loss functions, 3 of them applied to this problem for the first time. We benchmark their performance in offline settings on both public and proprietary datasets in conjunction with shallow and deep model architectures. We also discuss the engineering cost associated with implementing each loss function in a production environment. Finally, we carried out online experiments with the top performing methods, in order to validate their performance in a continuous training scheme. While training on 668 million in-house data points offline, our proposed methods outperform previous state-of-the-art by 3% relative cross entropy (RCE). During online experiments, we observed 55% gain in revenue per thousand requests (RPMq) against naive log loss.

Salim Arslan, Sofia Ira Ktena, Ben Glocker et al.

Graph convolutional networks (GCNs) allow to apply traditional convolution operations in non-Euclidean domains, where data are commonly modelled as irregular graphs. Medical imaging and, in particular, neuroscience studies often rely on such graph representations, with brain connectivity networks being a characteristic example, while ultimately seeking the locus of phenotypic or disease-related differences in the brain. These regions of interest (ROIs) are, then, considered to be closely associated with function and/or behaviour. Driven by this, we explore GCNs for the task of ROI identification and propose a visual attribution method based on class activation mapping. By undertaking a sex classification task as proof of concept, we show that this method can be used to identify salient nodes (brain regions) without prior node labels. Based on experiments conducted on neuroimaging data of more than 5000 participants from UK Biobank, we demonstrate the robustness of the proposed method in highlighting reproducible regions across individuals. We further evaluate the neurobiological relevance of the identified regions based on evidence from large-scale UK Biobank studies.

Sarah Parisot, Sofia Ira Ktena, Enzo Ferrante et al.

Graphs are widely used as a natural framework that captures interactions between individual elements represented as nodes in a graph. In medical applications, specifically, nodes can represent individuals within a potentially large population (patients or healthy controls) accompanied by a set of features, while the graph edges incorporate associations between subjects in an intuitive manner. This representation allows to incorporate the wealth of imaging and non-imaging information as well as individual subject features simultaneously in disease classification tasks. Previous graph-based approaches for supervised or unsupervised learning in the context of disease prediction solely focus on pairwise similarities between subjects, disregarding individual characteristics and features, or rather rely on subject-specific imaging feature vectors and fail to model interactions between them. In this paper, we present a thorough evaluation of a generic framework that leverages both imaging and non-imaging information and can be used for brain analysis in large populations. This framework exploits Graph Convolutional Networks (GCNs) and involves representing populations as a sparse graph, where its nodes are associated with imaging-based feature vectors, while phenotypic information is integrated as edge weights. The extensive evaluation explores the effect of each individual component of this framework on disease prediction performance and further compares it to different baselines. The framework performance is tested on two large datasets with diverse underlying data, ABIDE and ADNI, for the prediction of Autism Spectrum Disorder and conversion to Alzheimer's disease, respectively. Our analysis shows that our novel framework can improve over state-of-the-art results on both databases, with 70.4% classification accuracy for ABIDE and 80.0% for ADNI.

Nick Pawlowski, Sofia Ira Ktena, Matthew C. H. Lee et al.

We present DLTK, a toolkit providing baseline implementations for efficient experimentation with deep learning methods on biomedical images. It builds on top of TensorFlow and its high modularity and easy-to-use examples allow for a low-threshold access to state-of-the-art implementations for typical medical imaging problems. A comparison of DLTK's reference implementations of popular network architectures for image segmentation demonstrates new top performance on the publicly available challenge data "Multi-Atlas Labeling Beyond the Cranial Vault". The average test Dice similarity coefficient of $81.5$ exceeds the previously best performing CNN ($75.7$) and the accuracy of the challenge winning method ($79.0$).

Sofia Ira Ktena, Salim Arslan, Sarah Parisot et al.

Data-driven brain parcellations aim to provide a more accurate representation of an individual's functional connectivity, since they are able to capture individual variability that arises due to development or disease. This renders comparisons between the emerging brain connectivity networks more challenging, since correspondences between their elements are not preserved. Unveiling these correspondences is of major importance to keep track of local functional connectivity changes. We propose a novel method based on graph edit distance for the comparison of brain graphs directly in their domain, that can accurately reflect similarities between individual networks while providing the network element correspondences. This method is validated on a dataset of 116 twin subjects provided by the Human Connectome Project.

Sarah Parisot, Sofia Ira Ktena, Enzo Ferrante et al.

Exploiting the wealth of imaging and non-imaging information for disease prediction tasks requires models capable of representing, at the same time, individual features as well as data associations between subjects from potentially large populations. Graphs provide a natural framework for such tasks, yet previous graph-based approaches focus on pairwise similarities without modelling the subjects' individual characteristics and features. On the other hand, relying solely on subject-specific imaging feature vectors fails to model the interaction and similarity between subjects, which can reduce performance. In this paper, we introduce the novel concept of Graph Convolutional Networks (GCN) for brain analysis in populations, combining imaging and non-imaging data. We represent populations as a sparse graph where its vertices are associated with image-based feature vectors and the edges encode phenotypic information. This structure was used to train a GCN model on partially labelled graphs, aiming to infer the classes of unlabelled nodes from the node features and pairwise associations between subjects. We demonstrate the potential of the method on the challenging ADNI and ABIDE databases, as a proof of concept of the benefit from integrating contextual information in classification tasks. This has a clear impact on the quality of the predictions, leading to 69.5% accuracy for ABIDE (outperforming the current state of the art of 66.8%) and 77% for ADNI for prediction of MCI conversion, significantly outperforming standard linear classifiers where only individual features are considered.

Sofia Ira Ktena, Sarah Parisot, Enzo Ferrante et al.

Evaluating similarity between graphs is of major importance in several computer vision and pattern recognition problems, where graph representations are often used to model objects or interactions between elements. The choice of a distance or similarity metric is, however, not trivial and can be highly dependent on the application at hand. In this work, we propose a novel metric learning method to evaluate distance between graphs that leverages the power of convolutional neural networks, while exploiting concepts from spectral graph theory to allow these operations on irregular graphs. We demonstrate the potential of our method in the field of connectomics, where neuronal pathways or functional connections between brain regions are commonly modelled as graphs. In this problem, the definition of an appropriate graph similarity function is critical to unveil patterns of disruptions associated with certain brain disorders. Experimental results on the ABIDE dataset show that our method can learn a graph similarity metric tailored for a clinical application, improving the performance of a simple k-nn classifier by 11.9% compared to a traditional distance metric.

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.