From Intention To Implementation: Automating Biomedical Research via LLMs

Conventional biomedical research is increasingly labor-intensive due to the exponential growth of scientific literature and datasets. Artificial intelligence (AI), particularly Large Language Models (LLMs), has the potential to revolutionize this process by automating various steps. Still, significant challenges remain, including the need for multidisciplinary expertise, logicality of experimental design, and performance measurements. This paper introduces BioResearcher, the first end-to-end automated system designed to streamline the entire biomedical research process involving dry lab experiments. BioResearcher employs a modular multi-agent architecture, integrating specialized agents for search, literature processing, experimental design, and programming. By decomposing complex tasks into logically related sub-tasks and utilizing a hierarchical learning approach, BioResearcher effectively addresses the challenges of multidisciplinary requirements and logical complexity. Furthermore, BioResearcher incorporates an LLM-based reviewer for in-process quality control and introduces novel evaluation metrics to assess the quality and automation of experimental protocols. BioResearcher successfully achieves an average execution success rate of 63.07% across eight previously unmet research objectives. The generated protocols averagely outperform typical agent systems by 22.0% on five quality metrics. The system demonstrates significant potential to reduce researchers' workloads and accelerate biomedical discoveries, paving the way for future innovations in automated research systems.

GaussReg: Fast 3D Registration with Gaussian Splatting

Point cloud registration is a fundamental problem for large-scale 3D scene scanning and reconstruction. With the help of deep learning, registration methods have evolved significantly, reaching a nearly-mature stage. As the introduction of Neural Radiance Fields (NeRF), it has become the most popular 3D scene representation as its powerful view synthesis capabilities. Regarding NeRF representation, its registration is also required for large-scale scene reconstruction. However, this topic extremly lacks exploration. This is due to the inherent challenge to model the geometric relationship among two scenes with implicit representations. The existing methods usually convert the implicit representation to explicit representation for further registration. Most recently, Gaussian Splatting (GS) is introduced, employing explicit 3D Gaussian. This method significantly enhances rendering speed while maintaining high rendering quality. Given two scenes with explicit GS representations, in this work, we explore the 3D registration task between them. To this end, we propose GaussReg, a novel coarse-to-fine framework, both fast and accurate. The coarse stage follows existing point cloud registration methods and estimates a rough alignment for point clouds from GS. We further newly present an image-guided fine registration approach, which renders images from GS to provide more detailed geometric information for precise alignment. To support comprehensive evaluation, we carefully build a scene-level dataset called ScanNet-GSReg with 1379 scenes obtained from the ScanNet dataset and collect an in-the-wild dataset called GSReg. Experimental results demonstrate our method achieves state-of-the-art performance on multiple datasets. Our GaussReg is 44 times faster than HLoc (SuperPoint as the feature extractor and SuperGlue as the matcher) with comparable accuracy.

LaTiM: Longitudinal representation learning in continuous-time models to predict disease progression

This work proposes a novel framework for analyzing disease progression using time-aware neural ordinary differential equations (NODE). We introduce a "time-aware head" in a framework trained through self-supervised learning (SSL) to leverage temporal information in latent space for data augmentation. This approach effectively integrates NODEs with SSL, offering significant performance improvements compared to traditional methods that lack explicit temporal integration. We demonstrate the effectiveness of our strategy for diabetic retinopathy progression prediction using the OPHDIAT database. Compared to the baseline, all NODE architectures achieve statistically significant improvements in area under the ROC curve (AUC) and Kappa metrics, highlighting the efficacy of pre-training with SSL-inspired approaches. Additionally, our framework promotes stable training for NODEs, a commonly encountered challenge in time-aware modeling.

