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Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data

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Genomics, Proteomics & Bioinformatics 2022年第5期20卷 899-911页

作者： Yongbing Zhao Jinfeng Shao Yan W.Asmann department of quantitative health sciences Mayo ClinicJacksonvilleFL 32224USA The Laboratory of Malaria and Vector Research National Institute of Allergy and Infectious DiseasesNational Institutes of HealthRockvilleMD 20852USA

Explainable artificial intelligence aims to interpret how machine learning models make decisions,and many model explainers have been developed in the computer vision field.However,understanding of the applicability of these model explainers to biological data is still lacking.In this study,we comprehensively evaluated multiple explainers by interpreting pre-trained models for predicting tissue types from transcriptomic data and by identifying the top contributing genes from each sample with the greatest impacts on model prediction.To improve the reproducibility and interpretability of results generated by model explainers,we proposed a series of optimization strategies for each explainer on two different model architectures of multilayer perceptron(MLP)and convolutional neural network(CNN).We observed three groups of explainer and model architecture combinations with high reproducibility.Group II,which contains three model explainers on aggregated MLP models,identified top contributing genes in different tissues that exhibited tissue-specific manifestation and were potential cancer biomarkers.In summary,our work provides novel insights and guidance for exploring biological mechanisms using explainable machine learning models.

关键词： Machine learning Model interpretability Gene expression Marker gene Omics data mining

电磁导航支气管镜与CT引导下经皮肺穿刺肺周围结节的队列研究

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国际医学放射学杂志 2018年第3期 349-350页

作者： K.M.Bhatt Y.K.Tandon R.Graham C.T.Lau J.K.Lempel J.T.Azok 吕晓虹 department of Radiology Pulmonology and Quantitative Health Sciences Cleveland Clinic

摘要目的比较电磁导航支气管镜(ENB)引导与CT引导下经皮肺穿刺肺结节取样的诊断价值和并发症发生率。材料与方法回顾性分析2013—2015年间149例CT引导下经

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DNA methylation signature predicts cancer response to demethylation agents from profiling diverse cancer cell lines

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Cancer Communications 2022年第8期42卷 789-792页

作者： Zhifu Sun Xuewei Wang Pete Vedell Jean-Pierre Kocher Division of Computational Biology Department of Quantitative Health SciencesMayo ClinicRochesterMN 55905USA

Dear Editor,Abnormal DNA methylation,a process whereby tumor suppressors tend to be hypermethylated and silenced,is a hallmark of cancer cells[1].Removing the methylation by demethylation agents such as azacitidine and decitabine is one of the strategies to treat cancers and has been successfully used to treat certain hematological and solid tumors[2].However,there are no established DNA methylation markers or signatures that can accurately predict patients’response to treatment[2];thus,the identification of reliable predictive biomarkers for effective therapy remains a critical need in clinical practice.

关键词： cancer signature suppressor

Incident frailty and cognitive impairment by heart failure status in older patients with atrial fibrillation: the SAGE-AF study

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Journal of Geriatric Cardiology 2020年第11期17卷 653-658页

作者： Wei-Jia WANG Darleen Lessard Jane Saczynski Robert J Goldberg Alan S.Go Tenes Paul Ely Gracia David D McManus department of Medicine University of Massachusetts Medical SchoolWorcesterMAUSA department of Population and quantitative health sciences University of Massachusetts Medical SchoolWorcesterMAUSA department of Pharmacy and health System sciences Northeastern UniversityBostonMAUSA Division of Research Kaiser Permanente Northern CaliforniaOaklandCAUSA

Background Atrial fibrillation(AF) and heart failure(HF) frequently co-occur in older individuals. Among patients with AF, HF increases risks for stroke and death, but the associations between HF and incident cognition and physical impairment remain unknown. We aimed to examine the cross-sectional and prospective associations between HF, cognition, and frailty among older patients with AF. Methods The SAGE-AF(Systematic Assessment of Geriatric Elements in AF) study enrolled 1244 patients with AF(mean age 76 years, 48% women) from five practices in Massachusetts and Georgia. HF at baseline was identified from electronic health records using ICD-9/10 codes. At baseline and 1-year, frailty was assessed by Cardiovascular health Survey score and cognition was assessed by the Montreal Cognitive Assessment. Results Patients with prevalent HF(n = 463, 37.2%) were older, less likely to be non-Hispanic white, had less education, and had greater cardiovascular comorbidity burden and higher CHA2 DS2 VASC and HAS-BLED scores than patients without HF(all P's < 0.01). In multivariable adjusted regression models, HF(present vs. absent) was associated with both prevalent frailty(adjusted odds ratio [a OR]: 2.38, 95% confidence interval [CI]: 1.64-3.46) and incident frailty at 1 year(a OR: 2.48, 95% CI: 1.37-4.51). HF was also independently associated with baseline cognitive impairment(a OR: 1.60, 95% CI: 1.22-2.11), but not with developing cognitive impairment at 1 year(a OR 1.04, 95%CI: 0.64-1.70). Conclusions Among ambulatory older patients with AF, the co-existence of HF identifies individuals with physical and cognitive impairments who are at higher short-term risk for becoming frail. Preventive strategies to this vulnerable subgroup merit consideration.

