Medical domain knowledge in domain-agnostic generative AI.
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ABSTRACT:
SUBMITTER: Kather JN
PROVIDER: S-EPMC9273760 | biostudies-literature | 2022 Jul
REPOSITORIES: biostudies-literature
Publications
Medical domain knowledge in domain-agnostic generative AI.
Kather Jakob Nikolas JN Ghaffari Laleh Narmin N Foersch Sebastian S Truhn Daniel D
NPJ digital medicine 20220711 1
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Project description:BackgroundAI models have shown promise in performing many medical imaging tasks. However, our ability to explain what signals these models have learned is severely lacking. Explanations are needed in order to increase the trust of doctors in AI-based models, especially in domains where AI prediction capabilities surpass those of humans. Moreover, such explanations could enable novel scientific discovery by uncovering signals in the data that aren't yet known to experts.MethodsIn this paper, we present a workflow for generating hypotheses to understand which visual signals in images are correlated with a classification model's predictions for a given task. This approach leverages an automatic visual explanation algorithm followed by interdisciplinary expert review. We propose the following 4 steps: (i) Train a classifier to perform a given task to assess whether the imagery indeed contains signals relevant to the task; (ii) Train a StyleGAN-based image generator with an architecture that enables guidance by the classifier ("StylEx"); (iii) Automatically detect, extract, and visualize the top visual attributes that the classifier is sensitive towards. For visualization, we independently modify each of these attributes to generate counterfactual visualizations for a set of images (i.e., what the image would look like with the attribute increased or decreased); (iv) Formulate hypotheses for the underlying mechanisms, to stimulate future research. Specifically, present the discovered attributes and corresponding counterfactual visualizations to an interdisciplinary panel of experts so that hypotheses can account for social and structural determinants of health (e.g., whether the attributes correspond to known patho-physiological or socio-cultural phenomena, or could be novel discoveries).FindingsTo demonstrate the broad applicability of our approach, we present results on eight prediction tasks across three medical imaging modalities-retinal fundus photographs, external eye photographs, and chest radiographs. We showcase examples where many of the automatically-learned attributes clearly capture clinically known features (e.g., types of cataract, enlarged heart), and demonstrate automatically-learned confounders that arise from factors beyond physiological mechanisms (e.g., chest X-ray underexposure is correlated with the classifier predicting abnormality, and eye makeup is correlated with the classifier predicting low hemoglobin levels). We further show that our method reveals a number of physiologically plausible, previously-unknown attributes based on the literature (e.g., differences in the fundus associated with self-reported sex, which were previously unknown).InterpretationOur approach enables hypotheses generation via attribute visualizations and has the potential to enable researchers to better understand, improve their assessment, and extract new knowledge from AI-based models, as well as debug and design better datasets. Though not designed to infer causality, importantly, we highlight that attributes generated by our framework can capture phenomena beyond physiology or pathophysiology, reflecting the real world nature of healthcare delivery and socio-cultural factors, and hence interdisciplinary perspectives are critical in these investigations. Finally, we will release code to help researchers train their own StylEx models and analyze their predictive tasks of interest, and use the methodology presented in this paper for responsible interpretation of the revealed attributes.FundingGoogle.
| S-EPMC10993140 | biostudies-literature
Project description:Generative models are frequently used for de novo design in drug discovery projects to propose new molecules. However, the question of whether or not the generated molecules can be synthesized is not systematically taken into account during generation, even though being able to synthesize the generated molecules is a fundamental requirement for such methods to be useful in practice. Methods have been developed to estimate molecule "synthesizability", but, so far, there is no consensus on whether or not a molecule is synthesizable. In this paper we introduce the Retro-Score (RScore), which computes a synthetic accessibility score of molecules by performing a full retrosynthetic analysis through our data-driven synthetic planning software Spaya, and its dedicated API: Spaya-API (https://spaya.ai). We start by comparing several synthetic accessibility scores to a binary "chemist score" as estimated by chemists on a bench of generated molecules, as a first experimental validation that the RScore is a reliable synthetic accessibility score. We then describe a pipeline to generate molecules that validate a list of targets while still being easy to synthesize. We further this idea by performing experiments comparing molecular generator outputs across a range of constraints and conditions. We show that the RScore can be learned by a Neural Network, which leads to a new score: RSPred. We demonstrate that using the RScore or RSPred as a constraint during molecular generation enables our molecular generators to produce more synthesizable solutions, with higher diversity. The open-source Python code containing all the scores and the experiments can be found on ( https://github.com/iktos/generation-under-synthetic-constraint ).
