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Background Predicting protein function and structure from sequence is one important challenge for computational biology. For 26 years, most state-of-the-art approaches combined machine learning and evolutionary information. However, for some applications retrieving related proteins is becoming too time-consuming. Additionally, evolutionary information is less powerful for small families, e.g. for proteins from the Dark Proteome . Both these problems are addressed by the new methodology introduced here. Results We introduced a novel way to represent protein sequences as continuous vectors ( embeddings ) by using the language model ELMo taken from natural language processing. By modeling protein sequences, ELMo effectively captured the biophysical properties of the language of life from unlabeled big data (UniRef50). We refer to these new embeddings as SeqVec ( Seq uence-to- Vec tor) and demonstrate their effectiveness by training simple neural networks for two different tasks. At the per-residue level, secondary structure (Q3 = 79% ± 1, Q8 = 68% ± 1) and regions with intrinsic disorder (MCC = 0.59 ± 0.03) were predicted significantly better than through one-hot encoding or through Word2vec-like approaches. At the per-protein level, subcellular localization was predicted in ten classes (Q10 = 68% ± 1) and membrane-bound were distinguished from water-soluble proteins (Q2 = 87% ± 1). Although SeqVec embeddings generated the best predictions from single sequences, no solution improved over the best existing method using evolutionary information. Nevertheless, our approach improved over some popular methods using evolutionary information and for some proteins even did beat the best. Thus, they prove to condense the underlying principles of protein sequences. Overall, the important novelty is speed: where the lightning-fast HHblits needed on average about two minutes to generate the evolutionary information for a target protein, SeqVec created embeddings on average in 0.03 s. As this speed-up is independent of the size of growing sequence databases, SeqVec provides a highly scalable approach for the analysis of big data in proteomics, i.e. microbiome or metaproteome analysis. Conclusion Transfer-learning succeeded to extract information from unlabeled sequence databases relevant for various protein prediction tasks. SeqVec modeled the language of life, namely the principles underlying protein sequences better than any features suggested by textbooks and prediction methods. The exception is evolutionary information, however, that information is not available on the level of a single sequence.

This study aimed to examine an assumption regarding whether generative artificial intelligence (GAI) tools can overcome the cognitive intensity that humans suffer when solving problems. We examine the performance of ChatGPT and GPT-4 on NAEP science assessments and compare their performance to students by cognitive demands of the items. Fifty-four 2019 NAEP science assessment tasks were coded by content experts using a two-dimensional cognitive load framework, including task cognitive complexity and dimensionality. ChatGPT and GPT-4 answered the questions individually and were scored using the scoring keys provided by NAEP. The analysis of the available data for this study was based on the average student ability scores for students who answered each item correctly and the percentage of students who responded to individual items. The results showed that both ChatGPT and GPT-4 consistently outperformed most students who answered each individual item in the NAEP science assessments. As the cognitive demand for NAEP science assessments increases, statistically higher average student ability scores are required to correctly address the questions. This pattern was observed for Grades 4, 8, and 12 students respectively. However, ChatGPT and GPT-4 were not statistically sensitive to the increase of cognitive demands of the tasks, except for Grade 4. As the first study focusing on comparing cutting-edge GAI and K-12 students in problem-solving in science, this finding implies the need for changes to educational objectives to prepare students with competence to work with GAI tools such as ChatGPT and GPT-4 in the future. Education ought to emphasize the cultivation of advanced cognitive skills rather than depending solely on tasks that demand cognitive intensity. This approach would foster critical thinking, analytical skills, and the application of knowledge in novel contexts among students. Furthermore, the findings suggest that researchers should innovate assessment practices by moving away from cognitive intensity tasks toward creativity and analytical skills to more efficiently avoid the negative effects of GAI on testing.

