DeepNuParc: A Novel Deep Clustering Framework for Fine-scale Parcellation of Brain Nuclei Using Diffusion MRI Tractography

Brain nuclei are clusters of anatomically distinct neurons that serve as important hubs for processing and relaying information in various neural circuits. Fine-scale parcellation of the brain nuclei is vital for a comprehensive understanding of its anatomico-functional correlations. Diffusion MRI tractography is an advanced imaging technique that can estimate the brain's white matter structural connectivity to potentially reveal the topography of the nuclei of interest for studying its subdivisions. In this work, we present a deep clustering pipeline, namely DeepNuParc, to perform automated, fine-scale parcellation of brain nuclei using diffusion MRI tractography. First, we incorporate a newly proposed deep learning approach to enable accurate segmentation of the nuclei of interest directly on the dMRI data. Next, we design a novel streamline clustering-based structural connectivity feature for a robust representation of voxels within the nuclei. Finally, we improve the popular joint dimensionality reduction and k-means clustering approach to enable nuclei parcellation at a finer scale. We demonstrate DeepNuParc on two important brain structures, i.e. the amygdala and the thalamus, that are known to have multiple anatomically and functionally distinct nuclei subdivisions. Experimental results show that DeepNuParc enables consistent parcellation of the nuclei into multiple parcels across multiple subjects and achieves good correspondence with the widely used coarse-scale atlases. Our codes are available at https://github.com/HarlandZZC/deep_nuclei_parcellation.

Blind Video Super-Resolution based on Implicit Kernels

Blind video super-resolution (BVSR) is a low-level vision task which aims to generate high-resolution videos from low-resolution counterparts in unknown degradation scenarios. Existing approaches typically predict blur kernels that are spatially invariant in each video frame or even the entire video. These methods do not consider potential spatio-temporal varying degradations in videos, resulting in suboptimal BVSR performance. In this context, we propose a novel BVSR model based on Implicit Kernels, BVSR-IK, which constructs a multi-scale kernel dictionary parameterized by implicit neural representations. It also employs a newly designed recurrent Transformer to predict the coefficient weights for accurate filtering in both frame correction and feature alignment. Experimental results have demonstrated the effectiveness of the proposed BVSR-IK, when compared with four state-of-the-art BVSR models on three commonly used datasets, with BVSR-IK outperforming the second best approach, FMA-Net, by up to 0.59 dB in PSNR. Source code will be available at https://github.com.

MultiCo3D: Multi-Label Voxel Contrast for One-Shot Incremental Segmentation of 3D Neuroimages

3D neuroimages provide a comprehensive view of brain structure and function, aiding in precise localization and functional connectivity analysis. Segmentation of white matter (WM) tracts using 3D neuroimages is vital for understanding the brain's structural connectivity in both healthy and diseased states. One-shot Class Incremental Semantic Segmentation (OCIS) refers to effectively segmenting new (novel) classes using only a single sample while retaining knowledge of old (base) classes without forgetting. Voxel-contrastive OCIS methods adjust the feature space to alleviate the feature overlap problem between the base and novel classes. However, since WM tract segmentation is a multi-label segmentation task, existing single-label voxel contrastive-based methods may cause inherent contradictions. To address this, we propose a new multi-label voxel contrast framework called MultiCo3D for one-shot class incremental tract segmentation. Our method utilizes uncertainty distillation to preserve base tract segmentation knowledge while adjusting the feature space with multi-label voxel contrast to alleviate feature overlap when learning novel tracts and dynamically weighting multi losses to balance overall loss. We compare our method against several state-of-the-art (SOTA) approaches. The experimental results show that our method significantly enhances one-shot class incremental tract segmentation accuracy across five different experimental setups on HCP and Preto datasets.