| S-EPMC10507964 | biostudies-literature
Project description:One valuable application for generative artificial intelligence (AI) is summarizing research studies for non-academic readers. We submitted five articles to Chat Generative Pre-trained Transformer (ChatGPT) for summarization, and asked the article's author to rate the summaries. Higher ratings were assigned to more insight-oriented activities, such as the production of eighth-grade reading level summaries, and summaries highlighting the most important findings and real-world applications. The general summary request was rated lower. For the field of environmental health science, no-cost AI technology such as ChatGPT holds the promise to improve research translation, but it must continue to be improved (or improve itself) from its current capability.
| S-EPMC10369501 | biostudies-literature
Project description:In response to the COVID-19 crisis, Artificial Intelligence (AI) has been applied to a range of applications in healthcare and public health such as case identification or monitoring of the population. The urgency of the situation should not be to the detriment of considering the ethical implications of such apps. Implementing ethics in medical AI is a complex issue calling for a systems thinking approach engaging diverse representatives of the stakeholders in a consultative process. The participatory engagement aims to gather the different perspectives of the stakeholders about the app in a transparent and inclusive way. In this study, we engaged a group of clinicians, patients, and AI developers in conversations about a fictitious app which was an aggregate of actual COVID-19 apps. The app featured a COVID-19 symptoms monitoring function for both the patient and the clinician, as well as infection clusters tracking for health agencies. Anchored in Soft Systems Methodology and Critical Systems Thinking, participants were asked to map the flow of knowledge between the clinician, the patient, and the AI app system and answer questions about the ethical boundaries of the system. Because data and information are the resource and the product of the AI app, understanding the nature of the information and knowledge exchanged between the different agents of the system can reveal ethical issues. In this study, not only the output of the participatory process was analysed, but the process of the stakeholders' engagement itself was studied as well. To establish a strong foundation for the implementation of ethics in the AI app, the conversations among stakeholders need to be inclusive, respectful and allow for free and candid dialogues ensuring that the process is transparent for which a systemic intervention is well suited.
| S-EPMC10621848 | biostudies-literature
Project description:Question answering (QA) is a hot field of research in Natural Language Processing. A big challenge in this field is to answer questions from knowledge-dependable domain. Since traditional QA hardly satisfies some knowledge-dependable situations, such as disease diagnosis, drug recommendation, etc. In recent years, researches focus on knowledge-based question answering (KBQA). However, there still exist some problems in KBQA, traditional KBQA is limited by a range of historical cases and takes too much human labor. To address the problems, in this paper, we propose an approach of knowledge graph based question answering (KGQA) method for medical domain, which firstly constructs a medical knowledge graph by extracting named entities and relations between the entities from medical documents. Then, in order to understand a question, it extracts the key information in the question according to the named entities, and meanwhile, it recognizes the questions' intentions by adopting information gain. The next an inference method based on weighted path ranking on the knowledge graph is proposed to score the related entities according to the key information and intention of a given question. Finally, it extracts the inferred candidate entities to construct answers. Our approach can understand questions, connect the questions to the knowledge graph and inference the answers on the knowledge graph. Theoretical analysis and real-life experimental results show the efficiency of our approach.
| S-EPMC8444078 | biostudies-literature
Project description:BackgroundMental disorders have ranked among the top 10 prevalent causes of burden on a global scale. Generative artificial intelligence (GAI) has emerged as a promising and innovative technological advancement that has significant potential in the field of mental health care. Nevertheless, there is a scarcity of research dedicated to examining and understanding the application landscape of GAI within this domain.ObjectiveThis review aims to inform the current state of GAI knowledge and identify its key uses in the mental health domain by consolidating relevant literature.MethodsRecords were searched within 8 reputable sources including Web of Science, PubMed, IEEE Xplore, medRxiv, bioRxiv, Google Scholar, CNKI and Wanfang databases between 2013 and 2023. Our focus was on original, empirical research with either English or Chinese publications that use GAI technologies to benefit mental health. For an exhaustive search, we also checked the studies cited by relevant literature. Two reviewers were responsible for the data selection process, and all the extracted data were synthesized and summarized for brief and in-depth analyses depending on the GAI approaches used (traditional retrieval and rule-based techniques vs advanced GAI techniques).ResultsIn this review of 144 articles, 44 (30.6%) met the inclusion criteria for detailed analysis. Six key uses of advanced GAI emerged: mental disorder detection, counseling support, therapeutic application, clinical training, clinical decision-making support, and goal-driven optimization. Advanced GAI systems have been mainly focused on therapeutic applications (n=19, 43%) and counseling support (n=13, 30%), with clinical training being the least common. Most studies (n=28, 64%) focused broadly on mental health, while specific conditions such as anxiety (n=1, 2%), bipolar disorder (n=2, 5%), eating disorders (n=1, 2%), posttraumatic stress disorder (n=2, 5%), and schizophrenia (n=1, 2%) received limited attention. Despite prevalent use, the efficacy of ChatGPT in the detection of mental disorders remains insufficient. In addition, 100 articles on traditional GAI approaches were found, indicating diverse areas where advanced GAI could enhance mental health care.ConclusionsThis study provides a comprehensive overview of the use of GAI in mental health care, which serves as a valuable guide for future research, practical applications, and policy development in this domain. While GAI demonstrates promise in augmenting mental health care services, its inherent limitations emphasize its role as a supplementary tool rather than a replacement for trained mental health providers. A conscientious and ethical integration of GAI techniques is necessary, ensuring a balanced approach that maximizes benefits while mitigating potential challenges in mental health care practices.
