PRedictive Intelligence in MEdicine. PRIME (Workshop)最新文献

{"title":"Spectral Graph Sample Weighting for Interpretable Sub-cohort Analysis in Predictive Models for Neuroimaging.","authors":"Magdalini Paschali, Yu Hang Jiang, Spencer Siegel, Camila Gonzalez, Kilian M Pohl, Akshay Chaudhari, Qingyu Zhao","doi":"10.1007/978-3-031-74561-4_3","DOIUrl":"https://doi.org/10.1007/978-3-031-74561-4_3","url":null,"abstract":"<p><p>Recent advancements in medicine have confirmed that brain disorders often comprise multiple subtypes of mechanisms, developmental trajectories, or severity levels. Such heterogeneity is often associated with demographic aspects (e.g., sex) or disease-related contributors (e.g., genetics). Thus, the predictive power of machine learning models used for symptom prediction varies across subjects based on such factors. To model this heterogeneity, one can assign each training sample a factor-dependent weight, which modulates the subject's contribution to the overall objective loss function. To this end, we propose to model the subject weights as a linear combination of the eigenbases of a spectral population graph that captures the similarity of factors across subjects. In doing so, the learned weights smoothly vary across the graph, highlighting sub-cohorts with high and low predictability. Our proposed sample weighting scheme is evaluated on two tasks. First, we predict initiation of heavy alcohol drinking in young adulthood from imaging and neuropsychological measures from the National Consortium on Alcohol and NeuroDevelopment in Adolescence (NCANDA). Next, we detect Dementia <i>vs</i>. Mild Cognitive Impairment (MCI) using imaging and demographic measurements in subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Compared to existing sample weighting schemes, our sample weights improve interpretability and highlight sub-cohorts with distinct characteristics and varying model accuracy.</p>","PeriodicalId":92572,"journal":{"name":"PRedictive Intelligence in MEdicine. PRIME (Workshop)","volume":"15155 ","pages":"24-34"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549025/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SynthA1c: Towards Clinically Interpretable Patient Representations for Diabetes Risk Stratification.","authors":"Michael S Yao, Allison Chae, Matthew T MacLean, Anurag Verma, Jeffrey Duda, James C Gee, Drew A Torigian, Daniel Rader, Charles E Kahn, Walter R Witschey, Hersh Sagreiya","doi":"10.1007/978-3-031-46005-0_5","DOIUrl":"10.1007/978-3-031-46005-0_5","url":null,"abstract":"<p><p>Early diagnosis of Type 2 Diabetes Mellitus (T2DM) is crucial to enable timely therapeutic interventions and lifestyle modifications. As the time available for clinical office visits shortens and medical imaging data become more widely available, patient image data could be used to opportunistically identify patients for additional T2DM diagnostic workup by physicians. We investigated whether image-derived phenotypic data could be leveraged in tabular learning classifier models to predict T2DM risk in an automated fashion to flag high-risk patients <i>without</i> the need for additional blood laboratory measurements. In contrast to traditional binary classifiers, we leverage neural networks and decision tree models to represent patient data as 'SynthA1c' latent variables, which mimic blood hemoglobin A1c empirical lab measurements, that achieve sensitivities as high as 87.6%. To evaluate how SynthA1c models may generalize to other patient populations, we introduce a novel generalizable metric that uses vanilla data augmentation techniques to predict model performance on input out-of-domain covariates. We show that image-derived phenotypes and physical examination data together can accurately predict diabetes risk as a means of opportunistic risk stratification enabled by artificial intelligence and medical imaging. Our code is available at https://github.com/allisonjchae/DMT2RiskAssessment.</p>","PeriodicalId":92572,"journal":{"name":"PRedictive Intelligence in MEdicine. PRIME (Workshop)","volume":"14277 ","pages":"46-57"},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11217801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141494546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Imputing Brain Measurements Across Data Sets via Graph Neural Networks.","authors":"Yixin Wang, Wei Peng, Susan F Tapert, Qingyu Zhao, Kilian M Pohl","doi":"10.1007/978-3-031-46005-0_15","DOIUrl":"10.1007/978-3-031-46005-0_15","url":null,"abstract":"<p><p>Publicly available data sets of structural MRIs might not contain specific measurements of brain Regions of Interests (ROIs) that are important for training machine learning models. For example, the curvature scores computed by Freesurfer are not released by the Adolescent Brain Cognitive Development (ABCD) Study. One can address this issue by simply reapplying Freesurfer to the data set. However, this approach is generally computationally and labor intensive (e.g., requiring quality control). An alternative is to impute the missing measurements via a deep learning approach. However, the state-of-the-art is designed to estimate randomly missing values rather than entire measurements. We therefore propose to re-frame the imputation problem as a prediction task on another (public) data set that contains the missing measurements and shares some ROI measurements with the data sets of interest. A deep learning model is then trained to predict the missing measurements from the shared ones and afterwards is applied to the other data sets. Our proposed algorithm models the dependencies between ROI measurements via a graph neural network (GNN) and accounts for demographic differences in brain measurements (e.g. sex) by feeding the graph encoding into a parallel architecture. The architecture simultaneously optimizes a graph decoder to impute values and a classifier in predicting demographic factors. We test the approach, called <i>D</i>emographic <i>A</i>ware <i>G</i>raph-based <i>I</i>mputation (<i>DAGI</i>), on imputing those missing Freesurfer measurements of ABCD (N=3760; minimum age 12 years) by training the predictor on those publicly released by the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA, N=540). 