Publications

1. Sohn A, Turner AM, Speier W, Fonarow GC, Ong M, Arnold C. Patients with Heart Failure: Internet Use and Mobile Health Perceptions.. Applied clinical informatics, 2024.
2. Radhachandran A, Kinzel A, Chen J, Sant V, Patel M, Masamed R, Arnold CW, Speier W. A multitask approach for automated detection and segmentation of thyroid nodules in ultrasound images.. Computers in biology and medicine, 2024.
3. Ravipati Y, Pouratian N, Arnold C, Speier W. Evaluating Deep Learning Performance for P300 Neural Signal Classification.. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2024.
4. Zhuang L, Ivezic V, Feng J, Shen C, Radhachandran A, Sant V, Patel M, Masamed R, Arnold C, Speier W. Patient-level thyroid cancer classification using attention multiple instance learning on fused multi-scale ultrasound image features.. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2024.
5. Gibson D, Tran T, Raveendran V, Bonnet C, Siu N, Vinet M, Stoddard-Bennett T, Arnold C, Deng SX, Speier W. Latent diffusion augmentation enhances deep learning analysis of neuro-morphology in limbal stem cell deficiency.. Frontiers in medicine, 2023.
6. Panchavati S, Daida A, Edmonds B, Miyakoshi M, Oana S, Ahn SS, Arnold C, Salamon N, Sankar R, Fallah A, Speier W, Nariai H. Uncovering Spatiotemporal Dynamics of the Corticothalamic Network during Seizures.. medRxiv : the preprint server for health sciences, 2023.
7. Monsoor T, Zhang Y, Daida A, Oana S, Lu Q, Hussain SA, Fallah A, Sankar R, Staba RJ, Speier W, Roychowdhury V, Nariai H. Optimizing detection and deep learning-based classification of pathological high-frequency oscillations in epilepsy.. Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology, 2023.
8. Rao K, Speier W, Meng Y, Wang J, Ramesh N, Xie F, Su Y, Nowell WB, Curtis JR, Arnold C. Machine Learning Approaches to Classify Self-Reported Rheumatoid Arthritis Health Scores Using Activity Tracker Data: Longitudinal Observational Study.. JMIR formative research, 2023.
9. Monsoor T, Zhang Y, Daida A, Oana S, Lu Q, Hussain SA, Fallah A, Sankar R, Staba RJ, Speier W, Roychowdhury V, Nariai H. Optimizing Detection and Deep Learning-based Classification of Pathological High-Frequency Oscillations in Epilepsy.. medRxiv : the preprint server for health sciences, 2023.
10. Radhachandran A, Kinzel A, Chen J, Sant V, Patel M, Masamed R, Arnold CW, Speier W. A Multitask Approach for Automated Detection and Segmentation of Thyroid Nodules in Ultrasound Images.. medRxiv : the preprint server for health sciences, 2023.
11. Taira RK, Garlid AO, Speier W. Design considerations for a hierarchical semantic compositional framework for medical natural language understanding.. PloS one, 2023.
12. Chen C, Raymond C, Speier W, Jin X, Cloughesy TF, Enzmann D, Ellingson BM, Arnold CW. Synthesizing MR Image Contrast Enhancement Using 3D High-Resolution ConvNets.. IEEE transactions on bio-medical engineering, 2023.
13. Zhang Y, Chung H, Ngo JP, Monsoor T, Hussain SA, Matsumoto JH, Walshaw PD, Fallah A, Sim MS, Asano E, Sankar R, Staba RJ, Engel J, Speier W, Roychowdhury V, Nariai H. Characterizing physiological high-frequency oscillations using deep learning.. Journal of neural engineering, 2022.
14. Polson JS, Zhang H, Nael K, Salamon N, Yoo BY, El-Saden S, Starkman S, Kim N, Kang DW, Speier WF, Arnold CW. Identifying acute ischemic stroke patients within the thrombolytic treatment window using deep learning.. Journal of neuroimaging : official journal of the American Society of Neuroimaging, 2022.
15. Li W, Li J, Wang Z, Polson J, Sisk AE, Sajed DP, Speier W, Arnold CW. PathAL: An Active Learning Framework for Histopathology Image Analysis.. IEEE transactions on medical imaging, 2022.
16. Barsky L, Speier W, Fuller G, Cheng S, Kim A, Joung S, Arnold C, Dhawan S, Lopez M, Mastali M, van den Broek I, Wei J, Spiegel B, Van Eyk JE, Bairey Merz CN, Shufelt C. Sex-based differences in remote monitoring of biometric, psychometric and biomarker indices in stable ischemic heart disease.. Biology of sex differences, 2022.
