arXiv subjects

Yicong Li

Publications and source records attributed to Yicong Li.

49 records · Page 3Linked to original sources

arXiv2023

X-Ray2EM: Uncertainty-Aware Cross-Modality Image Reconstruction from X-Ray to Electron Microscopy in Connectomics

Comprehensive, synapse-resolution imaging of the brain will be crucial for understanding neuronal computations and function. In connectomics, this has been the sole purview of volume electron microscopy (EM), which entails an excruciatingly difficult process because it requires cutting tissue into many thin, fragile slices that then need to be imaged, aligned, and reconstructed. Unlike EM, hard X-ray imaging is compatible with thick tissues, eliminating the need for thin sectioning, and delivering fast acquisition, intrinsic alignment, and isotropic resolution. Unfortunately, current state-of-the-art X-ray microscopy provides much lower resolution, to the extent that segmenting membranes is very challenging. We propose an uncertainty-aware 3D reconstruction model that translates X-ray images to EM-like images with enhanced membrane segmentation quality, showing its potential for developing simpler, faster, and more accurate X-ray based connectomics pipelines.

eess.IV↗

arXiv2023

The XPRESS Challenge: Xray Projectomic Reconstruction -- Extracting Segmentation with Skeletons

The wiring and connectivity of neurons form a structural basis for the function of the nervous system. Advances in volume electron microscopy (EM) and image segmentation have enabled mapping of circuit diagrams (connectomics) within local regions of the mouse brain. However, applying volume EM over the whole brain is not currently feasible due to technological challenges. As a result, comprehensive maps of long-range connections between brain regions are lacking. Recently, we demonstrated that X-ray holographic nanotomography (XNH) can provide high-resolution images of brain tissue at a much larger scale than EM. In particular, XNH is wellsuited to resolve large, myelinated axon tracts (white matter) that make up the bulk of long-range connections (projections) and are critical for inter-region communication. Thus, XNH provides an imaging solution for brain-wide projectomics. However, because XNH data is typically collected at lower resolutions and larger fields-of-view than EM, accurate segmentation of XNH images remains an important challenge that we present here. In this task, we provide volumetric XNH images of cortical white matter axons from the mouse brain along with ground truth annotations for axon trajectories. Manual voxel-wise annotation of ground truth is a time-consuming bottleneck for training segmentation networks. On the other hand, skeleton-based ground truth is much faster to annotate, and sufficient to determine connectivity. Therefore, we encourage participants to develop methods to leverage skeleton-based training. To this end, we provide two types of ground-truth annotations: a small volume of voxel-wise annotations and a larger volume with skeleton-based annotations. Entries will be evaluated on how accurately the submitted segmentations agree with the ground-truth skeleton annotations.

cs.CV↗

arXiv2023

An Out-of-Domain Synapse Detection Challenge for Microwasp Brain Connectomes

The size of image stacks in connectomics studies now reaches the terabyte and often petabyte scales with a great diversity of appearance across brain regions and samples. However, manual annotation of neural structures, e.g., synapses, is time-consuming, which leads to limited training data often smaller than 0.001\% of the test data in size. Domain adaptation and generalization approaches were proposed to address similar issues for natural images, which were less evaluated on connectomics data due to a lack of out-of-domain benchmarks.

cs.CV↗

arXiv2023

Finding the Most Transferable Tasks for Brain Image Segmentation

Although many studies have successfully applied transfer learning to medical image segmentation, very few of them have investigated the selection strategy when multiple source tasks are available for transfer. In this paper, we propose a prior knowledge guided and transferability based framework to select the best source tasks among a collection of brain image segmentation tasks, to improve the transfer learning performance on the given target task. The framework consists of modality analysis, RoI (region of interest) analysis, and transferability estimation, such that the source task selection can be refined step by step. Specifically, we adapt the state-of-the-art analytical transferability estimation metrics to medical image segmentation tasks and further show that their performance can be significantly boosted by filtering candidate source tasks based on modality and RoI characteristics. Our experiments on brain matter, brain tumor, and white matter hyperintensities segmentation datasets reveal that transferring from different tasks under the same modality is often more successful than transferring from the same task under different modalities. Furthermore, within the same modality, transferring from the source task that has stronger RoI shape similarity with the target task can significantly improve the final transfer performance. And such similarity can be captured using the Structural Similarity index in the label space.

eess.IV↗

arXiv2022

Video Question Answering: Datasets, Algorithms and Challenges

Video Question Answering (VideoQA) aims to answer natural language questions according to the given videos. It has earned increasing attention with recent research trends in joint vision and language understanding. Yet, compared with ImageQA, VideoQA is largely underexplored and progresses slowly. Although different algorithms have continually been proposed and shown success on different VideoQA datasets, we find that there lacks a meaningful survey to categorize them, which seriously impedes its advancements. This paper thus provides a clear taxonomy and comprehensive analyses to VideoQA, focusing on the datasets, algorithms, and unique challenges. We then point out the research trend of studying beyond factoid QA to inference QA towards the cognition of video contents, Finally, we conclude some promising directions for future exploration.