关键词： Atrial fibrillation Cognitive impairment Heart failure Frailty

Does serotonin reuptake inhibitor therapy increase the risk of post-sphincterotomy bleeding in patients undergoing endoscopic retrograde cholangio-pancreatography?

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World Journal of Gastrointestinal Endoscopy 2017年第4期9卷 171-176页

作者： Divya Yadav John Vargo Rocio Lopez Prabhleen Chahal department of Gastroenterology and Hepatology Digestive Disease InstituteCleveland Clinic department of quantitative health sciences Cleveland Clinic

AIM To evaluate the risk of immediate and delayed bleeding following sphincterotomy procedure.METHODS This retrospective cohort study was conducted with all patients who underwent endoscopic sphincterotomy during January 2006 to September 2015 at a tertiary academic center. Patients were grouped according to pre procedural usage of serotonin reuptake inhibitors(SRIs). Both groups were matched for demographic and clinical characteristics. Patients with thrombocytopenia,increased international normalized ratio, or a history of bleeding or coagulation disorders, concurrent use of other antiplatelet/anticoagulants were excluded from the study.RESULTS A total of 447 patients were included, of which 219(45.9%) used SRIs and 228(54.1%) cases did not.There was no significant difference in acute or delayed bleeding during endoscopic sphincterotomy between the two groups.(8.2% vs 12.3%, P = 0.16).CONCLUSION The use of SRIs was not associated with an increased risk of post-sphincterotomy bleeding. To our best knowledge, this is the first study to explore this asso-ciation.

关键词：血清素举起禁止者柱子 -- sphincterotomy 流血内视镜检查法内视镜后退 cholangiopancreatography 胃肠的流血

Exposure to air pollutants in Vietnam:Assessing potential risk for tourists

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Journal of Environmental sciences 2018年第11期30卷 147-154页

作者： Pallavi Pant Whitney Huynh Richard E.Peltier department of Environmental health sciences School of Public Health and Health SciencesUniversity of Massachusetts

Tourism can form an important component of a nation＇s GDP, and Vietnam is among the most visited countries in Southeast Asia. Most studies on personal exposure focus on the general population, or occupational cohorts with exposure to specific pollutants. However, short-term exposure to air pollutants while visiting regions with high levels of air pollution can lead to acute health effects. A personal exposure study was conducted across three cities in Vietnam to estimate exposure to particulate matter （PM2.5） and black carbon for tourists. Measurements were conducted during the wet season in 2014 in Ho Chi Minh City, Da Lat and Nha Trang using portable instrumentation. Average 24-hr PM2.5 and BC exposures were estimated as 18.9 ± 9.24 and 3.41 ± 1.33 μg/m3 and among the three cities, Ho Chi Minh was found to have the highest PM2.5 concentrations. Environmental tobacco smoke, commuting and street food stands were found to contribute to highest levels of exposure to PM2.s and BC across all cities.

关键词： Vietnam PM2.5 BC Exposure ETS Commute

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维多珠单抗治疗慢性抗生素难治性储袋炎

Gastroenterology Report 2019年第2期7卷 121-126,I0002页

作者： Amandeep Singh Freeha Khan Rocio Lopez Bo Shen Jessica Philpott department of Gastroenterology Hepatology and NutritionCleveland Clinic9500 Euclid AvenueClevelandOH 44195USA Center for Populations health sciences&quantitative health sciences Cleveland Clinic9500 Euclid AvenueClevelandOH 44195USA

背景:慢性抗生素难治性储袋炎(CARP)是回肠储袋-肛管吻合术(IPAA)的一个并发症,治疗上存在巨大挑战。维多珠单抗是一种肠道选择性的抗α4β7整合素单克隆抗体,现已应用于CARP患者,但其疗效数据报道不多。本研究旨在评估维多珠单抗作为... 详细信息

