Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper, rather than pursuing state-of-the-art performance, we aim to evaluate capabilities of LLMs in a wide range of tasks across the chemistry domain. We identify three key chemistryrelated capabilities including understanding, reasoning and explaining to explore in LLMs and establish a benchmark containing eight chemistry tasks. Our analysis draws on widely recognized datasets facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Five LLMs (GPT-4, GPT-3.5, Davinci-003, Llama and Galactica) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. Our investigation found that GPT-4 outperformed other models and LLMs exhibit different competitive levels in eight chemistry tasks. In addition to the key findings from the comprehensive benchmark analysis, our work provides insights into the limitation of current LLMs and the impact of in-context learning settings on LLMs’ performance across various chemistry tasks. The code and datasets used in this study are available at https://github.com/ChemFoundationModels/ChemLLMBench.
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Biomedical knowledge graph-optimized prompt generation for large language models
Large language models (LLMs) are being adopted at an unprecedented rate, yet still face challenges in knowledge-intensive domains such as biomedicine. Solutions such as pretraining and domain-specific fine-tuning add substantial computational overhead, requiring further domain-expertise. Here, we introduce a token-optimized and robust Knowledge Graph-based Retrieval Augmented Generation (KG-RAG) framework by leveraging a massive biomedical KG (SPOKE) with LLMs such as Llama-2-13b, GPT-3.5-Turbo, and GPT-4, to generate meaningful biomedical text rooted in established knowledge.
Compared to the existing RAG technique for Knowledge Graphs, the proposed method utilizes minimal graph schema for context extraction and uses embedding methods for context pruning. This optimization in context extraction results in more than 50% reduction in token consumption without compromising the accuracy, making a cost-effective and robust RAG implementation on proprietary LLMs. KG-RAG consistently enhanced the performance of LLMs across diverse biomedical prompts by generating responses rooted in established knowledge, accompanied by accurate provenance and statistical evidence (if available) to substantiate the claims. Further benchmarking on human curated datasets, such as biomedical true/false and multiple-choice questions (MCQ), showed a remarkable 71% boost in the performance of the Llama-2 model on the challenging MCQ dataset, demonstrating the framework’s capacity to empower open-source models with fewer parameters for domain-specific questions. Furthermore, KG-RAG enhanced the performance of proprietary GPT models, such as GPT-3.5 and GPT-4. In summary, the proposed framework combines explicit and implicit knowledge of KG and LLM in a token optimized fashion, thus enhancing the adaptability of general-purpose LLMs to tackle domain-specific questions in a cost-effective fashion.
SPOKE KG can be accessed at https://spoke.rbvi.ucsf.edu/neighborhood.html. It can also be accessed using REST-API (https://spoke.rbvi.ucsf.edu/swagger/). KG-RAG code is made available at https://github.com/BaranziniLab/KG_RAG. Biomedical benchmark datasets used in this study are made available to the research community in the same GitHub repository.
- PAR ID:
- 10545314
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Bioinformatics
- Volume:
- 40
- Issue:
- 9
- ISSN:
- 1367-4811
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Motivation Knowledge graphs (KGs) are being adopted in industry, commerce and academia. Biomedical KG presents a challenge due to the complexity, size and heterogeneity of the underlying information.
Results In this work, we present the Scalable Precision Medicine Open Knowledge Engine (SPOKE), a biomedical KG connecting millions of concepts via semantically meaningful relationships. SPOKE contains 27 million nodes of 21 different types and 53 million edges of 55 types downloaded from 41 databases. The graph is built on the framework of 11 ontologies that maintain its structure, enable mappings and facilitate navigation. SPOKE is built weekly by python scripts which download each resource, check for integrity and completeness, and then create a ‘parent table’ of nodes and edges. Graph queries are translated by a REST API and users can submit searches directly via an API or a graphical user interface. Conclusions/Significance: SPOKE enables the integration of seemingly disparate information to support precision medicine efforts.
Availability and implementation The SPOKE neighborhood explorer is available at https://spoke.rbvi.ucsf.edu.
Supplementary information Supplementary data are available at Bioinformatics online.
