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Publications
LitLLM: A Toolkit for Scientific Literature Review
Conducting literature reviews for scientific papers is essential for understanding research, its limitations, and building on existing work.… (see more) It is a tedious task which makes an automatic literature review generator appealing. Unfortunately, many existing works that generate such reviews using Large Language Models (LLMs) have significant limitations. They tend to hallucinate-generate non-actual information-and ignore the latest research they have not been trained on. To address these limitations, we propose a toolkit that operates on Retrieval Augmented Generation (RAG) principles, specialized prompting and instructing techniques with the help of LLMs. Our system first initiates a web search to retrieve relevant papers by summarizing user-provided abstracts into keywords using an off-the-shelf LLM. Authors can enhance the search by supplementing it with relevant papers or keywords, contributing to a tailored retrieval process. Second, the system re-ranks the retrieved papers based on the user-provided abstract. Finally, the related work section is generated based on the re-ranked results and the abstract. There is a substantial reduction in time and effort for literature review compared to traditional methods, establishing our toolkit as an efficient alternative. Our open-source toolkit is accessible at https://github.com/shubhamagarwal92/LitLLM and Huggingface space (https://huggingface.co/spaces/shubhamagarwal92/LitLLM) with the video demo at https://youtu.be/E2ggOZBAFw0.
Conducting literature reviews for scientific papers is essential for understanding research, its limitations, and building on existing work.… (see more) It is a tedious task which makes an automatic literature review generator appealing. Unfortunately, many existing works that generate such reviews using Large Language Models (LLMs) have significant limitations. They tend to hallucinate-generate non-actual information-and ignore the latest research they have not been trained on. To address these limitations, we propose a toolkit that operates on Retrieval Augmented Generation (RAG) principles, specialized prompting and instructing techniques with the help of LLMs. Our system first initiates a web search to retrieve relevant papers by summarizing user-provided abstracts into keywords using an off-the-shelf LLM. Authors can enhance the search by supplementing it with relevant papers or keywords, contributing to a tailored retrieval process. Second, the system re-ranks the retrieved papers based on the user-provided abstract. Finally, the related work section is generated based on the re-ranked results and the abstract. There is a substantial reduction in time and effort for literature review compared to traditional methods, establishing our toolkit as an efficient alternative. Our open-source toolkit is accessible at https://github.com/shubhamagarwal92/LitLLM and Huggingface space (https://huggingface.co/spaces/shubhamagarwal92/LitLLM) with the video demo at https://youtu.be/E2ggOZBAFw0.
Conducting literature reviews for scientific papers is essential for understanding research, its limitations, and building on existing work.… (see more) It is a tedious task which makes an automatic literature review generator appealing. Unfortunately, many existing works that generate such reviews using Large Language Models (LLMs) have significant limitations. They tend to hallucinate-generate non-actual information-and ignore the latest research they have not been trained on. To address these limitations, we propose a toolkit that operates on Retrieval Augmented Generation (RAG) principles, specialized prompting and instructing techniques with the help of LLMs. Our system first initiates a web search to retrieve relevant papers by summarizing user-provided abstracts into keywords using an off-the-shelf LLM. Authors can enhance the search by supplementing it with relevant papers or keywords, contributing to a tailored retrieval process. Second, the system re-ranks the retrieved papers based on the user-provided abstract. Finally, the related work section is generated based on the re-ranked results and the abstract. There is a substantial reduction in time and effort for literature review compared to traditional methods, establishing our toolkit as an efficient alternative. Our open-source toolkit is accessible at https://github.com/shubhamagarwal92/LitLLM and Huggingface space (https://huggingface.co/spaces/shubhamagarwal92/LitLLM) with the video demo at https://youtu.be/E2ggOZBAFw0.
Abstract Precise identification of spinal nerve rootlets is relevant to delineate spinal levels for the study of functional activity in the … (see more)spinal cord. The goal of this study was to develop an automatic method for the semantic segmentation of spinal nerve rootlets from T2-weighted magnetic resonance imaging (MRI) scans. Images from two open-access 3T MRI datasets were used to train a 3D multi-class convolutional neural network using an active learning approach to segment C2-C8 dorsal nerve rootlets. Each output class corresponds to a spinal level. The method was tested on 3T T2-weighted images from three datasets unseen during training to assess inter-site, inter-session, and inter-resolution variability. The test Dice score was 0.67 ± 0.16 (mean ± standard deviation across testing images and rootlets levels), suggesting a good performance. The method also demonstrated low inter-vendor and inter-site variability (coefficient of variation ≤ 1.41%), as well as low inter-session variability (coefficient of variation ≤ 1.30%), indicating stable predictions across different MRI vendors, sites, and sessions. The proposed methodology is open-source and readily available in the Spinal Cord Toolbox (SCT) v6.2 and higher.
Abstract Precise identification of spinal nerve rootlets is relevant to delineate spinal levels for the study of functional activity in the … (see more)spinal cord. The goal of this study was to develop an automatic method for the semantic segmentation of spinal nerve rootlets from T2-weighted magnetic resonance imaging (MRI) scans. Images from two open-access 3T MRI datasets were used to train a 3D multi-class convolutional neural network using an active learning approach to segment C2-C8 dorsal nerve rootlets. Each output class corresponds to a spinal level. The method was tested on 3T T2-weighted images from three datasets unseen during training to assess inter-site, inter-session, and inter-resolution variability. The test Dice score was 0.67 ± 0.16 (mean ± standard deviation across testing images and rootlets levels), suggesting a good performance. The method also demonstrated low inter-vendor and inter-site variability (coefficient of variation ≤ 1.41%), as well as low inter-session variability (coefficient of variation ≤ 1.30%), indicating stable predictions across different MRI vendors, sites, and sessions. The proposed methodology is open-source and readily available in the Spinal Cord Toolbox (SCT) v6.2 and higher.
