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Survey and Improvement Strategies for Gene Prioritization with Large Language Models

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arXiv 2025年

作者： Neeley, Matthew B. Qi, Guantong Wang, Guanchu Tang, Ruixiang Mao, Dongxue Liu, Chaozhong Pasupuleti, Sasidhar Yuan, Bo Xia, Fan Liu, Pengfei Liu, Zhandong Hu, Xia Jan and Dan Duncan Neurological Research Institute Texas Children’s Hospital Houston United States Graduate School of Biomedical Sciences Program in Quantitative and Computational Biosciences Baylor College of Medicine Houston United States Graduate School of Biomedical Sciences Program in Genetics and Genomics Baylor College of Medicine Houston United States Department of Computer Science Rice University Houston United States Department of Computer Science Rutgers University NJ United States Department of Pediatrics Baylor College of Medicine Houston United States Department of Molecular and Human Genetics Baylor College of Medicine Houston United States Human Genome Sequencing Center Baylor College of Medicine Houston United States Baylor Genetics Houston United States

Background Rare diseases can be difficult to diagnose due to limited patient data and broad genetic diversity. Despite the advances in variant prioritization tools, many rare disease cases remain undiagnosed. While large language models (LLMs) have performed well in medical exams, their accuracy in diagnosing rare genetic diseases has not yet been evaluated. Methods To identify causal genes for genetic diseases, we benchmarked various LLMs for gene prioritization. We employed multi-agent and Human Phenotype Ontology (HPO) classification approaches to identify patient case groups based on phenotypes categorizing them into different levels of solvability. To address LLM limitations in ranking large gene sets, we used a divide-and-conquer strategy to break down the ranking task into smaller subsets. Mini-batching inputs and limiting the number of generated tokens improved efficiency. Results In its vanilla form, GPT-4 consistently outperformed the other LLMs with an accuracy around 30%. Multi-agent and HPO classification approaches aided us in distinguishing between confidently-solved and challenging cases. In addition, we observed bias towards well-studied genes and input order sensitivity which are drawbacks of LLMs in disease-causal gene prioritization. Our divide-and-conquer strategy enhanced accuracy by overcoming positional and gene frequency biases in literature. This framework, based on benchmarking insights and novel techniques, significantly optimizes the overall process when identifying disease-causal genes for genetic diseases when compared to our baseline evaluation, and thereby better enables the development of targeted diagnostic and therapeutic interventions. Conclusions Using HPO classification and our novel multi-agent techniques, and our LLM divide-and-conquer strategy (1) highlighted the importance of accounting for differences in patient case solvability and (2) yielded improved performance in identifying causal genes for rare diseases when compare

关键词： Gene Ontology

A proposal for removing πN-state contamination from the nucleon induced pseudoscalar form factor in lattice QCD

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arXiv 2025年

作者： Sasaki, Shoichi Aoki, Yasumichi Ishikawa, Ken-Ichi Kuramashi, Yoshinobu Sato, Kohei Shintan, Eigo Tsuji, Ryutaro Watanabe, Hiromasa Yamazaki, Takeshi Department of Physics Tohoku University Sendai980-8578 Japan RIKEN Center for Computational Science Kobe650-0047 Japan Core of Research for the Energetic Universe Graduate School of Advanced Science and Engineering Hiroshima University Higashi-Hiroshima739-8526 Japan Center for Computational Sciences University of Tsukuba Tsukuba305-8577 Japan Degree Programs in Pure and Applied Sciences Graduate School of Science and Technology University of Tsukuba Ibaraki305-8571 Japan Tsukuba305-0801 Japan Yukawa Institute for Theoretical Physics Kyoto University Kyoto606-8502 Japan Institute of pure and Applied Sciences University of Tsukuba Tsukuba305-8571 Japan

In the PACS10 project, the PACS collaboration has generated three sets of the PACS10 gauge configurations at the physical point with lattice volume larger than (10 fm)4 and three different lattice spacings. The isovector nucleon form factors had been already calculated by using two sets of the PACS10 gauge configurations. In our strategy, the smearing parameters of the nucleon interpolation operator were highly optimized to eliminate as much as possible the contribution of excited states in the nucleon two-point function. This strategy was quite successful in calculations of the electric (GE), magnetic (GM) and axial-vector (FA) form factors, while the induced pseudoscalar (FP) and pseudoscalar (GP) form factors remained strongly affected by residual contamination of πΝ-state contribution. In this work, we propose a simple method to remove the πΝ-state contamination from the FP form factor, and then evaluate the induced pseudoscalar charge g∗Ρ and the pion-nucleon coupling gπNN from existing data in a new analysis. Applying this method to the GP form factor is also considered with a help of the axial Ward-Takahashi identity. © 2025, CC BY.