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Kochmar, E ; Bexte, M ; Burstein, J ; Horbach, A ; Laarmann-Quante, R ; Tack, A ; Yaneva, V ; Yuan, Z (Ed.)The practice of soliciting self-explanations from students is widely recognized for its pedagogical benefits. However, the labor-intensive effort required to manually assess students’ explanations makes it impractical for classroom settings. As a result, many current solutions to gauge students’ understanding during class are often limited to multiple choice or fill-in-the-blank questions, which are less effective at exposing misconceptions or helping students to understand and integrate new concepts. Recent advances in large language models (LLMs) present an opportunity to assess student explanations in real-time, making explanation-based classroom response systems feasible for implementation. In this work, we investigate LLM-based approaches for assessing the correctness of students’ explanations in response to undergraduate computer science questions. We investigate alternative prompting approaches for multiple LLMs (i.e., Llama 2, GPT-3.5, and GPT-4) and compare their performance to FLAN-T5 models trained in a fine-tuning manner. The results suggest that the highest accuracy and weighted F1 score were achieved by fine-tuning FLAN-T5, while an in-context learning approach with GPT-4 attains the highest macro F1 score.more » « less
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Abstract Importance The study highlights the potential of large language models, specifically GPT-3.5 and GPT-4, in processing complex clinical data and extracting meaningful information with minimal training data. By developing and refining prompt-based strategies, we can significantly enhance the models’ performance, making them viable tools for clinical NER tasks and possibly reducing the reliance on extensive annotated datasets.
Objectives This study quantifies the capabilities of GPT-3.5 and GPT-4 for clinical named entity recognition (NER) tasks and proposes task-specific prompts to improve their performance.
Materials and Methods We evaluated these models on 2 clinical NER tasks: (1) to extract medical problems, treatments, and tests from clinical notes in the MTSamples corpus, following the 2010 i2b2 concept extraction shared task, and (2) to identify nervous system disorder-related adverse events from safety reports in the vaccine adverse event reporting system (VAERS). To improve the GPT models' performance, we developed a clinical task-specific prompt framework that includes (1) baseline prompts with task description and format specification, (2) annotation guideline-based prompts, (3) error analysis-based instructions, and (4) annotated samples for few-shot learning. We assessed each prompt's effectiveness and compared the models to BioClinicalBERT.
Results Using baseline prompts, GPT-3.5 and GPT-4 achieved relaxed F1 scores of 0.634, 0.804 for MTSamples and 0.301, 0.593 for VAERS. Additional prompt components consistently improved model performance. When all 4 components were used, GPT-3.5 and GPT-4 achieved relaxed F1 socres of 0.794, 0.861 for MTSamples and 0.676, 0.736 for VAERS, demonstrating the effectiveness of our prompt framework. Although these results trail BioClinicalBERT (F1 of 0.901 for the MTSamples dataset and 0.802 for the VAERS), it is very promising considering few training samples are needed.
Discussion The study’s findings suggest a promising direction in leveraging LLMs for clinical NER tasks. However, while the performance of GPT models improved with task-specific prompts, there's a need for further development and refinement. LLMs like GPT-4 show potential in achieving close performance to state-of-the-art models like BioClinicalBERT, but they still require careful prompt engineering and understanding of task-specific knowledge. The study also underscores the importance of evaluation schemas that accurately reflect the capabilities and performance of LLMs in clinical settings.
Conclusion While direct application of GPT models to clinical NER tasks falls short of optimal performance, our task-specific prompt framework, incorporating medical knowledge and training samples, significantly enhances GPT models' feasibility for potential clinical applications.
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Abstract Objectives To investigate approaches of reasoning with large language models (LLMs) and to propose a new prompting approach, ensemble reasoning, to improve medical question answering performance with refined reasoning and reduced inconsistency.
Materials and Methods We used multiple choice questions from the USMLE Sample Exam question files on 2 closed-source commercial and 1 open-source clinical LLM to evaluate our proposed approach ensemble reasoning.
Results On GPT-3.5 turbo and Med42-70B, our proposed ensemble reasoning approach outperformed zero-shot chain-of-thought with self-consistency on Steps 1, 2, and 3 questions (+3.44%, +4.00%, and +2.54%) and (2.3%, 5.00%, and 4.15%), respectively. With GPT-4 turbo, there were mixed results with ensemble reasoning again outperforming zero-shot chain-of-thought with self-consistency on Step 1 questions (+1.15%). In all cases, the results demonstrated improved consistency of responses with our approach. A qualitative analysis of the reasoning from the model demonstrated that the ensemble reasoning approach produces correct and helpful reasoning.
Conclusion The proposed iterative ensemble reasoning has the potential to improve the performance of LLMs in medical question answering tasks, particularly with the less powerful LLMs like GPT-3.5 turbo and Med42-70B, which may suggest that this is a promising approach for LLMs with lower capabilities. Additionally, the findings show that our approach helps to refine the reasoning generated by the LLM and thereby improve consistency even with the more powerful GPT-4 turbo. We also identify the potential and need for human-artificial intelligence teaming to improve the reasoning beyond the limits of the model.
