TractGraphCNN: anatomically informed graph CNN for classification using diffusion MRI tractography

The structure and variability of the brain's connections can be investigated via prediction of non-imaging phenotypes using neural networks. However, known neuroanatomical relationships between input features are generally ignored in network design. We propose TractGraphCNN, a novel, anatomically informed graph CNN framework for machine learning tasks using diffusion MRI tractography. An EdgeConv module aggregates features from anatomically similar white matter connections indicated by graph edges, and an attention module enables interpretation of predictive white matter tracts. Results in a sex prediction testbed task demonstrate strong performance of TractGraphCNN in two large datasets (HCP and ABCD). Graphs informed by white matter geometry demonstrate higher performance than graphs informed by gray matter connectivity. Overall, the bilateral cingulum and left middle longitudinal fasciculus are consistently highly predictive of sex. This work shows the potential of incorporating anatomical information, especially known anatomical similarities between input features, to guide convolutions in neural networks.

Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Text-guided mask-free local image retouching

In the realm of multi-modality, text-guided image retouching techniques emerged with the advent of deep learning. Most currently available text-guided methods, however, rely on object-level supervision to constrain the region that may be modified. This not only makes it more challenging to develop these algorithms, but it also limits how widely deep learning can be used for image retouching. In this paper, we offer a text-guided mask-free image retouching approach that yields consistent results to address this concern. In order to perform image retouching without mask supervision, our technique can construct plausible and edge-sharp masks based on the text for each object in the image. Extensive experiments have shown that our method can produce high-quality, accurate images based on spoken language. The source code will be released soon.

Purifier: Defending Data Inference Attacks via Transforming Confidence Scores

Neural networks are susceptible to data inference attacks such as the membership inference attack, the adversarial model inversion attack and the attribute inference attack, where the attacker could infer useful information such as the membership, the reconstruction or the sensitive attributes of a data sample from the confidence scores predicted by the target classifier. In this paper, we propose a method, namely PURIFIER, to defend against membership inference attacks. It transforms the confidence score vectors predicted by the target classifier and makes purified confidence scores indistinguishable in individual shape, statistical distribution and prediction label between members and non-members. The experimental results show that PURIFIER helps defend membership inference attacks with high effectiveness and efficiency, outperforming previous defense methods, and also incurs negligible utility loss. Besides, our further experiments show that PURIFIER is also effective in defending adversarial model inversion attacks and attribute inference attacks. For example, the inversion error is raised about 4+ times on the Facescrub530 classifier, and the attribute inference accuracy drops significantly when PURIFIER is deployed in our experiment.

Tractography-Based Parcellation of Cerebellar Dentate Nuclei via a Deep Nonnegative Matrix Factorization Clustering Method

As the largest human cerebellar nucleus, the dentate nucleus (DN) functions significantly in the communication between the cerebellum and the rest of the brain. Structural connectivity-based parcellation has the potential to reveal the topography of the DN and enable the study of its subregions. In this paper, we investigate a deep nonnegative matrix factorization clustering method (DNMFC) for parcellation of the human DN based on its structural connectivity using diffusion MRI tractography. We propose to describe the connectivity of the DN using a set of curated tractography fiber clusters within the cerebellum. Experiments are conducted on the diffusion MRI data of 50 healthy adults from the Human Connectome Project. In comparison with state-of-the-art clustering methods, DN parcellations resulting from DNMFC show better quality and consistency of parcels across subjects.

DeepRGVP: A Novel Microstructure-Informed Supervised Contrastive Learning Framework for Automated Identification Of The Retinogeniculate Pathway Using dMRI Tractography

The retinogeniculate pathway (RGVP) is responsible for carrying visual information from the retina to the lateral geniculate nucleus. Identification and visualization of the RGVP are important in studying the anatomy of the visual system and can inform treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced imaging method that uniquely enables in vivo mapping of the 3D trajectory of the RGVP. Currently, identification of the RGVP from tractography data relies on expert (manual) selection of tractography streamlines, which is time-consuming, has high clinical and expert labor costs, and affected by inter-observer variability. In this paper, we present what we believe is the first deep learning framework, namely DeepRGVP, to enable fast and accurate identification of the RGVP from dMRI tractography data. We design a novel microstructure-informed supervised contrastive learning method that leverages both streamline label and tissue microstructure information to determine positive and negative pairs. We propose a simple and successful streamline-level data augmentation method to address highly imbalanced training data, where the number of RGVP streamlines is much lower than that of non-RGVP streamlines. We perform comparisons with several state-of-the-art deep learning methods that were designed for tractography parcellation, and we show superior RGVP identification results using DeepRGVP.