The increasing application of generative artificial intelligence large language models (LLMs) in various fields, including dentistry, raises questions about their accuracy. This study aims to comparatively evaluate the answers provided by 4 LLMs, namely Bard (Google LLC), ChatGPT-3.5 and ChatGPT-4 (OpenAI), and Bing Chat (Microsoft Corp), to clinically relevant questions from the field of dentistry. The LLMs were queried with 20 open-type, clinical dentistry-related questions from different disciplines, developed by the respective faculty of the School of Dentistry, European University Cyprus. The LLMs' answers were graded 0 (minimum) to 10 (maximum) points against strong, traditionally collected scientific evidence, such as guidelines and consensus statements, using a rubric, as if they were examination questions posed to students, by 2 experienced faculty members. The scores were statistically compared to identify the best-performing model using the Friedman and Wilcoxon tests. Moreover, the evaluators were asked to provide a qualitative evaluation of the comprehensiveness, scientific accuracy, clarity, and relevance of the LLMs' answers. Overall, no statistically significant difference was detected between the scores given by the 2 evaluators; therefore, an average score was computed for every LLM. Although ChatGPT-4 statistically outperformed ChatGPT-3.5 (P=.008), Bing Chat (P=.049), and Bard (P=.045), all models occasionally exhibited inaccuracies, generality, outdated content, and a lack of source references. The evaluators noted instances where the LLMs delivered irrelevant information, vague answers, or information that was not fully accurate. This study demonstrates that although LLMs hold promising potential as an aid in the implementation of evidence-based dentistry, their current limitations can lead to potentially harmful health care decisions if not used judiciously. Therefore, these tools should not replace the dentist's critical thinking and in-depth understanding of the subject matter. Further research, clinical validation, and model improvements are necessary for these tools to be fully integrated into dental practice. Dental practitioners must be aware of the limitations of LLMs, as their imprudent use could potentially impact patient care. Regulatory measures should be established to oversee the use of these evolving technologies.

ChatGPT is a generative language model tool launched by OpenAI on November 30, 2022, enabling the public to converse with a machine on a broad range of topics. In January 2023, ChatGPT reached over 100 million users, making it the fastest-growing consumer application to date. This interview with ChatGPT is part 2 of a larger interview with ChatGPT. It provides a snapshot of the current capabilities of ChatGPT and illustrates the vast potential for medical education, research, and practice but also hints at current problems and limitations. In this conversation with Gunther Eysenbach, the founder and publisher of JMIR Publications, ChatGPT generated some ideas on how to use chatbots in medical education. It also illustrated its capabilities to generate a virtual patient simulation and quizzes for medical students; critiqued a simulated doctor-patient communication and attempts to summarize a research article (which turned out to be fabricated); commented on methods to detect machine-generated text to ensure academic integrity; generated a curriculum for health professionals to learn about artificial intelligence (AI); and helped to draft a call for papers for a new theme issue to be launched in JMIR Medical Education on ChatGPT. The conversation also highlighted the importance of proper “prompting.” Although the language generator does make occasional mistakes, it admits these when challenged. The well-known disturbing tendency of large language models to hallucinate became evident when ChatGPT fabricated references. The interview provides a glimpse into the capabilities and limitations of ChatGPT and the future of AI-supported medical education. Due to the impact of this new technology on medical education, JMIR Medical Education is launching a call for papers for a new e-collection and theme issue. The initial draft of the call for papers was entirely machine generated by ChatGPT, but will be edited by the human guest editors of the theme issue.

Medical knowledge graphs (MKGs) are the basis for intelligent health care, and they have been in use in a variety of intelligent medical applications. Thus, understanding the research and application development of MKGs will be crucial for future relevant research in the biomedical field. To this end, we offer an in-depth review of MKG in this work. Our research begins with the examination of four types of medical information sources, knowledge graph creation methodologies, and six major themes for MKG development. Furthermore, three popular models of reasoning from the viewpoint of knowledge reasoning are discussed. A reasoning implementation path (RIP) is proposed as a means of expressing the reasoning procedures for MKG. In addition, we explore intelligent medical applications based on RIP and MKG and classify them into nine major types. Finally, we summarize the current state of MKG research based on more than 130 publications and future challenges and opportunities.

Large language models, in particular ChatGPT, have showcased remarkable language processing capabilities. Given the substantial workload of university medical staff, this study aims to assess the quality of multiple-choice questions (MCQs) produced by ChatGPT for use in graduate medical examinations, compared to questions written by university professoriate staffs based on standard medical textbooks. 50 MCQs were generated by ChatGPT with reference to two standard undergraduate medical textbooks (Harrison's, and Bailey & Love's). Another 50 MCQs were drafted by two university professoriate staff using the same medical textbooks. All 100 MCQ were individually numbered, randomized and sent to five independent international assessors for MCQ quality assessment using a standardized assessment score on five assessment domains, namely, appropriateness of the question, clarity and specificity, relevance, discriminative power of alternatives, and suitability for medical graduate examination. The total time required for ChatGPT to create the 50 questions was 20 minutes 25 seconds, while it took two human examiners a total of 211 minutes 33 seconds to draft the 50 questions. When a comparison of the mean score was made between the questions constructed by A.I. with those drafted by humans, only in the relevance domain that the A.I. was inferior to humans (A.I.: 7.56 +/- 0.94 vs human: 7.88 +/- 0.52; p = 0.04). There was no significant difference in question quality between questions drafted by A.I. versus humans, in the total assessment score as well as in other domains. Questions generated by A.I. yielded a wider range of scores, while those created by humans were consistent and within a narrower range. ChatGPT has the potential to generate comparable-quality MCQs for medical graduate examinations within a significantly shorter time.

