SELMA3D challenge: Self-supervised learning for 3D light-sheet microscopy image segmentation

Recent innovations in light sheet microscopy, paired with developments in tissue clearing techniques, enable the 3D imaging of large mammalian tissues with cellular resolution. Combined with the progress in large-scale data analysis, driven by deep learning, these innovations empower researchers to rapidly investigate the morphological and functional properties of diverse biological samples. Segmentation, a crucial preliminary step in the analysis process, can be automated using domain-specific deep learning models with expert-level performance. However, these models exhibit high sensitivity to domain shifts, leading to a significant drop in accuracy when applied to data outside their training distribution. To address this limitation, and inspired by the recent success of self-supervised learning in training generalizable models, we organized the SELMA3D Challenge during the MICCAI 2024 conference. SELMA3D provides a vast collection of light-sheet images from cleared mice and human brains, comprising 35 large 3D images-each with over 1000^3 voxels-and 315 annotated small patches for finetuning, preliminary testing and final testing. The dataset encompasses diverse biological structures, including vessel-like and spot-like structures. Five teams participated in all phases of the challenge, and their proposed methods are reviewed in this paper. Quantitative and qualitative results from most participating teams demonstrate that self-supervised learning on large datasets improves segmentation model performance and generalization. We will continue to support and extend SELMA3D as an inaugural MICCAI challenge focused on self-supervised learning for 3D microscopy image segmentation.

Stochastically Constrained Best Arm Identification with Thompson Sampling

We consider the problem of the best arm identification in the presence of stochastic constraints, where there is a finite number of arms associated with multiple performance measures. The goal is to identify the arm that optimizes the objective measure subject to constraints on the remaining measures. We will explore the popular idea of Thompson sampling (TS) as a means to solve it. To the best of our knowledge, it is the first attempt to extend TS to this problem. We will design a TS-based sampling algorithm, establish its asymptotic optimality in the rate of posterior convergence, and demonstrate its superior performance using numerical examples.

Salient Region Matching for Fully Automated MR-TRUS Registration

Prostate cancer is a leading cause of cancer-related mortality in men. The registration of magnetic resonance (MR) and transrectal ultrasound (TRUS) can provide guidance for the targeted biopsy of prostate cancer. In this study, we propose a salient region matching framework for fully automated MR-TRUS registration. The framework consists of prostate segmentation, rigid alignment and deformable registration. Prostate segmentation is performed using two segmentation networks on MR and TRUS respectively, and the predicted salient regions are used for the rigid alignment. The rigidly-aligned MR and TRUS images serve as initialization for the deformable registration. The deformable registration network has a dual-stream encoder with cross-modal spatial attention modules to facilitate multi-modality feature learning, and a salient region matching loss to consider both structure and intensity similarity within the prostate region. Experiments on a public MR-TRUS dataset demonstrate that our method achieves satisfactory registration results, outperforming several cutting-edge methods. The code is publicly available at https://github.com/mock1ngbrd/salient-region-matching.

Interpretable Load Forecasting via Representation Learning of Geo-distributed Meteorological Factors

Meteorological factors (MF) are crucial in day-ahead load forecasting as they significantly influence the electricity consumption behaviors of consumers. Numerous studies have incorporated MF into the load forecasting model to achieve higher accuracy. Selecting MF from one representative location or the averaged MF as the inputs of the forecasting model is a common practice. However, the difference in MF collected in various locations within a region may be significant, which poses a challenge in selecting the appropriate MF from numerous locations. A representation learning framework is proposed to extract geo-distributed MF while considering their spatial relationships. In addition, this paper employs the Shapley value in the graph-based model to reveal connections between MF collected in different locations and loads. To reduce the computational complexity of calculating the Shapley value, an acceleration method is adopted based on Monte Carlo sampling and weighted linear regression. Experiments on two real-world datasets demonstrate that the proposed method improves the day-ahead forecasting accuracy, especially in extreme scenarios such as the "accumulation temperature effect" in summer and "sudden temperature change" in winter. We also find a significant correlation between the importance of MF in different locations and the corresponding area's GDP and mainstay industry.

VideoChat-Flash: Hierarchical Compression for Long-Context Video Modeling

Long-context modeling is a critical capability for multimodal large language models (MLLMs), enabling them to process long-form contents with implicit memorization. Despite its advances, handling extremely long videos remains challenging due to the difficulty in maintaining crucial features over extended sequences. This paper introduces a Hierarchical visual token Compression (HiCo) method designed for high-fidelity representation and a practical context modeling system VideoChat-Flash tailored for multimodal long-sequence processing. HiCo capitalizes on the redundancy of visual information in long videos to compress long video context from the clip-level to the video-level, reducing the compute significantly while preserving essential details. VideoChat-Flash features a multi-stage short-to-long learning scheme, a rich dataset of real-world long videos named LongVid, and an upgraded "Needle-In-A-video-Haystack" (NIAH) for evaluating context capacities. In extensive experiments, VideoChat-Flash shows the leading performance on both mainstream long and short video benchmarks at the 7B model scale. It firstly gets 99.1% accuracy over 10,000 frames in NIAH among open-source models.

