Large Language Models for Bioinformatics

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

Label-Efficient Data Augmentation with Video Diffusion Models for Guidewire Segmentation in Cardiac Fluoroscopy

The accurate segmentation of guidewires in interventional cardiac fluoroscopy videos is crucial for computer-aided navigation tasks. Although deep learning methods have demonstrated high accuracy and robustness in wire segmentation, they require substantial annotated datasets for generalizability, underscoring the need for extensive labeled data to enhance model performance. To address this challenge, we propose the Segmentation-guided Frame-consistency Video Diffusion Model (SF-VD) to generate large collections of labeled fluoroscopy videos, augmenting the training data for wire segmentation networks. SF-VD leverages videos with limited annotations by independently modeling scene distribution and motion distribution. It first samples the scene distribution by generating 2D fluoroscopy images with wires positioned according to a specified input mask, and then samples the motion distribution by progressively generating subsequent frames, ensuring frame-to-frame coherence through a frame-consistency strategy. A segmentation-guided mechanism further refines the process by adjusting wire contrast, ensuring a diverse range of visibility in the synthesized image. Evaluation on a fluoroscopy dataset confirms the superior quality of the generated videos and shows significant improvements in guidewire segmentation.

Pre-training a Density-Aware Pose Transformer for Robust LiDAR-based 3D Human Pose Estimation

With the rapid development of autonomous driving, LiDAR-based 3D Human Pose Estimation (3D HPE) is becoming a research focus. However, due to the noise and sparsity of LiDAR-captured point clouds, robust human pose estimation remains challenging. Most of the existing methods use temporal information, multi-modal fusion, or SMPL optimization to correct biased results. In this work, we try to obtain sufficient information for 3D HPE only by modeling the intrinsic properties of low-quality point clouds. Hence, a simple yet powerful method is proposed, which provides insights both on modeling and augmentation of point clouds. Specifically, we first propose a concise and effective density-aware pose transformer (DAPT) to get stable keypoint representations. By using a set of joint anchors and a carefully designed exchange module, valid information is extracted from point clouds with different densities. Then 1D heatmaps are utilized to represent the precise locations of the keypoints. Secondly, a comprehensive LiDAR human synthesis and augmentation method is proposed to pre-train the model, enabling it to acquire a better human body prior. We increase the diversity of point clouds by randomly sampling human positions and orientations and by simulating occlusions through the addition of laser-level masks. Extensive experiments have been conducted on multiple datasets, including IMU-annotated LidarHuman26M, SLOPER4D, and manually annotated Waymo Open Dataset v2.0 (Waymo), HumanM3. Our method demonstrates SOTA performance in all scenarios. In particular, compared with LPFormer on Waymo, we reduce the average MPJPE by $10.0mm$. Compared with PRN on SLOPER4D, we notably reduce the average MPJPE by $20.7mm$.

FD2-Net: Frequency-Driven Feature Decomposition Network for Infrared-Visible Object Detection

Infrared-visible object detection (IVOD) seeks to harness the complementary information in infrared and visible images, thereby enhancing the performance of detectors in complex environments. However, existing methods often neglect the frequency characteristics of complementary information, such as the abundant high-frequency details in visible images and the valuable low-frequency thermal information in infrared images, thus constraining detection performance. To solve this problem, we introduce a novel Frequency-Driven Feature Decomposition Network for IVOD, called FD2-Net, which effectively captures the unique frequency representations of complementary information across multimodal visual spaces. Specifically, we propose a feature decomposition encoder, wherein the high-frequency unit (HFU) utilizes discrete cosine transform to capture representative high-frequency features, while the low-frequency unit (LFU) employs dynamic receptive fields to model the multi-scale context of diverse objects. Next, we adopt a parameter-free complementary strengths strategy to enhance multimodal features through seamless inter-frequency recoupling. Furthermore, we innovatively design a multimodal reconstruction mechanism that recovers image details lost during feature extraction, further leveraging the complementary information from infrared and visible images to enhance overall representational capacity. Extensive experiments demonstrate that FD2-Net outperforms state-of-the-art (SOTA) models across various IVOD benchmarks, i.e. LLVIP (96.2% mAP), FLIR (82.9% mAP), and M3FD (83.5% mAP).