DDCSR: A Novel End-to-End Deep Learning Framework for Cortical Surface Reconstruction from Diffusion MRI

Diffusion MRI (dMRI) plays a crucial role in studying brain white matter connectivity. Cortical surface reconstruction (CSR), including the inner whiter matter (WM) and outer pial surfaces, is one of the key tasks in dMRI analyses such as fiber tractography and multimodal MRI analysis. Existing CSR methods rely on anatomical T1-weighted data and map them into the dMRI space through inter-modality registration. However, due to the low resolution and image distortions of dMRI data, inter-modality registration faces significant challenges. This work proposes a novel end-to-end learning framework, DDCSR, which for the first time enables CSR directly from dMRI data. DDCSR consists of two major components, including: (1) an implicit learning module to predict a voxel-wise intermediate surface representation, and (2) an explicit learning module to predict the 3D mesh surfaces. Compared to several baseline and advanced CSR methods, we show that the proposed DDCSR can largely increase both accuracy and efficiency. Furthermore, we demonstrate a high generalization ability of DDCSR to data from different sources, despite the differences in dMRI acquisitions and populations.

A Novel Streamline-based diffusion MRI Tractography Registration Method with Probabilistic Keypoint Detection

Registration of diffusion MRI tractography is an essential step for analyzing group similarities and variations in the brain's white matter (WM). Streamline-based registration approaches can leverage the 3D geometric information of fiber pathways to enable spatial alignment after registration. Existing methods usually rely on the optimization of the spatial distances to identify the optimal transformation. However, such methods overlook point connectivity patterns within the streamline itself, limiting their ability to identify anatomical correspondences across tractography datasets. In this work, we propose a novel unsupervised approach using deep learning to perform streamline-based dMRI tractography registration. The overall idea is to identify corresponding keypoint pairs across subjects for spatial alignment of tractography datasets. We model tractography as point clouds to leverage the graph connectivity along streamlines. We propose a novel keypoint detection method for streamlines, framed as a probabilistic classification task to identify anatomically consistent correspondences across unstructured streamline sets. In the experiments, we compare several existing methods and show highly effective and efficient tractography registration performance.

TractCloud-FOV: Deep Learning-based Robust Tractography Parcellation in Diffusion MRI with Incomplete Field of View

Tractography parcellation classifies streamlines reconstructed from diffusion MRI into anatomically defined fiber tracts for clinical and research applications. However, clinical scans often have incomplete fields of view (FOV) where brain regions are partially imaged, leading to partial or truncated fiber tracts. To address this challenge, we introduce TractCloud-FOV, a deep learning framework that robustly parcellates tractography under conditions of incomplete FOV. We propose a novel training strategy, FOV-Cut Augmentation (FOV-CA), in which we synthetically cut tractograms to simulate a spectrum of real-world inferior FOV cutoff scenarios. This data augmentation approach enriches the training set with realistic truncated streamlines, enabling the model to achieve superior generalization. We evaluate the proposed TractCloud-FOV on both synthetically cut tractography and two real-life datasets with incomplete FOV. TractCloud-FOV significantly outperforms several state-of-the-art methods on all testing datasets in terms of streamline classification accuracy, generalization ability, tract anatomical depiction, and computational efficiency. Overall, TractCloud-FOV achieves efficient and consistent tractography parcellation in diffusion MRI with incomplete FOV.

Towards an AI co-scientist

Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance. The system's design incorporates a generate, debate, and evolve approach to hypothesis generation, inspired by the scientific method and accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute, improving hypothesis quality. While general purpose, we focus development and validation in three biomedical areas: drug repurposing, novel target discovery, and explaining mechanisms of bacterial evolution and anti-microbial resistance. For drug repurposing, the system proposes candidates with promising validation findings, including candidates for acute myeloid leukemia that show tumor inhibition in vitro at clinically applicable concentrations. For novel target discovery, the AI co-scientist proposed new epigenetic targets for liver fibrosis, validated by anti-fibrotic activity and liver cell regeneration in human hepatic organoids. Finally, the AI co-scientist recapitulated unpublished experimental results via a parallel in silico discovery of a novel gene transfer mechanism in bacterial evolution. These results, detailed in separate, co-timed reports, demonstrate the potential to augment biomedical and scientific discovery and usher an era of AI empowered scientists.