5-fold cross-validation on NCANDA reveals that the imputed scores are more accurate than those generated by linear regressors and deep learning models. Adding them also to a classifier trained in identifying sex results in higher accuracy than only using those Freesurfer scores provided by ABCD.</p>","PeriodicalId":92572,"journal":{"name":"PRedictive Intelligence in MEdicine. PRIME (Workshop)","volume":"14277 ","pages":"172-183"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72016422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple Instance Neuroimage Transformer.","authors":"Ayush Singla, Qingyu Zhao, Daniel K Do, Yuyin Zhou, Kilian M Pohl, Ehsan Adeli","doi":"10.1007/978-3-031-16919-9_4","DOIUrl":"10.1007/978-3-031-16919-9_4","url":null,"abstract":"<p><p>For the first time, we propose using a multiple instance learning based convolution-free transformer model, called Multiple Instance Neuroimage Transformer (MINiT), for the classification of T1-weighted (T1w) MRIs. We first present several variants of transformer models adopted for neuroimages. These models extract non-overlapping 3D blocks from the input volume and perform multi-headed self-attention on a sequence of their linear projections. MINiT, on the other hand, treats each of the non-overlapping 3D blocks of the input MRI as its own instance, splitting it further into non-overlapping 3D patches, on which multi-headed self-attention is computed. As a proof-of-concept, we evaluate the efficacy of our model by training it to identify sex from T1w-MRIs of two public datasets: Adolescent Brain Cognitive Development (ABCD) and the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA). The learned attention maps highlight voxels contributing to identifying sex differences in brain morphometry. The code is available at https://github.com/singlaayush/MINIT.</p>","PeriodicalId":92572,"journal":{"name":"PRedictive Intelligence in MEdicine. PRIME (Workshop)","volume":"13564 ","pages":"36-48"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9629332/pdf/nihms-1844680.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40665498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridging the Gap between Deep Learning and Hypothesis-Driven Analysis via Permutation Testing.","authors":"Magdalini Paschali, Qingyu Zhao, Ehsan Adeli, Kilian M Pohl","doi":"10.1007/978-3-031-16919-9_2","DOIUrl":"10.1007/978-3-031-16919-9_2","url":null,"abstract":"<p><p>A fundamental approach in neuroscience research is to test hypotheses based on neuropsychological and behavioral measures, i.e., whether certain factors (e.g., related to life events) are associated with an outcome (e.g., depression). In recent years, deep learning has become a potential alternative approach for conducting such analyses by predicting an outcome from a collection of factors and identifying the most \"informative\" ones driving the prediction. However, this approach has had limited impact as its findings are not linked to statistical significance of factors supporting hypotheses. In this article, we proposed a flexible and scalable approach based on the concept of permutation testing that integrates hypothesis testing into the data-driven deep learning analysis. We apply our approach to the yearly self-reported assessments of 621 adolescent participants of the National Consortium of Alcohol and Neurodevelopment in Adolescence (NCANDA) to predict negative valence, a symptom of major depressive disorder according to the NIMH Research Domain Criteria (RDoC). Our method successfully identifies categories of risk factors that further explain the symptom.</p>","PeriodicalId":92572,"journal":{"name":"PRedictive Intelligence in MEdicine. PRIME (Workshop)","volume":"13564 ","pages":"13-23"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9632755/pdf/nihms-1844547.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40671061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple Instance Neuroimage Transformer","authors":"Ayush Singla, Qingyu Zhao, Daniel K. Do, Yuyin Zhou, K. Pohl, E. Adeli","doi":"10.48550/arXiv.2208.09567","DOIUrl":"https://doi.org/10.48550/arXiv.2208.09567","url":null,"abstract":"For the first time, we propose using a multiple instance learning based convolution-free transformer model, called Multiple Instance Neuroimage Transformer (MINiT), for the classification of T1-weighted (T1w) MRIs. We first present several variants of transformer models adopted for neuroimages. These models extract non-overlapping 3D blocks from the input volume and perform multi-headed self-attention on a sequence of their linear projections. MINiT, on the other hand, treats each of the non-overlapping 3D blocks of the input MRI as its own