Long-Tailed Object Detection Pre-training: Dynamic Rebalancing Contrastive Learning with Dual Reconstruction

Pre-training plays a vital role in various vision tasks, such as object recognition and detection. Commonly used pre-training methods, which typically rely on randomized approaches like uniform or Gaussian distributions to initialize model parameters, often fall short when confronted with long-tailed distributions, especially in detection tasks. This is largely due to extreme data imbalance and the issue of simplicity bias. In this paper, we introduce a novel pre-training framework for object detection, called Dynamic Rebalancing Contrastive Learning with Dual Reconstruction (2DRCL). Our method builds on a Holistic-Local Contrastive Learning mechanism, which aligns pre-training with object detection by capturing both global contextual semantics and detailed local patterns. To tackle the imbalance inherent in long-tailed data, we design a dynamic rebalancing strategy that adjusts the sampling of underrepresented instances throughout the pre-training process, ensuring better representation of tail classes. Moreover, Dual Reconstruction addresses simplicity bias by enforcing a reconstruction task aligned with the self-consistency principle, specifically benefiting underrepresented tail classes. Experiments on COCO and LVIS v1.0 datasets demonstrate the effectiveness of our method, particularly in improving the mAP/AP scores for tail classes.

Evaluation of OpenAI o1: Opportunities and Challenges of AGI

This comprehensive study evaluates the performance of OpenAI's o1-preview large language model across a diverse array of complex reasoning tasks, spanning multiple domains, including computer science, mathematics, natural sciences, medicine, linguistics, and social sciences. Through rigorous testing, o1-preview demonstrated remarkable capabilities, often achieving human-level or superior performance in areas ranging from coding challenges to scientific reasoning and from language processing to creative problem-solving. Key findings include: -83.3% success rate in solving complex competitive programming problems, surpassing many human experts. -Superior ability in generating coherent and accurate radiology reports, outperforming other evaluated models. -100% accuracy in high school-level mathematical reasoning tasks, providing detailed step-by-step solutions. -Advanced natural language inference capabilities across general and specialized domains like medicine. -Impressive performance in chip design tasks, outperforming specialized models in areas such as EDA script generation and bug analysis. -Remarkable proficiency in anthropology and geology, demonstrating deep understanding and reasoning in these specialized fields. -Strong capabilities in quantitative investing. O1 has comprehensive financial knowledge and statistical modeling skills. -Effective performance in social media analysis, including sentiment analysis and emotion recognition. The model excelled particularly in tasks requiring intricate reasoning and knowledge integration across various fields. While some limitations were observed, including occasional errors on simpler problems and challenges with certain highly specialized concepts, the overall results indicate significant progress towards artificial general intelligence.

Auxiliary Input in Training: Incorporating Catheter Features into Deep Learning Models for ECG-Free Dynamic Coronary Roadmapping

Dynamic coronary roadmapping is a technology that overlays the vessel maps (the "roadmap") extracted from an offline image sequence of X-ray angiography onto a live stream of X-ray fluoroscopy in real-time. It aims to offer navigational guidance for interventional surgeries without the need for repeated contrast agent injections, thereby reducing the risks associated with radiation exposure and kidney failure. The precision of the roadmaps is contingent upon the accurate alignment of angiographic and fluoroscopic images based on their cardiac phases, as well as precise catheter tip tracking. The former ensures the selection of a roadmap that closely matches the vessel shape in the current frame, while the latter uses catheter tips as reference points to adjust for translational motion between the roadmap and the present vessel tree. Training deep learning models for both tasks is challenging and underexplored. However, incorporating catheter features into the models could offer substantial benefits, given humans heavily rely on catheters to complete the tasks. To this end, we introduce a simple but effective method, auxiliary input in training (AIT), and demonstrate that it enhances model performance across both tasks, outperforming baseline methods in knowledge incorporation and transfer learning.

