Benchmarking AI scientists in omics data-driven biological research

The rise of large language models and multi-agent systems has sparked growing interest in AI scientists capable of autonomous biological research. However, existing benchmarks either focus on reasoning without data or on data analysis with predefined statistical answers, lacking realistic, data-driven evaluation settings. Here, we introduce the Biological AI Scientist Benchmark (BaisBench), a benchmark designed to assess AI scientists' ability to generate biological discoveries through data analysis and reasoning with external knowledge. BaisBench comprises two tasks: cell type annotation on 31 expert-labeled single-cell datasets, and scientific discovery through answering 198 multiple-choice questions derived from the biological insights of 41 recent single-cell studies. Systematic experiments on state-of-the-art AI scientists and LLM agents showed that while promising, current models still substantially underperform human experts on both tasks. We hope BaisBench will fill this gap and serve as a foundation for advancing and evaluating AI models for scientific discovery. The benchmark can be found at: https://github.com/EperLuo/BaisBench.

Intelligent Spatial Perception by Building Hierarchical 3D Scene Graphs for Indoor Scenarios with the Help of LLMs

This paper addresses the high demand in advanced intelligent robot navigation for a more holistic understanding of spatial environments, by introducing a novel system that harnesses the capabilities of Large Language Models (LLMs) to construct hierarchical 3D Scene Graphs (3DSGs) for indoor scenarios. The proposed framework constructs 3DSGs consisting of a fundamental layer with rich metric-semantic information, an object layer featuring precise point-cloud representation of object nodes as well as visual descriptors, and higher layers of room, floor, and building nodes. Thanks to the innovative application of LLMs, not only object nodes but also nodes of higher layers, e.g., room nodes, are annotated in an intelligent and accurate manner. A polling mechanism for room classification using LLMs is proposed to enhance the accuracy and reliability of the room node annotation. Thorough numerical experiments demonstrate the system's ability to integrate semantic descriptions with geometric data, creating an accurate and comprehensive representation of the environment instrumental for context-aware navigation and task planning.

QueST: Querying Functional and Structural Niches on Spatial Transcriptomics Data via Contrastive Subgraph Embedding

The functional or structural spatial regions within tissues, referred to as spatial niches, are elements for illustrating the spatial contexts of multicellular organisms. A key challenge is querying shared niches across diverse tissues, which is crucial for achieving a comprehensive understanding of the organization and phenotypes of cell populations. However, current data analysis methods predominantly focus on creating spatial-aware embeddings for cells, neglecting the development of niche-level representations for effective querying. To address this gap, we introduce QueST, a novel niche representation learning model designed for querying spatial niches across multiple samples. QueST utilizes a novel subgraph contrastive learning approach to explicitly capture niche-level characteristics and incorporates adversarial training to mitigate batch effects. We evaluate QueST on established benchmarks using human and mouse datasets, demonstrating its superiority over state-of-the-art graph representation learning methods in accurate niche queries. Overall, QueST offers a specialized model for spatial niche queries, paving the way for deeper insights into the patterns and mechanisms of cell spatial organization across tissues. Source code can be found at https://github.com/cmhimself/QueST.

StraightPCF: Straight Point Cloud Filtering

Point cloud filtering is a fundamental 3D vision task, which aims to remove noise while recovering the underlying clean surfaces. State-of-the-art methods remove noise by moving noisy points along stochastic trajectories to the clean surfaces. These methods often require regularization within the training objective and/or during post-processing, to ensure fidelity. In this paper, we introduce StraightPCF, a new deep learning based method for point cloud filtering. It works by moving noisy points along straight paths, thus reducing discretization errors while ensuring faster convergence to the clean surfaces. We model noisy patches as intermediate states between high noise patch variants and their clean counterparts, and design the VelocityModule to infer a constant flow velocity from the former to the latter. This constant flow leads to straight filtering trajectories. In addition, we introduce a DistanceModule that scales the straight trajectory using an estimated distance scalar to attain convergence near the clean surface. Our network is lightweight and only has $\sim530K$ parameters, being 17% of IterativePFN (a most recent point cloud filtering network). Extensive experiments on both synthetic and real-world data show our method achieves state-of-the-art results. Our method also demonstrates nice distributions of filtered points without the need for regularization. The implementation code can be found at: https://github.com/ddsediri/StraightPCF.