AquaNeRF: Neural Radiance Fields in Underwater Media with Distractor Removal

Neural radiance field (NeRF) research has made significant progress in modeling static video content captured in the wild. However, current models and rendering processes rarely consider scenes captured underwater, which are useful for studying and filming ocean life. They fail to address visual artifacts unique to underwater scenes, such as moving fish and suspended particles. This paper introduces a novel NeRF renderer and optimization scheme for an implicit MLP-based NeRF model. Our renderer reduces the influence of floaters and moving objects that interfere with static objects of interest by estimating a single surface per ray. We use a Gaussian weight function with a small offset to ensure that the transmittance of the surrounding media remains constant. Additionally, we enhance our model with a depth-based scaling function to upscale gradients for near-camera volumes. Overall, our method outperforms the baseline Nerfacto by approximately 7.5\% and SeaThru-NeRF by 6.2% in terms of PSNR. Subjective evaluation also shows a significant reduction of artifacts while preserving details of static targets and background compared to the state of the arts.

Bridging the Gap: Transforming Natural Language Questions into SQL Queries via Abstract Query Pattern and Contextual Schema Markup

Large language models have demonstrated excellent performance in many tasks, including Text-to-SQL, due to their powerful in-context learning capabilities. They are becoming the mainstream approach for Text-to-SQL. However, these methods still have a significant gap compared to human performance, especially on complex questions. As the complexity of questions increases, the gap between questions and SQLs increases. We identify two important gaps: the structural mapping gap and the lexical mapping gap. To tackle these two gaps, we propose PAS-SQL, an efficient SQL generation pipeline based on LLMs, which alleviates gaps through Abstract Query Pattern (AQP) and Contextual Schema Markup (CSM). AQP aims to obtain the structural pattern of the question by removing database-related information, which enables us to find structurally similar demonstrations. CSM aims to associate database-related text span in the question with specific tables or columns in the database, which alleviates the lexical mapping gap. Experimental results on the Spider and BIRD datasets demonstrate the effectiveness of our proposed method. Specifically, PAS-SQL + GPT-4o sets a new state-of-the-art on the Spider benchmark with an execution accuracy of 87.9\%, and achieves leading results on the BIRD dataset with an execution accuracy of 64.67\%.

AFDM-Enabled Integrated Sensing and Communication: Theoretical Framework and Pilot Design

The integrated sensing and communication (ISAC) has been envisioned as one representative usage scenario of sixth-generation (6G) network. However, the unprecedented characteristics of 6G, especially the doubly dispersive channel, make classical ISAC waveforms rather challenging to guarantee a desirable performance level. The recently proposed affine frequency division multiplexing (AFDM) can attain full diversity even under doubly dispersive effects, thus becoming a competitive candidate for next-generation ISAC waveforms. Relevant investigations are still at an early stage, which involve only straightforward design lacking explicit theoretical analysis. This paper provides an in-depth investigation on AFDM waveform design for ISAC applications. Specifically, the closed-form Cr\'{a}mer-Rao bounds of target detection for AFDM are derived, followed by a demonstration on its merits over existing counterparts. Furthermore, we formulate the ambiguity function of the pilot-assisted AFDM waveform for the first time, revealing conditions for stable sensing performance. To further enhance both the communication and sensing performance of the AFDM waveform, we propose a novel pilot design by exploiting the characteristics of AFDM signals. The proposed design is analytically validated to be capable of optimizing the ambiguity function property and channel estimation accuracy simultaneously as well as overcoming the sensing and channel estimation range limitation originated from the pilot spacing. Numerical results have verified the superiority of the proposed pilot design in terms of dual-functional performance.