cs.CV↗

arXiv2022

Equivariant and Invariant Grounding for Video Question Answering

Video Question Answering (VideoQA) is the task of answering the natural language questions about a video. Producing an answer requires understanding the interplay across visual scenes in video and linguistic semantics in question. However, most leading VideoQA models work as black boxes, which make the visual-linguistic alignment behind the answering process obscure. Such black-box nature calls for visual explainability that reveals ``What part of the video should the model look at to answer the question?''. Only a few works present the visual explanations in a post-hoc fashion, which emulates the target model's answering process via an additional method. Nonetheless, the emulation struggles to faithfully exhibit the visual-linguistic alignment during answering. Instead of post-hoc explainability, we focus on intrinsic interpretability to make the answering process transparent. At its core is grounding the question-critical cues as the causal scene to yield answers, while rolling out the question-irrelevant information as the environment scene. Taking a causal look at VideoQA, we devise a self-interpretable framework, Equivariant and Invariant Grounding for Interpretable VideoQA (EIGV). Specifically, the equivariant grounding encourages the answering to be sensitive to the semantic changes in the causal scene and question; in contrast, the invariant grounding enforces the answering to be insensitive to the changes in the environment scene. By imposing them on the answering process, EIGV is able to distinguish the causal scene from the environment information, and explicitly present the visual-linguistic alignment. Extensive experiments on three benchmark datasets justify the superiority of EIGV in terms of accuracy and visual interpretability over the leading baselines.

cs.CL↗

arXiv2022

Invariant Grounding for Video Question Answering

Video Question Answering (VideoQA) is the task of answering questions about a video. At its core is understanding the alignments between visual scenes in video and linguistic semantics in question to yield the answer. In leading VideoQA models, the typical learning objective, empirical risk minimization (ERM), latches on superficial correlations between video-question pairs and answers as the alignments. However, ERM can be problematic, because it tends to over-exploit the spurious correlations between question-irrelevant scenes and answers, instead of inspecting the causal effect of question-critical scenes. As a result, the VideoQA models suffer from unreliable reasoning. In this work, we first take a causal look at VideoQA and argue that invariant grounding is the key to ruling out the spurious correlations. Towards this end, we propose a new learning framework, Invariant Grounding for VideoQA (IGV), to ground the question-critical scene, whose causal relations with answers are invariant across different interventions on the complement. With IGV, the VideoQA models are forced to shield the answering process from the negative influence of spurious correlations, which significantly improves the reasoning ability. Experiments on three benchmark datasets validate the superiority of IGV in terms of accuracy, visual explainability, and generalization ability over the leading baselines.

cs.CV↗

arXiv2022

Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning

Vision Transformers (ViTs) and their multi-scale and hierarchical variations have been successful at capturing image representations but their use has been generally studied for low-resolution images (e.g. - 256x256, 384384). For gigapixel whole-slide imaging (WSI) in computational pathology, WSIs can be as large as 150000x150000 pixels at 20X magnification and exhibit a hierarchical structure of visual tokens across varying resolutions: from 16x16 images capture spatial patterns among cells, to 4096x4096 images characterizing interactions within the tissue microenvironment. We introduce a new ViT architecture called the Hierarchical Image Pyramid Transformer (HIPT), which leverages the natural hierarchical structure inherent in WSIs using two levels of self-supervised learning to learn high-resolution image representations. HIPT is pretrained across 33 cancer types using 10,678 gigapixel WSIs, 408,218 4096x4096 images, and 104M 256x256 images. We benchmark HIPT representations on 9 slide-level tasks, and demonstrate that: 1) HIPT with hierarchical pretraining outperforms current state-of-the-art methods for cancer subtyping and survival prediction, 2) self-supervised ViTs are able to model important inductive biases about the hierarchical structure of phenotypes in the tumor microenvironment.

cs.CV↗

arXiv2022

Video as Conditional Graph Hierarchy for Multi-Granular Question Answering

Video question answering requires the models to understand and reason about both the complex video and language data to correctly derive the answers. Existing efforts have been focused on designing sophisticated cross-modal interactions to fuse the information from two modalities, while encoding the video and question holistically as frame and word sequences. Despite their success, these methods are essentially revolving around the sequential nature of video- and question-contents, providing little insight to the problem of question-answering and lacking interpretability as well. In this work, we argue that while video is presented in frame sequence, the visual elements (e.g., objects, actions, activities and events) are not sequential but rather hierarchical in semantic space. To align with the multi-granular essence of linguistic concepts in language queries, we propose to model video as a conditional graph hierarchy which weaves together visual facts of different granularity in a level-wise manner, with the guidance of corresponding textual cues. Despite the simplicity, our extensive experiments demonstrate the superiority of such conditional hierarchical graph architecture, with clear performance improvements over prior methods and also better generalization across different type of questions. Further analyses also demonstrate the model's reliability as it shows meaningful visual-textual evidences for the predicted answers.