scDiffusion: conditional generation of high-quality single-cell data using diffusion model

Single-cell RNA sequencing (scRNA-seq) data are important for studying the biology of development or diseases at single-cell level. To better understand the properties of the data, to build controlled benchmark data for testing downstream methods, and to augment data when collecting sufficient real data is challenging, generative models have been proposed to computationally generate synthetic scRNA-seq data. However, the data generated with current models are not very realistic yet, especially when we need to generate data with controlled conditions. In the meantime, the Diffusion models have shown their power in generating data in computer vision at high fidelity, providing a new opportunity for scRNA-seq generation. In this study, we developed scDiffusion, a diffusion-based model to generate high-quality scRNA-seq data with controlled conditions. We designed multiple classifiers to guide the diffusion process simultaneously, enabling scDiffusion to generate data under multiple condition combinations. We also proposed a new control strategy called Gradient Interpolation. This strategy allows the model to generate continuous trajectories of cell development from a given cell state. Experiments showed that scDiffusion can generate single-cell gene expression data closely resembling real scRNA-seq data, surpassing state-of-the-art models in multiple metrics. Also, scDiffusion can conditionally produce data on specific cell types including rare cell types. Furthermore, we could use the multiple-condition generation of scDiffusion to generate cell type that was out of the training data. Leveraging the Gradient Interpolation strategy, we generated a continuous developmental trajectory of mouse embryonic cells. These experiments demonstrate that scDiffusion is a powerful tool for augmenting the real scRNA-seq data and can provide insights into cell fate research.

TIMS: A Tactile Internet-Based Micromanipulation System with Haptic Guidance for Surgical Training

Microsurgery involves the dexterous manipulation of delicate tissue or fragile structures such as small blood vessels, nerves, etc., under a microscope. To address the limitation of imprecise manipulation of human hands, robotic systems have been developed to assist surgeons in performing complex microsurgical tasks with greater precision and safety. However, the steep learning curve for robot-assisted microsurgery (RAMS) and the shortage of well-trained surgeons pose significant challenges to the widespread adoption of RAMS. Therefore, the development of a versatile training system for RAMS is necessary, which can bring tangible benefits to both surgeons and patients. In this paper, we present a Tactile Internet-Based Micromanipulation System (TIMS) based on a ROS-Django web-based architecture for microsurgical training. This system can provide tactile feedback to operators via a wearable tactile display (WTD), while real-time data is transmitted through the internet via a ROS-Django framework. In addition, TIMS integrates haptic guidance to `guide' the trainees to follow a desired trajectory provided by expert surgeons. Learning from demonstration based on Gaussian Process Regression (GPR) was used to generate the desired trajectory. User studies were also conducted to verify the effectiveness of our proposed TIMS, comparing users' performance with and without tactile feedback and/or haptic guidance.

Explainable Hierarchical Imitation Learning for Robotic Drink Pouring

To accurately pour drinks into various containers is an essential skill for service robots. However, drink pouring is a dynamic process and difficult to model. Traditional deep imitation learning techniques for implementing autonomous robotic pouring have an inherent black-box effect and require a large amount of demonstration data for model training. To address these issues, an Explainable Hierarchical Imitation Learning (EHIL) method is proposed in this paper such that a robot can learn high-level general knowledge and execute low-level actions across multiple drink pouring scenarios. Moreover, with EHIL, a logical graph can be constructed for task execution, through which the decision-making process for action generation can be made explainable to users and the causes of failure can be traced out. Based on the logical graph, the framework is manipulable to achieve different targets while the adaptability to unseen scenarios can be achieved in an explainable manner. A series of experiments have been conducted to verify the effectiveness of the proposed method. Results indicate that EHIL outperforms the traditional behavior cloning method in terms of success rate, adaptability, manipulability and explainability.