17. Chen C, Chen Z, Jin X, Li L, Speier W, Arnold CW. Attention-Guided Discriminative Region Localization and Label Distribution Learning for Bone Age Assessment.. IEEE journal of biomedical and health informatics, 2022.
18. Loizidou P, Rios E, Marttini A, Keluo-Udeke O, Soetedjo J, Belay J, Perifanos K, Pouratian N, Speier W. Extending Brain-Computer Interface Access with a Multilingual Language Model in the P300 Speller.. Brain computer interfaces (Abingdon, England), 2021.
19. Li W, Li J, Polson J, Wang Z, Speier W, Arnold C. High resolution histopathology image generation and segmentation through adversarial training.. Medical image analysis, 2021.
20. Zhang Y, Lu Q, Monsoor T, Hussain SA, Qiao JX, Salamon N, Fallah A, Sim MS, Asano E, Sankar R, Staba RJ, Engel J, Speier W, Roychowdhury V, Nariai H. Refining epileptogenic high-frequency oscillations using deep learning: a reverse engineering approach.. Brain communications, 2021.
21. Polson J, Zhang H, Nael K, Salamon N, Yoo B, Kim N, Kang DW, Speier W, Arnold CW. A Semi-Supervised Learning Framework to Leverage Proxy Information for Stroke MRI Analysis.. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference, 2021.
22. Grzenda A, Speier W, Siddarth P, Pant A, Krause-Sorio B, Narr K, Lavretsky H. Machine Learning Prediction of Treatment Outcome in Late-Life Depression.. Frontiers in psychiatry, 2021.
23. Zhang H, Polson J, Nael K, Salamon N, Yoo B, Speier W, Arnold C. A Machine Learning Approach to Predict Acute Ischemic Stroke Thrombectomy Reperfusion using Discriminative MR Image Features.. ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics, 2021.
24. Meng Y, Speier W, Ong MK, Arnold CW. Bidirectional Representation Learning From Transformers Using Multimodal Electronic Health Record Data to Predict Depression.. IEEE journal of biomedical and health informatics, 2021.
25. Sarma KV, Raman AG, Dhinagar NJ, Priester AM, Harmon S, Sanford T, Mehralivand S, Turkbey B, Marks LS, Raman SS, Speier W, Arnold CW. Harnessing clinical annotations to improve deep learning performance in prostate segmentation.. PloS one, 2021.
26. Sarma KV, Harmon S, Sanford T, Roth HR, Xu Z, Tetreault J, Xu D, Flores MG, Raman AG, Kulkarni R, Wood BJ, Choyke PL, Priester AM, Marks LS, Raman SS, Enzmann D, Turkbey B, Speier W, Arnold CW. Federated learning improves site performance in multicenter deep learning without data sharing.. Journal of the American Medical Informatics Association : JAMIA, 2021.
27. Sheth J, Tankus A, Tran M, Pouratian N, Fried I, Speier W. Generalizing neural signal-to-text brain-computer interfaces.. Biomedical physics & engineering express, 2021.
28. Raman AG, Sarma KV, Raman SS, Priester AM, Mirak SA, Riskin-Jones HH, Dhinagar N, Speier W, Felker E, Sisk AE, Lu D, Kinnaird A, Reiter RE, Marks LS, Arnold CW. Optimizing Spatial Biopsy Sampling for the Detection of Prostate Cancer.. The Journal of urology, 2021.
29. Zhang H, Polson JS, Nael K, Salamon N, Yoo B, El-Saden S, Scalzo F, Speier W, Arnold CW. Intra-domain task-adaptive transfer learning to determine acute ischemic stroke onset time.. Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society, 2021.
30. Meng Y, Speier W, Ong M, Arnold CW. HCET: Hierarchical Clinical Embedding With Topic Modeling on Electronic Health Records for Predicting Future Depression.. IEEE journal of biomedical and health informatics, 2021.
31. Li J, Li W, Sisk A, Ye H, Wallace WD, Speier W, Arnold CW. A multi-resolution model for histopathology image classification and localization with multiple instance learning.. Computers in biology and medicine, 2021.
32. Dhinagar NJ, Speier W, Sarma KV, Raman A, Kinnaird A, Raman SS, Marks LS, Arnold CW. Semi-automated PIRADS scoring via mpMRI analysis.. Journal of medical imaging (Bellingham, Wash.), 2020.
33. Sohn A, Speier W, Lan E, Aoki K, Fonarow GC, Ong MK, Arnold CW. Integrating remote monitoring into heart failure patients' care regimen: A pilot study.. PloS one, 2020.