关键词： Lattice theory

Comparison of Fitness Tracking Using Three Different Smartwatches during Free Activities in Daily Life

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Open Journal of Nursing 2023年第10期13卷 625-640页

作者： Eriko Terasawa Yoshihiro Asano Makiko Aoki Hisayo Okayama Doctorial Program in Nursing Graduate School of Comprehensive Human Sciences University of Tsukuba Ibaraki Japan School of Medicine Department of Health Sciences Shinshu University Nagano Japan Faculty of Health Science of Nursing Juntendo University Shizuoka Japan Nursing Science and Engineering/Women’s Health Nursing Institute of Medicine University of Tsukuba Ibaraki Japan

Background: Young women of reproductive age experience various physiological changes, which they measure and track using various devices, including fitness trackers and smartwatches. However, fitness tracking assessment methods are ambiguous because they may differ from model to model. Objective: This study aimed to compare the stress level, heart rate, sleep time, number of steps, and distance traveled, which were calculated using fitness tracking methods for daily-life free activity installed in various smartwatches. Materials and Methodology: Healthy women in their 20s to 30s were recruited for this study, which was conducted from December 2021 to June 2022. The finalized participants wore three different smartwatch models (Mi smartband 6, vivosmart^®4, and Band 6) simultaneously on their person for 48 hours and performed their daily activities and recorded them on an hour-based activity chart. Each smartwatch’s measured data (e.g., age, height, weight, and oral medications) were extracted into five datasets: heart rate, stress level, number of steps, distance, and sleep time. Data analyses were conducted using Spearman’s rank correlation coefficient ρ (for comparing heart rates) and Bland-Altman plots (for assessing heart rate agreement). The smartwatches’ fitness trackers were compared using the mean absolute percentage error. Results: The correlation coefficient showed that vivosmart^®4 and Band 6 had a higher heart rate agreement (ρ = 0.684). The Bland-Altman plots showed high agreement between Band 6, Mi smartband 6, and vivosmart^®4. The heart rate measurement method used under free movement was found to be consistent. The examined smartwatches were able to measure heart rate at the same level even under daily-life free movements. Conclusion: Several different smartwatches’ calculated measured values for heart rate had a high agreement. The smartwatches provided accurate heart rate measurements under daily-life free movement co

关键词： Wearable Device Fitness Tracking Daily Life Smartwatches

Development of Simultaneous Quantitative Analytical Method for Three Active Components of Agastache Rugosa in Human Plasma Using Ultra-High-Performance Liquid Chromatography–Tandem Mass Spectrometry

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SSRN

SSRN 2023年

作者： Rinik, Urmi Rahman Kim, Ji Eon Lee, Eunok Kwon, Oran Jung, Byung Hwa Center for Advanced Biomolecular Recognition Korea Institute of Science and Technology Seoul02792 Korea Republic of Division of Bio-medical Science and Technology KIST School University of Science and Technology Daejeon34113 Korea Republic of Department of Nutritional Science and Food Management Graduate Program in System Health Science and Engineering Ewha Womans University Korea Republic of