Large language models (LLMs) have the potential to enhance clinical flow and improve medical education, but they encounter challenges related to specialized knowledge in ophthalmology. This study aims to enhance ophthalmic knowledge by refining a general LLM into an ophthalmology-specialized assistant for patient inquiries and medical education. We transformed Llama2 into an ophthalmology-specialized LLM, termed EyeGPT, through the following 3 strategies: prompt engineering for role-playing, fine-tuning with publicly available data sets filtered for eye-specific terminology (83,919 samples), and retrieval-augmented generation leveraging a medical database and 14 ophthalmology textbooks. The efficacy of various EyeGPT variants was evaluated by 4 board-certified ophthalmologists through comprehensive use of 120 diverse category questions in both simple and complex question-answering scenarios. The performance of the best EyeGPT model was then compared with that of the unassisted human physician group and the EyeGPT+human group. We proposed 4 metrics for assessment: accuracy, understandability, trustworthiness, and empathy. The proportion of hallucinations was also reported. The best fine-tuned model significantly outperformed the original Llama2 model at providing informed advice (mean 9.30, SD 4.42 vs mean 13.79, SD 5.70; P<.001) and mitigating hallucinations (97/120, 80.8% vs 53/120, 44.2%, P<.001). Incorporating information retrieval from reliable sources, particularly ophthalmology textbooks, further improved the model's response compared with solely the best fine-tuned model (mean 13.08, SD 5.43 vs mean 15.14, SD 4.64; P=.001) and reduced hallucinations (71/120, 59.2% vs 57/120, 47.4%, P=.02). Subgroup analysis revealed that EyeGPT showed robustness across common diseases, with consistent performance across different users and domains. Among the variants, the model integrating fine-tuning and book retrieval ranked highest, closely followed by the combination of fine-tuning and the manual database, standalone fine-tuning, and pure role-playing methods. EyeGPT demonstrated competitive capabilities in understandability and empathy when compared with human ophthalmologists. With the assistance of EyeGPT, the performance of the ophthalmologist was notably enhanced. We pioneered and introduced EyeGPT by refining a general domain LLM and conducted a comprehensive comparison and evaluation of different strategies to develop an ophthalmology-specific assistant. Our results highlight EyeGPT's potential to assist ophthalmologists and patients in medical settings.

ChatGPT (Generative Pre-trained Transformer) is a chatbot that was launched by Open AI as a prototype on November 30, 2022. ChatGPT has quickly gained attention for its detailed and well-formulated answers in many areas of knowledge. It can write computer programmes, poetry, business correspondence, or generate seemingly technical texts, depending on the verbal assignment. This article analyses and compares text in Czech language describing hydrostatic pressure produced by ChatGPT, from lower-secondary physics textbook and other sources. A text difficulty analysis was performed on the selected texts. The text-difficulty analysis by Nestler was chosen to assess the didactic properties. The results of the text-difficulty analysis and the selected partial coefficients are discussed.

Foundation models are the next generation of artificial intelligence that has the potential to provide novel use cases for healthcare. Large language models (LLMs), a type of foundation model, are capable of language comprehension and the ability to generate human-like text. Researchers and developers have been tuning LLMs to optimise their performance in specific tasks, such as medical challenge problems. Until recently, tuning required technical programming expertise, but the release of custom generative pre-trained transformers (GPTs) by OpenAI has allowed users to tune their own GPTs with natural language. This has the potential to democratise access to high-quality bespoke LLMs globally. In this review, we provide an overview of LLMs, how they are tuned and how custom GPTs work. We provide three use cases of custom GPTs in ophthalmology to demonstrate the versatility and effectiveness of these tools. First, we present ‘EyeTeacher’, an educational aid that generates questions from clinical guidelines to facilitate learning. Second, we built ‘EyeAssistant’, a clinical support tool that is tuned with clinical guidelines to respond to various physician queries. Lastly, we design ‘The GPT for GA’, which offers clinicians a comprehensive summary of emerging management strategies for geographic atrophy by analysing peer-reviewed documents. The review underscores the significance of custom instructions and information retrieval in tuning GPTs for specific tasks in ophthalmology. We also discuss the evaluation of LLM responses and address critical aspects such as privacy and accountability in their clinical application. Finally, we discuss their potential in ophthalmic education and clinical practice.