Line Drawing Guided Progressive Inpainting of Mural Damages

Mural image inpainting refers to repairing the damage or missing areas in a mural image to restore the visual appearance. Most existing image-inpainting methods tend to take a target image as the only input and directly repair the damage to generate a visually plausible result. These methods obtain high performance in restoration or completion of some specific objects, e.g., human face, fabric texture, and printed texts, etc., however, are not suitable for repairing murals with varied subjects, especially for murals with large damaged areas. Moreover, due to the discrete colors in paints, mural inpainting may suffer from apparent color bias as compared to natural image inpainting. To this end, in this paper, we propose a line drawing guided progressive mural inpainting method. It divides the inpainting process into two steps: structure reconstruction and color correction, executed by a structure reconstruction network (SRN) and a color correction network (CCN), respectively. In the structure reconstruction, line drawings are used by SRN as a guarantee for large-scale content authenticity and structural stability. In the color correction, CCN operates a local color adjustment for missing pixels which reduces the negative effects of color bias and edge jumping. The proposed approach is evaluated against the current state-of-the-art image inpainting methods. Qualitative and quantitative results demonstrate the superiority of the proposed method in mural image inpainting. The codes and data are available at {https://github.com/qinnzou/mural-image-inpainting}.

Age Prediction Performance Varies Across Deep, Superficial, and Cerebellar White Matter Connections

The brain's white matter (WM) undergoes developmental and degenerative processes during the human lifespan. To investigate the relationship between WM anatomical regions and age, we study diffusion magnetic resonance imaging tractography that is finely parcellated into fiber clusters in the deep, superficial, and cerebellar WM. We propose a deep-learning-based age prediction model that leverages large convolutional kernels and inverted bottlenecks. We improve performance using novel discrete multi-faceted mix data augmentation and a novel prior-knowledge-based loss function that encourages age predictions in the expected range. We study a dataset of 965 healthy young adults (22-37 years) derived from the Human Connectome Project (HCP). Experimental results demonstrate that the proposed model achieves a mean absolute error of 2.59 years and outperforms compared methods. We find that the deep WM is the most informative for age prediction in this cohort, while the superficial WM is the least informative. Overall, the most predictive WM tracts are the thalamo-frontal tract from the deep WM and the intracerebellar input and Purkinje tract from the cerebellar WM.

Are we really making much progress in unsupervised graph outlier detection? Revisiting the problem with new insight and superior method

A large number of studies on Graph Outlier Detection (GOD) have emerged in recent years due to its wide applications, in which Unsupervised Node Outlier Detection (UNOD) on attributed networks is an important area. UNOD focuses on detecting two kinds of typical outliers in graphs: the structural outlier and the contextual outlier. Most existing works conduct the experiments based on the datasets with injected outliers. However, we find that the most widely-used outlier injection approach has a serious data leakage issue. By only utilizing such data leakage, a simple approach can achieve the state-of-the-art performance in detecting outliers. In addition, we observe that most existing algorithms have performance drops with varied injection settings. The other major issue is on balanced detection performance between the two types of outliers, which has not been considered by existing studies. In this paper, we analyze the cause of the data leakage issue in depth since the injection approach is a building block to advance UNOD. Moreover, we devise a novel variance-based model to detect structural outliers, which is more robust to different injection settings. On top of this, we propose a new framework, Variance-based Graph Outlier Detection (VGOD), which combines our variance-based model and attribute reconstruction model to detect outliers in a balanced way. Finally, we conduct extensive experiments to demonstrate the effectiveness and the efficiency of VGOD. The results on 5 real-world datasets validate that VGOD achieves not only the best performance in detecting outliers but also a balanced detection performance between structural and contextual outliers.

A Novel Supervised Contrastive Regression Framework for Prediction of Neurocognitive Measures Using Multi-Site Harmonized Diffusion MRI Tractography

Neuroimaging-based prediction of neurocognitive measures is valuable for studying how the brain's structure relates to cognitive function. However, the accuracy of prediction using popular linear regression models is relatively low. We propose Supervised Contrastive Regression (SCR), a simple yet effective method that allows full supervision for contrastive learning in regression tasks. SCR performs supervised contrastive representation learning by using the absolute difference between continuous regression labels (i.e. neurocognitive scores) to determine positive and negative pairs. We apply SCR to analyze a large-scale dataset including multi-site harmonized diffusion MRI and neurocognitive data from 8735 participants in the Adolescent Brain Cognitive Development (ABCD) Study. We extract white matter microstructural measures using a fine parcellation of white matter tractography into fiber clusters. We predict three scores related to domains of higher-order cognition (general cognitive ability, executive function, and learning/memory). To identify important fiber clusters for prediction of these neurocognitive scores, we propose a permutation feature importance method for high-dimensional data. We find that SCR improves the accuracy of neurocognitive score prediction compared to other state-of-the-art methods. We find that the most predictive fiber clusters are predominantly located within the superficial white matter and projection tracts, particularly the superficial frontal white matter and striato-frontal connections. Overall, our results demonstrate the utility of contrastive representation learning methods for regression, and in particular for improving neuroimaging-based prediction of higher-order cognitive abilities.