Reconstruction of Cortical Surfaces with Spherical Topology from Infant Brain MRI via Recurrent Deformation Learning

Cortical surface reconstruction (CSR) from MRI is key to investigating brain structure and function. While recent deep learning approaches have significantly improved the speed of CSR, a substantial amount of runtime is still needed to map the cortex to a topologically-correct spherical manifold to facilitate downstream geometric analyses. Moreover, this mapping is possible only if the topology of the surface mesh is homotopic to a sphere. Here, we present a method for simultaneous CSR and spherical mapping efficiently within seconds. Our approach seamlessly connects two sub-networks for white and pial surface generation. Residual diffeomorphic deformations are learned iteratively to gradually warp a spherical template mesh to the white and pial surfaces while preserving mesh topology and uniformity. The one-to-one vertex correspondence between the template sphere and the cortical surfaces allows easy and direct mapping of geometric features like convexity and curvature to the sphere for visualization and downstream processing. We demonstrate the efficacy of our approach on infant brain MRI, which poses significant challenges to CSR due to tissue contrast changes associated with rapid brain development during the first postnatal year. Performance evaluation based on a dataset of infants from 0 to 12 months demonstrates that our method substantially enhances mesh regularity and reduces geometric errors, outperforming state-of-the-art deep learning approaches, all while maintaining high computational efficiency.

DBCopilot: Scaling Natural Language Querying to Massive Databases

Text-to-SQL simplifies database interactions by enabling non-experts to convert their natural language (NL) questions into Structured Query Language (SQL) queries. While recent advances in large language models (LLMs) have improved the zero-shot text-to-SQL paradigm, existing methods face scalability challenges when dealing with massive, dynamically changing databases. This paper introduces DBCopilot, a framework that addresses these challenges by employing a compact and flexible copilot model for routing across massive databases. Specifically, DBCopilot decouples the text-to-SQL process into schema routing and SQL generation, leveraging a lightweight sequence-to-sequence neural network-based router to formulate database connections and navigate natural language questions through databases and tables. The routed schemas and questions are then fed into LLMs for efficient SQL generation. Furthermore, DBCopilot also introduced a reverse schema-to-question generation paradigm, which can learn and adapt the router over massive databases automatically without requiring manual intervention. Experimental results demonstrate that DBCopilot is a scalable and effective solution for real-world text-to-SQL tasks, providing a significant advancement in handling large-scale schemas.

Versatile Medical Image Segmentation Learned from Multi-Source Datasets via Model Self-Disambiguation

A versatile medical image segmentation model applicable to imaging data collected with diverse equipment and protocols can facilitate model deployment and maintenance. However, building such a model typically requires a large, diverse, and fully annotated dataset, which is rarely available due to the labor-intensive and costly data curation. In this study, we develop a cost-efficient method by harnessing readily available data with partially or even sparsely annotated segmentation labels. We devise strategies for model self-disambiguation, prior knowledge incorporation, and imbalance mitigation to address challenges associated with inconsistently labeled data from various sources, including label ambiguity and imbalances across modalities, datasets, and segmentation labels. Experimental results on a multi-modal dataset compiled from eight different sources for abdominal organ segmentation have demonstrated our method's effectiveness and superior performance over alternative state-of-the-art methods, highlighting its potential for optimizing the use of existing annotated data and reducing the annotation efforts for new data to further enhance model capability.

Offline Pseudo Relevance Feedback for Efficient and Effective Single-pass Dense Retrieval

Dense retrieval has made significant advancements in information retrieval (IR) by achieving high levels of effectiveness while maintaining online efficiency during a single-pass retrieval process. However, the application of pseudo relevance feedback (PRF) to further enhance retrieval effectiveness results in a doubling of online latency. To address this challenge, this paper presents a single-pass dense retrieval framework that shifts the PRF process offline through the utilization of pre-generated pseudo-queries. As a result, online retrieval is reduced to a single matching with the pseudo-queries, hence providing faster online retrieval. The effectiveness of the proposed approach is evaluated on the standard TREC DL and HARD datasets, and the results demonstrate its promise. Our code is openly available at https://github.com/Rosenberg37/OPRF.