Retrieval-augmented Few-shot Medical Image Segmentation with Foundation Models

Medical image segmentation is crucial for clinical decision-making, but the scarcity of annotated data presents significant challenges. Few-shot segmentation (FSS) methods show promise but often require retraining on the target domain and struggle to generalize across different modalities. Similarly, adapting foundation models like the Segment Anything Model (SAM) for medical imaging has limitations, including the need for finetuning and domain-specific adaptation. To address these issues, we propose a novel method that adapts DINOv2 and Segment Anything Model 2 (SAM 2) for retrieval-augmented few-shot medical image segmentation. Our approach uses DINOv2's feature as query to retrieve similar samples from limited annotated data, which are then encoded as memories and stored in memory bank. With the memory attention mechanism of SAM 2, the model leverages these memories as conditions to generate accurate segmentation of the target image. We evaluated our framework on three medical image segmentation tasks, demonstrating superior performance and generalizability across various modalities without the need for any retraining or finetuning. Overall, this method offers a practical and effective solution for few-shot medical image segmentation and holds significant potential as a valuable annotation tool in clinical applications.

Preference-Guided Reinforcement Learning for Efficient Exploration

In this paper, we investigate preference-based reinforcement learning (PbRL) that allows reinforcement learning (RL) agents to learn from human feedback. This is particularly valuable when defining a fine-grain reward function is not feasible. However, this approach is inefficient and impractical for promoting deep exploration in hard-exploration tasks with long horizons and sparse rewards. To tackle this issue, we introduce LOPE: Learning Online with trajectory Preference guidancE, an end-to-end preference-guided RL framework that enhances exploration efficiency in hard-exploration tasks. Our intuition is that LOPE directly adjusts the focus of online exploration by considering human feedback as guidance, avoiding learning a separate reward model from preferences. Specifically, LOPE includes a two-step sequential policy optimization process consisting of trust-region-based policy improvement and preference guidance steps. We reformulate preference guidance as a novel trajectory-wise state marginal matching problem that minimizes the maximum mean discrepancy distance between the preferred trajectories and the learned policy. Furthermore, we provide a theoretical analysis to characterize the performance improvement bound and evaluate the LOPE's effectiveness. When assessed in various challenging hard-exploration environments, LOPE outperforms several state-of-the-art methods regarding convergence rate and overall performance. The code used in this study is available at \url{https://github.com/buaawgj/LOPE}.

Auto-Multilift: Distributed Learning and Control for Cooperative Load Transportation With Quadrotors

Designing motion control and planning algorithms for multilift systems remains challenging due to the complexities of dynamics, collision avoidance, actuator limits, and scalability. Existing methods that use optimization and distributed techniques effectively address these constraints and scalability issues. However, they often require substantial manual tuning, leading to suboptimal performance. This paper proposes Auto-Multilift, a novel framework that automates the tuning of model predictive controllers (MPCs) for multilift systems. We model the MPC cost functions with deep neural networks (DNNs), enabling fast online adaptation to various scenarios. We develop a distributed policy gradient algorithm to train these DNNs efficiently in a closed-loop manner. Central to our algorithm is distributed sensitivity propagation, which parallelizes gradient computation across quadrotors, focusing on actual system state sensitivities relative to key MPC parameters. We also provide theoretical guarantees for the convergence of this algorithm. Extensive simulations show rapid convergence and favorable scalability to a large number of quadrotors. Our method outperforms a state-of-the-art open-loop MPC tuning approach by effectively learning adaptive MPCs from trajectory tracking errors and handling the unique dynamics couplings within the multilift system. Additionally, our framework can learn an adaptive reference for reconfigurating the system when traversing through multiple narrow slots.