cs.CV↗

arXiv2022

Unsupervised Graph Poisoning Attack via Contrastive Loss Back-propagation

Graph contrastive learning is the state-of-the-art unsupervised graph representation learning framework and has shown comparable performance with supervised approaches. However, evaluating whether the graph contrastive learning is robust to adversarial attacks is still an open problem because most existing graph adversarial attacks are supervised models, which means they heavily rely on labels and can only be used to evaluate the graph contrastive learning in a specific scenario. For unsupervised graph representation methods such as graph contrastive learning, it is difficult to acquire labels in real-world scenarios, making traditional supervised graph attack methods difficult to be applied to test their robustness. In this paper, we propose a novel unsupervised gradient-based adversarial attack that does not rely on labels for graph contrastive learning. We compute the gradients of the adjacency matrices of the two views and flip the edges with gradient ascent to maximize the contrastive loss. In this way, we can fully use multiple views generated by the graph contrastive learning models and pick the most informative edges without knowing their labels, and therefore can promisingly support our model adapted to more kinds of downstream tasks. Extensive experiments show that our attack outperforms unsupervised baseline attacks and has comparable performance with supervised attacks in multiple downstream tasks including node classification and link prediction. We further show that our attack can be transferred to other graph representation models as well.

cs.LG↗

arXiv2021

Reinforcement Learning based Path Exploration for Sequential Explainable Recommendation

Recent advances in path-based explainable recommendation systems have attracted increasing attention thanks to the rich information provided by knowledge graphs. Most existing explainable recommendations only utilize static knowledge graphs and ignore the dynamic user-item evolutions, leading to less convincing and inaccurate explanations. Although there are some works that realize that modelling user's temporal sequential behaviour could boost the performance and explainability of the recommender systems, most of them either only focus on modelling user's sequential interactions within a path or independently and separately of the recommendation mechanism. In this paper, we propose a novel Temporal Meta-path Guided Explainable Recommendation leveraging Reinforcement Learning (TMER-RL), which utilizes reinforcement item-item path modelling between consecutive items with attention mechanisms to sequentially model dynamic user-item evolutions on dynamic knowledge graph for explainable recommendation. Compared with existing works that use heavy recurrent neural networks to model temporal information, we propose simple but effective neural networks to capture users' historical item features and path-based context to characterize the next purchased item. Extensive evaluations of TMER on two real-world datasets show state-of-the-art performance compared against recent strong baselines.

cs.IR↗

arXiv2021

Hyperbolic Hypergraphs for Sequential Recommendation

Hypergraphs have been becoming a popular choice to model complex, non-pairwise, and higher-order interactions for recommender system. However, compared with traditional graph-based methods, the constructed hypergraphs are usually much sparser, which leads to a dilemma when balancing the benefits of hypergraphs and the modelling difficulty. Moreover, existing sequential hypergraph recommendation overlooks the temporal modelling among user relationships, which neglects rich social signals from the recommendation data. To tackle the above shortcomings of the existing hypergraph-based sequential recommendations, we propose a novel architecture named Hyperbolic Hypergraph representation learning method for Sequential Recommendation (H2SeqRec) with pre-training phase. Specifically, we design three self-supervised tasks to obtain the pre-training item embeddings to feed or fuse into the following recommendation architecture (with two ways to use the pre-trained embeddings). In the recommendation phase, we learn multi-scale item embeddings via a hierarchical structure to capture multiple time-span information. To alleviate the negative impact of sparse hypergraphs, we utilize a hyperbolic space-based hypergraph convolutional neural network to learn the dynamic item embeddings. Also, we design an item enhancement module to capture dynamic social information at each timestamp to improve effectiveness. Extensive experiments are conducted on two real-world datasets to prove the effectiveness and high performance of the model.

cs.SI↗

arXiv2021

Temporal Meta-path Guided Explainable Recommendation

This paper utilizes well-designed item-item path modelling between consecutive items with attention mechanisms to sequentially model dynamic user-item evolutions on dynamic knowledge graph for explainable recommendations. Compared with existing works that use heavy recurrent neural networks to model temporal information, we propose simple but effective neural networks to capture user historical item features and path-based context to characterise next purchased item. Extensive evaluations of TMER on three real-world benchmark datasets show state-of-the-art performance compared against recent strong baselines.

cs.SI↗