背景:慢性抗生素难治性储袋炎(CARP)是回肠储袋-肛管吻合术(IPAA)的一个并发症,治疗上存在巨大挑战。维多珠单抗是一种肠道选择性的抗α4β7整合素单克隆抗体,现已应用于CARP患者,但其疗效数据报道不多。本研究旨在评估维多珠单抗作为诱导治疗,应用于CARP患者的有效性和安全性。方法:从一个单中心的历史队列中,筛选出2015年1月至2017年6月间接受维多珠单抗治疗的CARP患者。病例纳入标准:改良储袋疾病严重指数(mPDAI)评分≥5的急性储袋炎;但如果没有mPDAI评分则以临床医生作出急性储袋炎的诊断为准。于治疗前及治疗后3个月,通过储袋镜和门诊检查来进行mPDAI评分。结果:19例患者纳入研究,平均年龄(26.7612.8)岁,其中男性10例(53%)。9例(47%)在结肠切除术前曾接受抗肿瘤坏死因子(TNF)药物治疗,10例(53%)患者在IPAA术后接受过抗TNF药物治疗。维多珠单抗治疗后,6例(32%)患者mPDAI症状评分显著改善(P=0.031);14例(74%)患者mPDAI内镜评分和总评分均显著改善,中位下降均为2分(P=0.031)。仅2例(11%)患者出现药物不良反应,另有4例(21%)患者需针对CARP行再次手术治疗。结论:本研究显示,维多珠单抗治疗CARP患者安全有效。而这些结果尚需更大样本量的研究证实。

关键词： Vedolizumab chronic antibiotic-refractory puchitits modified pouch disease activity index

Matching mechanism in global public goods games:a case of climate protection

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Chinese Journal of Population,Resources and Environment 2017年第4期15卷 273-284页

作者： Chongwu Yu Guocheng Wang department of quantitative & Technical Economics Graduate School of Chinese Academy of Social Sciences Institute of quantitative & Technical Economics Chinese Academy of Social Sciences

In the setting of dealing with climate change, this article designs a matching mechanism for global public goods provision with the aggregative game approach. Given endowment and the technology of each country, we propose the conditions under which the matching mechanism is able to guarantee full participation and Pareto efficient provision, respectively, in the cases with certain and uncertain preference information. These conditions cannot only be adopted in international negotiation and cooperation, but also refines the theory of matching game. In comparative static analyses, we discover that: First, changes of initial stock of climate goods produce a wealth effect and the crowd-out effect is less than 1. Second, climate tax policies affect the supply and welfare of each country only when they produce wealth effects, and if tax revenue is transferred into climate goods with more advanced technology, they will produce positive wealth effects. Third, modifying matching plans dynamically and appropriately can urge countries to improve technology, and especially given a Pareto optimal mechanism, adjusting the matching plan to keep marginal rates of transformation unchanged as technology changes is still able to ensure full participation and efficient supply of climate goods.

关键词：气候保护匹配商品机制比赛 Pareto 盒子气候变化

Probing the electrostatic aggregation of nanoparticles with oppositely charged molecular ions

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聚集体(英文)

聚集体(英文) 2023年第4期4卷 185-194页

作者： Jianxiang Huang Damiano Buratto Ruhong Zhou Institute of quantitative Biology College of Life SciencesHangzhouChina department of Chemistry Columbia UniversityNew YorkNew YorkUSA

The co-assembly of charged nanoparticles with oppositely charged molecular ions has emerged as a promising technique in the fabrication of nanoparticle superstructures.However,the underlying mechanism behind these molecular ions in mediating the repulsion between these charged nanoparticles remains elusive.Herein,coarsegrained molecular dynamics simulations are used to elucidate the effects of valency,shape,and size of molecular anions on their co-assembly with gold nanoparticles coated with positively charged ligands.The findings suggest that the valency,shape,and size of molecular anions significantly influence the repulsion and aggregating dynamics among these positively charged nanoparticles.Moreover,the free energy calculations reveal that ring-shaped molecular anions with higher valences and larger sizes are more effective at reducing the repulsion between these gold nanoparticles and thus enhance the stability of the aggregate.This study contributes to a better understanding of the critical roles of valence,shape,and size of ions in mediating the electrostatic co-assembly of nanoparticles with oppositely charged ions,and it also guides the future design of DNA templates and DNA origami in co-assembly with oppositely charged nanoparticles.

关键词： aggregation coarse-grained molecular dynamics simulation co-assembly electrostatic interaction nanoparticle