L-MAE: Longitudinal masked auto-encoder with time and severity-aware encoding for diabetic retinopathy progression prediction

Pre-training strategies based on self-supervised learning (SSL) have proven to be effective pretext tasks for many downstream tasks in computer vision. Due to the significant disparity between medical and natural images, the application of typical SSL is not straightforward in medical imaging. Additionally, those pretext tasks often lack context, which is critical for computer-aided clinical decision support. In this paper, we developed a longitudinal masked auto-encoder (MAE) based on the well-known Transformer-based MAE. In particular, we explored the importance of time-aware position embedding as well as disease progression-aware masking. Taking into account the time between examinations instead of just scheduling them offers the benefit of capturing temporal changes and trends. The masking strategy, for its part, evolves during follow-up to better capture pathological changes, ensuring a more accurate assessment of disease progression. Using OPHDIAT, a large follow-up screening dataset targeting diabetic retinopathy (DR), we evaluated the pre-trained weights on a longitudinal task, which is to predict the severity label of the next visit within 3 years based on the past time series examinations. Our results demonstrated the relevancy of both time-aware position embedding and masking strategies based on disease progression knowledge. Compared to popular baseline models and standard longitudinal Transformers, these simple yet effective extensions significantly enhance the predictive ability of deep classification models.

An Enhanced Prompt-Based LLM Reasoning Scheme via Knowledge Graph-Integrated Collaboration

While Large Language Models (LLMs) demonstrate exceptional performance in a multitude of Natural Language Processing (NLP) tasks, they encounter challenges in practical applications, including issues with hallucinations, inadequate knowledge updating, and limited transparency in the reasoning process. To overcome these limitations, this study innovatively proposes a collaborative training-free reasoning scheme involving tight cooperation between Knowledge Graph (KG) and LLMs. This scheme first involves using LLMs to iteratively explore KG, selectively retrieving a task-relevant knowledge subgraph to support reasoning. The LLMs are then guided to further combine inherent implicit knowledge to reason on the subgraph while explicitly elucidating the reasoning process. Through such a cooperative approach, our scheme achieves more reliable knowledge-based reasoning and facilitates the tracing of the reasoning results. Experimental results show that our scheme significantly progressed across multiple datasets, notably achieving over a 10% improvement on the QALD10 dataset compared to the best baseline and the fine-tuned state-of-the-art (SOTA) work. Building on this success, this study hopes to offer a valuable reference for future research in the fusion of KG and LLMs, thereby enhancing LLMs' proficiency in solving complex issues.

DISCOVER: 2-D Multiview Summarization of Optical Coherence Tomography Angiography for Automatic Diabetic Retinopathy Diagnosis

Diabetic Retinopathy (DR), an ocular complication of diabetes, is a leading cause of blindness worldwide. Traditionally, DR is monitored using Color Fundus Photography (CFP), a widespread 2-D imaging modality. However, DR classifications based on CFP have poor predictive power, resulting in suboptimal DR management. Optical Coherence Tomography Angiography (OCTA) is a recent 3-D imaging modality offering enhanced structural and functional information (blood flow) with a wider field of view. This paper investigates automatic DR severity assessment using 3-D OCTA. A straightforward solution to this task is a 3-D neural network classifier. However, 3-D architectures have numerous parameters and typically require many training samples. A lighter solution consists in using 2-D neural network classifiers processing 2-D en-face (or frontal) projections and/or 2-D cross-sectional slices. Such an approach mimics the way ophthalmologists analyze OCTA acquisitions: 1) en-face flow maps are often used to detect avascular zones and neovascularization, and 2) cross-sectional slices are commonly analyzed to detect macular edemas, for instance. However, arbitrary data reduction or selection might result in information loss. Two complementary strategies are thus proposed to optimally summarize OCTA volumes with 2-D images: 1) a parametric en-face projection optimized through deep learning and 2) a cross-sectional slice selection process controlled through gradient-based attribution. The full summarization and DR classification pipeline is trained from end to end. The automatic 2-D summary can be displayed in a viewer or printed in a report to support the decision. We show that the proposed 2-D summarization and classification pipeline outperforms direct 3-D classification with the advantage of improved interpretability.