Understanding Differential Search Index for Text Retrieval

The Differentiable Search Index (DSI) is a novel information retrieval (IR) framework that utilizes a differentiable function to generate a sorted list of document identifiers in response to a given query. However, due to the black-box nature of the end-to-end neural architecture, it remains to be understood to what extent DSI possesses the basic indexing and retrieval abilities. To mitigate this gap, in this study, we define and examine three important abilities that a functioning IR framework should possess, namely, exclusivity, completeness, and relevance ordering. Our analytical experimentation shows that while DSI demonstrates proficiency in memorizing the unidirectional mapping from pseudo queries to document identifiers, it falls short in distinguishing relevant documents from random ones, thereby negatively impacting its retrieval effectiveness. To address this issue, we propose a multi-task distillation approach to enhance the retrieval quality without altering the structure of the model and successfully endow it with improved indexing abilities. Through experiments conducted on various datasets, we demonstrate that our proposed method outperforms previous DSI baselines.

Brain Tissue Segmentation Across the Human Lifespan via Supervised Contrastive Learning

Automatic segmentation of brain MR images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) is critical for tissue volumetric analysis and cortical surface reconstruction. Due to dramatic structural and appearance changes associated with developmental and aging processes, existing brain tissue segmentation methods are only viable for specific age groups. Consequently, methods developed for one age group may fail for another. In this paper, we make the first attempt to segment brain tissues across the entire human lifespan (0-100 years of age) using a unified deep learning model. To overcome the challenges related to structural variability underpinned by biological processes, intensity inhomogeneity, motion artifacts, scanner-induced differences, and acquisition protocols, we propose to use contrastive learning to improve the quality of feature representations in a latent space for effective lifespan tissue segmentation. We compared our approach with commonly used segmentation methods on a large-scale dataset of 2,464 MR images. Experimental results show that our model accurately segments brain tissues across the lifespan and outperforms existing methods.

Groupwise Query Performance Prediction with BERT

While large-scale pre-trained language models like BERT have advanced the state-of-the-art in IR, its application in query performance prediction (QPP) is so far based on pointwise modeling of individual queries. Meanwhile, recent studies suggest that the cross-attention modeling of a group of documents can effectively boost performances for both learning-to-rank algorithms and BERT-based re-ranking. To this end, a BERT-based groupwise QPP model is proposed, in which the ranking contexts of a list of queries are jointly modeled to predict the relative performance of individual queries. Extensive experiments on three standard TREC collections showcase effectiveness of our approach. Our code is available at https://github.com/VerdureChen/Group-QPP.

SkullEngine: A Multi-stage CNN Framework for Collaborative CBCT Image Segmentation and Landmark Detection

We propose a multi-stage coarse-to-fine CNN-based framework, called SkullEngine, for high-resolution segmentation and large-scale landmark detection through a collaborative, integrated, and scalable JSD model and three segmentation and landmark detection refinement models. We evaluated our framework on a clinical dataset consisting of 170 CBCT/CT images for the task of segmenting 2 bones (midface and mandible) and detecting 175 clinically common landmarks on bones, teeth, and soft tissues.

Co-BERT: A Context-Aware BERT Retrieval Model Incorporating Local and Query-specific Context

BERT-based text ranking models have dramatically advanced the state-of-the-art in ad-hoc retrieval, wherein most models tend to consider individual query-document pairs independently. In the mean time, the importance and usefulness to consider the cross-documents interactions and the query-specific characteristics in a ranking model have been repeatedly confirmed, mostly in the context of learning to rank. The BERT-based ranking model, however, has not been able to fully incorporate these two types of ranking context, thereby ignoring the inter-document relationships from the ranking and the differences among queries. To mitigate this gap, in this work, an end-to-end transformer-based ranking model, named Co-BERT, has been proposed to exploit several BERT architectures to calibrate the query-document representations using pseudo relevance feedback before modeling the relevance of a group of documents jointly. Extensive experiments on two standard test collections confirm the effectiveness of the proposed model in improving the performance of text re-ranking over strong fine-tuned BERT-Base baselines. We plan to make our implementation open source to enable further comparisons.