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Project description:Incorporating generative artificial intelligence (GAI) in education has become crucial in contemporary educational environments. This research article thoroughly investigates the ramifications of implementing GAI in the higher education context of Saudi Arabia, employing a blend of quantitative and qualitative research approaches. Survey-based quantitative data reveals a noteworthy correlation between educators' awareness of GAI and the frequency of its application. Notably, around half of the surveyed educators are at stages characterized by understanding and familiarity with GAI integration, indicating a tangible readiness for its adoption. Moreover, the study's quantitative findings underscore the perceived value and ease associated with integrating GAI, thus reinforcing the assumption that educators are motivated and inclined to integrate GAI tools like ChatGPT into their teaching methodologies. In addition to the quantitative analysis, qualitative insights from in-depth interviews with educators unveil a rich tapestry of perspectives. The qualitative data emphasizes GAI's role as a catalyst for collaborative learning, contributing to professional development, and fostering innovative teaching practices.
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Project description:Enzymes, as paramount protein catalysts, occupy a central role in fostering remarkable progress across numerous fields. However, the intricacy of sequence-function relationships continues to obscure our grasp of enzyme behaviors and curtails our capabilities in rational enzyme engineering. Generative artificial intelligence (AI), known for its proficiency in handling intricate data distributions, holds the potential to offer novel perspectives in enzyme research. By applying generative models, we could discern elusive patterns within the vast sequence space and uncover new functional enzyme sequences. This review highlights the recent advancements in employing generative AI for enzyme sequence analysis. We delve into the impact of generative AI in predicting mutation effects on enzyme fitness, activity, and stability, rationalizing the laboratory evolution of de novo enzymes, decoding protein sequence semantics, and its applications in enzyme engineering. Notably, the prediction of enzyme activity and stability using natural enzyme sequences serves as a vital link, indicating how enzyme catalysis shapes enzyme evolution. Overall, we foresee that the integration of generative AI into enzyme studies will remarkably enhance our knowledge of enzymes and expedite the creation of superior biocatalysts.
| S-EPMC10592750 | biostudies-literature
Project description:Artificial intelligence (AI)-based molecular design methods, especially deep generative models for generating novel molecule structures, have gratified our imagination to explore unknown chemical space without relying on brute-force exploration. However, whether designed by AI or human experts, the molecules need to be accessibly synthesized and biologically evaluated, and the trial-and-error process remains a resources-intensive endeavor. Therefore, AI-based drug design methods face a major challenge of how to prioritize the molecular structures with potential for subsequent drug development. This study indicates that common filtering approaches based on traditional screening metrics fail to differentiate AI-designed molecules. To address this issue, we propose a novel molecular filtering method, MolFilterGAN, based on a progressively augmented generative adversarial network. Comparative analysis shows that MolFilterGAN outperforms conventional screening approaches based on drug-likeness or synthetic ability metrics. Retrospective analysis of AI-designed discoidin domain receptor 1 (DDR1) inhibitors shows that MolFilterGAN significantly increases the efficiency of molecular triaging. Further evaluation of MolFilterGAN on eight external ligand sets suggests that MolFilterGAN is useful in triaging or enriching bioactive compounds across a wide range of target types. These results highlighted the importance of MolFilterGAN in evaluating molecules integrally and further accelerating molecular discovery especially combined with advanced AI generative models.
| S-EPMC10082991 | biostudies-literature
Project description:Generative pretrained models represent a significant advancement in natural language processing and computer vision, which can generate coherent and contextually relevant content based on the pre-training on large general datasets and fine-tune for specific tasks. Building foundation models using large scale omic data is promising to decode and understand the complex signaling language patterns within cells. Different from existing foundation models of omic data, we build a foundation model, mosGraphGPT, for multi-omic signaling (mos) graphs, in which the multi-omic data was integrated and interpreted using a multi-level signaling graph. The model was pretrained using multi-omic data of cancers in The Cancer Genome Atlas (TCGA), and fine-turned for multi-omic data of Alzheimer's Disease (AD). The experimental evaluation results showed that the model can not only improve the disease classification accuracy, but also is interpretable by uncovering disease targets and signaling interactions. And the model code are uploaded via GitHub with link: https://github.com/mosGraph/mosGraphGPT.
| S-EPMC11326168 | biostudies-literature