instance, splitting it further into non-overlapping 3D patches, on which multi-headed self-attention is computed. As a proof-of-concept, we evaluate the efficacy of our model by training it to identify sex from T1w-MRIs of two public datasets: Adolescent Brain Cognitive Development (ABCD) and the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA). The learned attention maps highlight voxels contributing to identifying sex differences in brain morphometry. The code is available at https://github.com/singlaayush/MINIT.","PeriodicalId":92572,"journal":{"name":"PRedictive Intelligence in MEdicine. PRIME (Workshop)","volume":"40 1","pages":"36-48"},"PeriodicalIF":0.0,"publicationDate":"2022-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90210281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridging the Gap between Deep Learning and Hypothesis-Driven Analysis via Permutation Testing","authors":"Magdalini Paschali, Qingyu Zhao, E. Adeli, K. Pohl","doi":"10.48550/arXiv.2207.14349","DOIUrl":"https://doi.org/10.48550/arXiv.2207.14349","url":null,"abstract":"A fundamental approach in neuroscience research is to test hypotheses based on neuropsychological and behavioral measures, i.e., whether certain factors (e.g., related to life events) are associated with an outcome (e.g., depression). In recent years, deep learning has become a potential alternative approach for conducting such analyses by predicting an outcome from a collection of factors and identifying the most \"informative\" ones driving the prediction. However, this approach has had limited impact as its findings are not linked to statistical significance of factors supporting hypotheses. In this article, we proposed a flexible and scalable approach based on the concept of permutation testing that integrates hypothesis testing into the data-driven deep learning analysis. We apply our approach to the yearly self-reported assessments of 621 adolescent participants of the National Consortium of Alcohol and Neurodevelopment in Adolescence (NCANDA) to predict negative valence, a symptom of major depressive disorder according to the NIMH Research Domain Criteria (RDoC). Our method successfully identifies categories of risk factors that further explain the symptom.","PeriodicalId":92572,"journal":{"name":"PRedictive Intelligence in MEdicine. PRIME (Workshop)","volume":"3 1","pages":"13-23"},"PeriodicalIF":0.0,"publicationDate":"2022-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85637288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predictive Intelligence in Medicine: 5th International Workshop, PRIME 2022, Held in Conjunction with MICCAI 2022, Singapore, September 22, 2022, Proceedings","authors":"","doi":"10.1007/978-3-031-16919-9","DOIUrl":"https://doi.org/10.1007/978-3-031-16919-9","url":null,"abstract":"","PeriodicalId":92572,"journal":{"name":"PRedictive Intelligence in MEdicine. PRIME (Workshop)","volume":"44 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78553975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adversarial Bayesian Optimization for Quantifying Motion Artifact Within MRI.","authors":"Anastasia Butskova,&nbsp;Rain Juhl,&nbsp;Dženan Zukić,&nbsp;Aashish Chaudhary,&nbsp;Kilian M Pohl,&nbsp;Qingyu Zhao","doi":"10.1007/978-3-030-87602-9_8","DOIUrl":"https://doi.org/10.1007/978-3-030-87602-9_8","url":null,"abstract":"<p><p>Subject motion during an MRI sequence can cause ghosting effects or diffuse image noise in the phase-encoding direction and hence is likely to bias findings in neuroimaging studies. Detecting motion artifacts often relies on experts visually inspecting MRIs, which is subjective and expensive. To improve this detection, we develop a framework to automatically quantify the severity of motion artifact within a brain MRI. We formulate this task as a regression problem and train the regressor from a data set of MRIs with various amounts of motion artifacts. To resolve the issue of missing fine-grained ground-truth labels (level of artifacts), we propose Adversarial Bayesian Optimization (ABO) to infer the distribution of motion parameters (i.e., rotation and translation) underlying the acquired MRI data and then inject synthetic motion artifacts sampled from that estimated distribution into motion-free MRIs. After training the regressor on the synthetic data, we applied the model to quantify the motion level in 990 MRIs collected by the National Consortium on Alcohol and Neurodevelopment in Adolescence. Results show that the motion level derived by our approach is more reliable than the traditional metric based on Entropy Focus Criterion and manually defined binary labels.</p>","PeriodicalId":92572,"journal":{"name":"PRedictive Intelligence in MEdicine. PRIME (Workshop)","volume":"12928 ","pages":"83-92"},"PeriodicalIF":0.0,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9212065/pdf/nihms-1816521.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40397338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predictive Intelligence in Medicine: 4th International Workshop, PRIME 2021, Held in Conjunction with MICCAI 2021, Strasbourg, France, October 1, 2021, Proceedings","authors":"","doi":"10.1007/978-3-030-87602-9","DOIUrl":"https://doi.org/10.1007/978-3-030-87602-9","url":null,"abstract":"","PeriodicalId":92572,"journal":{"name":"PRedictive Intelligence in MEdicine. PRIME (Workshop)","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77626012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}