Task Preference Optimization: Improving Multimodal Large Language Models with Vision Task Alignment

Current multimodal large language models (MLLMs) struggle with fine-grained or precise understanding of visuals though they give comprehensive perception and reasoning in a spectrum of vision applications. Recent studies either develop tool-using or unify specific visual tasks into the autoregressive framework, often at the expense of overall multimodal performance. To address this issue and enhance MLLMs with visual tasks in a scalable fashion, we propose Task Preference Optimization (TPO), a novel method that utilizes differentiable task preferences derived from typical fine-grained visual tasks. TPO introduces learnable task tokens that establish connections between multiple task-specific heads and the MLLM. By leveraging rich visual labels during training, TPO significantly enhances the MLLM's multimodal capabilities and task-specific performance. Through multi-task co-training within TPO, we observe synergistic benefits that elevate individual task performance beyond what is achievable through single-task training methodologies. Our instantiation of this approach with VideoChat and LLaVA demonstrates an overall 14.6% improvement in multimodal performance compared to baseline models. Additionally, MLLM-TPO demonstrates robust zero-shot capabilities across various tasks, performing comparably to state-of-the-art supervised models. The code will be released at https://github.com/OpenGVLab/TPO

Tracking the Feature Dynamics in LLM Training: A Mechanistic Study

Understanding training dynamics and feature evolution is crucial for the mechanistic interpretability of large language models (LLMs). Although sparse autoencoders (SAEs) have been used to identify features within LLMs, a clear picture of how these features evolve during training remains elusive. In this study, we: (1) introduce SAE-Track, a method to efficiently obtain a continual series of SAEs; (2) formulate the process of feature formation and conduct a mechanistic analysis; and (3) analyze and visualize feature drift during training. Our work provides new insights into the dynamics of features in LLMs, enhancing our understanding of training mechanisms and feature evolution.

LLM Agent for Fire Dynamics Simulations

Significant advances have been achieved in leveraging foundation models, such as large language models (LLMs), to accelerate complex scientific workflows. In this work we introduce FoamPilot, a proof-of-concept LLM agent designed to enhance the usability of FireFOAM, a specialized solver for fire dynamics and fire suppression simulations built using OpenFOAM, a popular open-source toolbox for computational fluid dynamics (CFD). FoamPilot provides three core functionalities: code insight, case configuration and simulation evaluation. Code insight is an alternative to traditional keyword searching leveraging retrieval-augmented generation (RAG) and aims to enable efficient navigation and summarization of the FireFOAM source code for developers and experienced users. For case configuration, the agent interprets user requests in natural language and aims to modify existing simulation setups accordingly to support intermediate users. FoamPilot's job execution functionality seeks to manage the submission and execution of simulations in high-performance computing (HPC) environments and provide preliminary analysis of simulation results to support less experienced users. Promising results were achieved for each functionality, particularly for simple tasks, and opportunities were identified for significant further improvement for more complex tasks. The integration of these functionalities into a single LLM agent is a step aimed at accelerating the simulation workflow for engineers and scientists employing FireFOAM for complex simulations critical for improving fire safety.

QSM-RimDS: A highly sensitive paramagnetic rim lesion detection and segmentation tool for multiple sclerosis lesions

Paramagnetic rim lesions (PRLs) are imaging biomarker of the innate immune response in MS lesions. QSM-RimNet, a state-of-the-art tool for PRLs detection on QSM, can identify PRLs but requires precise QSM lesion mask and does not provide rim segmentation. Therefore, the aims of this study are to develop QSM-RimDS algorithm to detect PRLs using the readily available FLAIR lesion mask and to provide rim segmentation for microglial quantification. QSM-RimDS, a deep-learning based tool for joint PRL rim segmentation and PRL detection has been developed. QSM-RimDS has obtained state-of-the art performance in PRL detection and therefore has the potential to be used in clinical practice as a tool to assist human readers for the time-consuming PRL detection and segmentation task. QSM-RimDS is made publicly available [https://github.com/kennyha85/QSM_RimDS]

Bootstrapping Language-Guided Navigation Learning with Self-Refining Data Flywheel

Creating high-quality data for training robust language-instructed agents is a long-lasting challenge in embodied AI. In this paper, we introduce a Self-Refining Data Flywheel (SRDF) that generates high-quality and large-scale navigational instruction-trajectory pairs by iteratively refining the data pool through the collaboration between two models, the instruction generator and the navigator, without any human-in-the-loop annotation. Specifically, SRDF starts with using a base generator to create an initial data pool for training a base navigator, followed by applying the trained navigator to filter the data pool. This leads to higher-fidelity data to train a better generator, which can, in turn, produce higher-quality data for training the next-round navigator. Such a flywheel establishes a data self-refining process, yielding a continuously improved and highly effective dataset for large-scale language-guided navigation learning. Our experiments demonstrate that after several flywheel rounds, the navigator elevates the performance boundary from 70% to 78% SPL on the classic R2R test set, surpassing human performance (76%) for the first time. Meanwhile, this process results in a superior generator, evidenced by a SPICE increase from 23.5 to 26.2, better than all previous VLN instruction generation methods. Finally, we demonstrate the scalability of our method through increasing environment and instruction diversity, and the generalization ability of our pre-trained navigator across various downstream navigation tasks, surpassing state-of-the-art methods by a large margin in all cases.