Abstract: Agastache rugosa contains phenolic compounds and flavonoids, and has been extensively used as a traditional herbal medicine. The major components in Agastache rugosa are rosmarinic acid, tilianin, and acacetin, for which several analytical techniques have been reported. However, these substances have yet to be simultaneously quantified in human plasma. In this study, we aimed to simultaneously determine the three active components of Agastacherugosa in human plasma by developing a reliable quantitative analytical method using ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS). Chromatographic separation of the plasma samples was achieved using an ACQUITY UPLC® BEH C18 column with a gradient mobile phase of water and acetonitrile containing 0.1% formic acid. Mass spectrometric detection was performed using a triple quadrupole tandem mass spectrometer in negative electrospray ionization (ESI−) and multiple reaction monitoring (MRM) modes. The developed quantitative method was validated for the three active components. All three analytes exhibited a linear response over the ranges of 0.5–50 ng/mL for rosmarinic acid, 0.1–20 ng/mL for acacetin, and 0.5–20 ng/mL for tilianin with a weighting factor of 1/x (where x is the concentration). At three quality control (QC) concentration levels (low, medium, and high), including the lower limit of quantitation (LLOQ), acceptable accuracy (±15%) was achieved in the intra- and interday validations. The concentration of rosmarinic acid was highest in plasma. Tilianin and acacetin appeared and were eliminated earlier in the plasma than rosmarinic acid. This study provides a successfully validated method that can be used in further clinical applications of Agastache rugosa extracts. © 2023, The Authors. All rights reserved.

关键词： Mass spectrometers

CLINICAL DETERIORATION PREDICTION IN BRAZILIAN HOSPITALS BASED ON ARTIFICIAL NEURAL NETWORKS AND TREE DECISION MODELS

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arXiv 2022年

作者： Yazdanpanah, Hamed Silva, Augusto C.M. Guedes, Murilo Morales, Hugo M.P. Coelho, Leandro dos S. Moro, Fernando G. Department of Research Robô Laura PR Curitiba Brazil Department of Computer Science University of São Paulo SP São Paulo Brazil Industrial and Systems Engineering Graduate Program Pontifical Catholic University of Parana PR Curitiba Brazil Electrical Engineering Graduate Program Federal University of Parana PR Curitiba Brazil

Early recognition of clinical deterioration (CD) has vital importance in patients' survival from exacerbation or death. Electronic health records (EHRs) data have been widely employed in Early Warning Scores (EWS) to measure CD risk in hospitalized patients. Recently, EHRs data have been utilized in Machine Learning (ML) models to predict mortality and CD. The ML models have shown superior performance in CD prediction compared to EWS. Since EHRs data are structured and tabular, conventional ML models are generally applied to them, and less effort is put into evaluating the artificial neural network's performance on EHRs data. Thus, in this article, an extremely boosted neural network (XBNet) is used to predict CD, and its performance is compared to eXtreme Gradient Boosting (XGBoost) and random forest (RF) models. For this purpose, 103,105 samples from thirteen Brazilian hospitals are used to generate the models. Moreover, the principal component analysis (PCA) is employed to verify whether it can improve the adopted models' performance. The performance of ML models and Modified Early Warning Score (MEWS), an EWS candidate, are evaluated in CD prediction regarding the accuracy, precision, recall, F1-score, and geometric mean (G-mean) metrics in a 10-fold cross-validation approach. According to the experiments, the XGBoost model obtained the best results in predicting CD among Brazilian hospitals' data. © 2022, CC BY-NC-SA.

关键词： Machine learning

Optimal Planning of Hybrid Energy Storage Systems Using Curtailed Renewable Energy Through Deep Reinforcement Learning

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SSRN

SSRN 2023年

作者： Kang, Dongju Kang, Doeun Hwangbo, Sumin Niaz, Haider Lee, Won Bo Liu, J. Jay Na, Jonggeol School of Chemical and Biological Engineering Seoul National University Gwanak-ro 1 Gwanak-gu Seoul08826 Korea Republic of Department of Chemical Engineering and Materials Science Ewha Womans University Seoul03760 Korea Republic of Graduate Program in System Health Science and Engineering Ewha Womans University Seoul03760 Korea Republic of Department of Chemical Engineering Pukyong National University Busan48513 Korea Republic of