Automated Detection of Myopic Maculopathy in MMAC 2023: Achievements in Classification, Segmentation, and Spherical Equivalent Prediction

Myopic macular degeneration is the most common complication of myopia and the primary cause of vision loss in individuals with pathological myopia. Early detection and prompt treatment are crucial in preventing vision impairment due to myopic maculopathy. This was the focus of the Myopic Maculopathy Analysis Challenge (MMAC), in which we participated. In task 1, classification of myopic maculopathy, we employed the contrastive learning framework, specifically SimCLR, to enhance classification accuracy by effectively capturing enriched features from unlabeled data. This approach not only improved the intrinsic understanding of the data but also elevated the performance of our classification model. For Task 2 (segmentation of myopic maculopathy plus lesions), we have developed independent segmentation models tailored for different lesion segmentation tasks and implemented a test-time augmentation strategy to further enhance the model's performance. As for Task 3 (prediction of spherical equivalent), we have designed a deep regression model based on the data distribution of the dataset and employed an integration strategy to enhance the model's prediction accuracy. The results we obtained are promising and have allowed us to position ourselves in the Top 6 of the classification task, the Top 2 of the segmentation task, and the Top 1 of the prediction task. The code is available at \url{https://github.com/liyihao76/MMAC_LaTIM_Solution}.

VeryFL: A Verify Federated Learning Framework Embedded with Blockchain

Blockchain-empowered federated learning (FL) has provoked extensive research recently. Various blockchain-based federated learning algorithm, architecture and mechanism have been designed to solve issues like single point failure and data falsification brought by centralized FL paradigm. Moreover, it is easier to allocate incentives to nodes with the help of the blockchain. Various centralized federated learning frameworks like FedML, have emerged in the community to help boost the research on FL. However, decentralized blockchain-based federated learning framework is still missing, which cause inconvenience for researcher to reproduce or verify the algorithm performance based on blockchain. Inspired by the above issues, we have designed and developed a blockchain-based federated learning framework by embedding Ethereum network. This report will present the overall structure of this framework, which proposes a code practice paradigm for the combination of FL with blockchain and, at the same time, compatible with normal FL training task. In addition to implement some blockchain federated learning algorithms on smart contract to help execute a FL training, we also propose a model ownership authentication architecture based on blockchain and model watermarking to protect the intellectual property rights of models. These mechanism on blockchain shows an underlying support of blockchain for federated learning to provide a verifiable training, aggregation and incentive distribution procedure and thus we named this framework VeryFL (A Verify Federated Learninig Framework Embedded with Blockchain). The source code is avaliable on https://github.com/GTMLLab/VeryFL.

Tokenized Model: A Blockchain-Empowered Decentralized Model Ownership Verification Platform

With the development of practical deep learning models like generative AI, their excellent performance has brought huge economic value. For instance, ChatGPT has attracted more than 100 million users in three months. Since the model training requires a lot of data and computing power, a well-performing deep learning model is behind a huge effort and cost. Facing various model attacks, unauthorized use and abuse from the network that threaten the interests of model owners, in addition to considering legal and other administrative measures, it is equally important to protect the model's copyright from the technical means. By using the model watermarking technology, we point out the possibility of building a unified platform for model ownership verification. Given the application history of blockchain in copyright verification and the drawbacks of a centralized third-party, this paper considers combining model watermarking technology and blockchain to build a unified model copyright protection platform. By a new solution we called Tokenized Model, it protects the model's copyright by reliable ownership record and verification mechanism. It also promotes the financial value of model by constructing the model's transaction process and contribution shares of a model. In the typical case study, we also study the various performance under usual scenario to verify the effectiveness of this platform.

FIRST: A Million-Entry Dataset for Text-Driven Fashion Synthesis and Design

Text-driven fashion synthesis and design is an extremely valuable part of artificial intelligence generative content(AIGC), which has the potential to propel a tremendous revolution in the traditional fashion industry. To advance the research on text-driven fashion synthesis and design, we introduce a new dataset comprising a million high-resolution fashion images with rich structured textual(FIRST) descriptions. In the FIRST, there is a wide range of attire categories and each image-paired textual description is organized at multiple hierarchical levels. Experiments on prevalent generative models trained over FISRT show the necessity of FIRST. We invite the community to further develop more intelligent fashion synthesis and design systems that make fashion design more creative and imaginative based on our dataset. The dataset will be released soon.