While imaging techniques at macro and mesoscales have garnered substantial attention and resources, microscale Volume Electron Microscopy (vEM) imaging, capable of revealing intricate vascular details, has lacked the necessary benchmarking infrastructure. In this paper, we address a significant gap in this field of neuroimaging by introducing the first-in-class public benchmark, BvEM, designed specifically for cortical blood vessel segmentation in vEM images. Our BvEM benchmark is based on vEM image volumes from three mammals: adult mouse, macaque, and human. We standardized the resolution, addressed imaging variations, and meticulously annotated blood vessels through semi-automatic, manual, and quality control processes, ensuring high-quality 3D segmentation. Furthermore, we developed a zero-shot cortical blood vessel segmentation method named TriSAM, which leverages the powerful segmentation model SAM for 3D segmentation. To extend SAM from 2D to 3D volume segmentation, TriSAM employs a multi-seed tracking framework, leveraging the reliability of certain image planes for tracking while using others to identify potential turning points. This approach effectively achieves long-term 3D blood vessel segmentation without model training or fine-tuning. Experimental results show that TriSAM achieved superior performances on the BvEM benchmark across three species.

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We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.

Automatic annotation of short-text data to a large number of target labels, referred to as Short Text Extreme Classification, has found numerous applications including prediction of related searches and product recommendation. In this paper, we propose a convolutional architecture InceptionXML which is light-weight, yet powerful, and robust to the inherent lack of word-order in short-text queries encountered in search and recommendation. We demonstrate the efficacy of applying convolutions by recasting the operation along the embedding dimension instead of the word dimension as applied in conventional CNNs for text classification. Towards scaling our model to datasets with millions of labels, we also propose SyncXML pipeline which improves upon the shortcomings of the recently proposed dynamic hard-negative mining technique for label shortlisting by synchronizing the label-shortlister and extreme classifier. SyncXML not only reduces the inference time to half but is also an order of magnitude smaller than state-of-the-art Astec in terms of model size. Through a comprehensive empirical comparison, we show that not only can InceptionXML outperform existing approaches on benchmark datasets but also the transformer baselines requiring only 2% FLOPs. The code for InceptionXML is available at https://github.com/xmc-aalto.

Extreme Multi-label Text Classification (XMC) involves learning a classifier that can assign an input with a subset of most relevant labels from millions of label choices. Recent approaches, such as XR-Transformer and LightXML, leverage a transformer instance to achieve state-of-the-art performance. However, in this process, these approaches need to make various trade-offs between performance and computational requirements. A major shortcoming, as compared to the Bi-LSTM based AttentionXML, is that they fail to keep separate feature representations for each resolution in a label tree. We thus propose CascadeXML, an end-to-end multi-resolution learning pipeline, which can harness the multi-layered architecture of a transformer model for attending to different label resolutions with separate feature representations. CascadeXML significantly outperforms all existing approaches with non-trivial gains obtained on benchmark datasets consisting of up to three million labels. Code for CascadeXML will be made publicly available at https://github.com/xmc-aalto/cascadexml.