Energy management systems (EMS) are becoming increasingly important in order to utilize the continuously growing curtailed renewable energy. Promising energy storage systems (ESS), such as batteries and green hydrogen should be employed to maximize the efficiency of energy stakeholders. However, optimal decision-making, i.e., planning the leveraging between different strategies, is confronted with the complexity and uncertainties of large-scale problems. Here, we propose a sophisticated deep reinforcement learning (DRL) methodology with a policy-based algorithm to realize the real-time optimal ESS planning under the curtailed renewable energy uncertainty. A quantitative performance comparison proved that the DRL agent outperforms the scenario-based stochastic optimization (SO) algorithm, even with a wide action and observation space. Owing to the uncertainty rejection capability of the DRL, we could confirm a robust performance, under a large uncertainty of the curtailed renewable energy, with a maximizing net profit and stable system. Action-mapping was performed for visually assessing the action taken by the DRL agent according to the state. The corresponding results confirmed that the DRL agent learns the way like what a human expert would do, suggesting reliable application of the proposed methodology. © 2023, The Authors. All rights reserved.

关键词： Reinforcement learning

Finite-Time Optimization of Quantum Szilard heat engine

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arXiv 2023年

作者： Zhou, Tan-Ji Ma, Yu-Han Sun, C.P. Graduate School of China Academy of Engineering Physics No. 10 Xibeiwang East Road Haidian District Beijing100193 China Department of Physics Peking University China Department of Physics Beijing Normal University Beijing100875 China Beijing Computational Science Research Center Beijing100193 China

We propose a finite-time quantum Szilard engine (QSE) with a quantum particle with spin as the working substance (WS) to accelerate the operation of information engines. A Maxwell’s demon (MD) is introduced to probe the spin state within a finite measurement time tM to capture the which-way information of the particle, quantified by the mutual information I(tM) between WS and MD. We establish that the efficiency η of QSE is bounded by η ≤ 1 - (1 - ηC)ln2/I(tM), where I(tM)/ln2 characterizes the ideality of quantum measurement, and approaches 1 for the Carnot efficiency reached under ideal measurement in quasi-static regime. We find that the power of QSE scales as P ∝ t3M in the short-time regime and as P ∝ t-M1 in the long-time regime. Additionally, considering the energy cost for erasing the MD’s memory required by Landauer’s principle, there exists a threshold time that guarantees QSE to output positive work. Copyright © 2023, The Authors. All rights reserved.

关键词： Heat engines

Exploration of the polarization angle variability of the Crab Nebula with POLARBEAR and its application to the search for axionlike particles

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Physical Review D 2024年第6期110卷 063013页

作者： Shunsuke Adachi Tylor Adkins Carlo Baccigalupi Yuji Chinone Kevin T. Crowley Josquin Errard Giulio Fabbian Chang Feng Takuro Fujino Masaya Hasegawa Masashi Hazumi Oliver Jeong Daisuke Kaneko Brian Keating Akito Kusaka Adrian T. Lee Anto I. Lonappan Yuto Minami Masaaki Murata Lucio Piccirillo Christian L. Reichardt Praween Siritanasak Jacob Spisak Satoru Takakura Grant P. Teply Kyohei Yamada Hakubi Center for Advanced Research Department of Physics Astrophysics and Cosmology QUP (WPI) Kavli Institute for the Physics and Mathematics of the Universe (WPI) UTIAS CNRS Astroparticule et Cosmologie F-75013 Paris France Center for Computational Astrophysics School of Physics and Astronomy CAS Key Laboratory for Research in Galaxies and Cosmology Department of Astronomy School of Astronomy and Space Science Graduate School of Engineering Science Institute of Particle and Nuclear Studies (IPNS) School of High Energy Accelerator Science Japan Aerospace Exploration Agency (JAXA) Department of Physics Graduate School of Science Physics Division Research Center for the Early Universe Dipartimento di Fisica Osaka University Osaka 567-0047 Japan Jodrell Bank Centre for Astrophysics School of Physics and Astronomy School of Physics Chiangmai 50180 Thailand Department of Physics Faculty of Science

The Crab Nebula, also known as Tau A, is a polarized astronomical source at millimeter wavelengths. It has been used as a stable light source for polarization angle calibration in millimeter-wave astronomy. However, it is known that its intensity and polarization vary as a function of time at a variety of wavelengths. Thus, it is of interest to verify the stability of the millimeter-wave polarization. If detected, polarization variability may be used to better understand the dynamics of Tau A, and for understanding the validity of Tau A as a calibrator. One intriguing application of such observation is to use it for the search of axionlike particles (ALPs). Ultralight ALPs couple to photons through a Chern-Simons term, and induce a temporal oscillation in the polarization angle of linearly polarized sources. After assessing a number of systematic errors and testing for internal consistency, we evaluate the variability of the polarization angle of the Crab Nebula using 2015 and 2016 observations with the 150 GHz Polarbear instrument. We place a median 95% upper bound of polarization oscillation amplitude A<0.065° over the oscillation frequencies from 0.75 year−1 to 0.66 hour−1. Assuming that no sources other than ALP are causing Tau A’s polarization angle variation, that the ALP constitutes all the dark matter, and that the ALP field is a stochastic Gaussian field, this bound translates into a median 95% upper bound of ALP-photon coupling gaγγ<2.16×10−12 GeV−1×(ma/10−21 eV) in the mass range from 9.9×10−23 eV to 7.7×10−19 eV. This demonstrates that this type of analysis using bright polarized sources is as competitive as those using the polarization of cosmic microwave background in constraining ALPs.

关键词： Cosmic microwave background Dark matter Radio, microwave, & sub-mm astronomy

Throughfall and stemflow chemical dynamics of Satoyama, a traditional secondary forest system under threat in Japan

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Journal of Forestry Research 2022年第3期33卷 813-826页

作者： Satoshi Asaoka Fuyuhiko Sumikawa Yoshifumi Watanabe Waqar Azeem Jadoon Masaki Ohno Nobumichi Shutoh Yuki Wakamatsu Lawrence M.Liao Akane Kanazawa Yuka Sato Natsumi Fujiwara Graduate School of Integrated Sciences for Life Hiroshima University1-4-4 KagamiyamaHigashi-Hiroshima739-8528Japan Research Center for Inland Seas Kobe University5-1-1 FukaeminamiHigashinadaKobe658-0022Japan Naragakuen Senior High School 430 YamadaYamatokoriyamaNara639-1093Japan Department of Environmental Sciences Faculty of Natural and Computational SciencesHazara UniversityDhodiaMansehra21130Khyber PakhtunkhwaPakistan Niigata University of Pharmacy and Applied Life Sciences 265-1 HigashijimaAkihaNiigata956-8603Japan Faculty of Science and Engineering Kindai University3-4-1 KowakaeHigashi-OsakaOsaka577-8502Japan Department of Maritime Science and Technology Japan Coast Guard Academy5 WakabaKureHiroshima737-8512Japan

The term 'Satoyama' refers to traditional and unique secondary forests in Japan that occupy intermediate zones between villages ('sato') and hills or mountains ('yama'). Satoyama landscapes help sustain ecosystem services and the diversity of secondary natural environments. As Japan relies more heavily on foreign timber imports, the traditional role of Satoyama in providing forest products has diminished, and this has led to their abandonment and poor management. The chemical behavior of cations, anions, and dissolved organic matter in throughfall and stemflow from one such threatened Satoyama system in central Japan was investigated. From autumn to winter, the atmospheric deposition of sulfates and nitrates was 2.5–6.0 times higher compared to the amounts in summer due to the intrusion of air masses from the Asian continent. The dissolved organic matter in the throughfall and stemflow was composed mainly of humic substances and protein derivatives. The deposition fluxes of dissolved organic carbon from throughfall (7.31–10.1 g m^(−2) a^(−1)) and stemflow (1.79–3.84 g m^(−2) a^(−1)) in this study were within ranges seen in temperate forests in previous studies. The deposition flux of sulfates was low compared to that in other forest types because canopy interaction was lower, suggesting higher canopy openness than in primary forests. If a shift from a mixed species Satoyama forest to a conifer-dominated forest occurs after the mass mortality of oak, the deposition flux of dissolved organic carbon and K^(+) might decrease by 33% and 62%, respectively, while NO_(3)^(−) might increase by 20%. In the near future, the degradation of Satoyama landscapes might change the levels of dissolved organic carbon and nitrogen loads, resulting in imbalances in river-ocean linkages affecting forested catchments and aquatic ecosystems in Japan.

关键词： Atmospheric deposition Dissolved organic matter Humic substance Mass mortality Oak trees Sustainable development goals