34. Shufelt CL, Kim A, Joung S, Barsky L, Arnold C, Cheng S, Dhawan S, Fuller G, Speier W, Lopez M, Mastali M, Mouapi K, van den Broek I, Wei J, Spiegel B, Van Eyk JE, Bairey-Merz CN. Biometric and Psychometric Remote Monitoring and Cardiovascular Risk Biomarkers in Ischemic Heart Disease.. Journal of the American Heart Association, 2020.
35. Sohn A, Speier W, Lan E, Aoki K, Fonarow G, Ong M, Arnold C. Assessment of Heart Failure Patients' Interest in Mobile Health Apps for Self-Care: Survey Study.. JMIR cardio, 2019.
36. Shufelt C, Dzubur E, Joung S, Fuller G, Mouapi KN, Van Den Broek I, Lopez M, Dhawan S, Arnold CW, Speier W, Mastali M, Fu Q, Van Eyk JE, Spiegel B, Merz CNB. A protocol integrating remote patient monitoring patient reported outcomes and cardiovascular biomarkers.. NPJ digital medicine, 2019.
37. Petousis P, Winter A, Speier W, Aberle DR, Hsu W, Bui AAT. Using Sequential Decision Making to Improve Lung Cancer Screening Performance.. IEEE access : practical innovations, open solutions, 2019.
38. Meng Y, Speier W, Shufelt C, Joung S, E Van Eyk J, Bairey Merz CN, Lopez M, Spiegel B, Arnold CW. A Machine Learning Approach to Classifying Self-Reported Health Status in a Cohort of Patients With Heart Disease Using Activity Tracker Data.. IEEE journal of biomedical and health informatics, 2019.
39. Ho KC, Scalzo F, Sarma KV, Speier W, El-Saden S, Arnold C. Predicting ischemic stroke tissue fate using a deep convolutional neural network on source magnetic resonance perfusion images.. Journal of medical imaging (Bellingham, Wash.), 2019.
40. Ho KC, Speier W, Zhang H, Scalzo F, El-Saden S, Arnold CW. A Machine Learning Approach for Classifying Ischemic Stroke Onset Time From Imaging.. IEEE transactions on medical imaging, 2019.
41. Speier W, Dzubur E, Zide M, Shufelt C, Joung S, Van Eyk JE, Bairey Merz CN, Lopez M, Spiegel B, Arnold C. Evaluating utility and compliance in a patient-based eHealth study using continuous-time heart rate and activity trackers.. Journal of the American Medical Informatics Association : JAMIA, 2018.
42. Li J, Speier W, Ho KC, Sarma KV, Gertych A, Knudsen BS, Arnold CW. An EM-based semi-supervised deep learning approach for semantic segmentation of histopathological images from radical prostatectomies.. Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society, 2018.
43. Neufeld EV, Dolezal BA, Speier W, Cooper CB. Effect of altering breathing frequency on maximum voluntary ventilation in healthy adults.. BMC pulmonary medicine, 2018.
44. Matiasz NJ, Wood J, Doshi P, Speier W, Beckemeyer B, Wang W, Hsu W, Silva AJ. ResearchMaps.org for integrating and planning research.. PloS one, 2018.
45. Ho KC, Speier W, El-Saden S, Arnold CW. Classifying Acute Ischemic Stroke Onset Time using Deep Imaging Features.. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2018.
46. Speier W, Arnold C, Chandravadia N, Roberts D, Pendekanti S, Pouratian N. Improving P300 Spelling Rate using Language Models and Predictive Spelling.. Brain computer interfaces (Abingdon, England), 2017.
47. Tsolaki E, Downes A, Speier W, Elias WJ, Pouratian N. The potential value of probabilistic tractography-based for MR-guided focused ultrasound thalamotomy for essential tremor.. NeuroImage. Clinical, 2017.
48. Hollada JL, Zide M, Speier W, Roter DL. Readability Assessment of Patient-Centered should be capitalized entered Outcomes Research Institute Public Abstracts in Relation to Accessibility.. Epidemiology (Cambridge, Mass.), 2017.
49. Speier W, Deshpande A, Cui L, Chandravadia N, Roberts D, Pouratian N. A comparison of stimulus types in online classification of the P300 speller using language models.. PloS one, 2017.
50. Speier W, Chandravadia N, Roberts D, Pendekanti S, Pouratian N. Online BCI Typing using Language Model Classifiers by ALS Patients in their Homes.. Brain computer interfaces (Abingdon, England), 2016.
51. Speier W, Arnold C, Pouratian N. Integrating language models into classifiers for BCI communication: a review.. Journal of neural engineering, 2016.
52. Speier W, Ong MK, Arnold CW. Using phrases and document metadata to improve topic modeling of clinical reports.. Journal of biomedical informatics, 2016.
53. Arnold CW, Oh A, Chen S, Speier W. Evaluating topic model interpretability from a primary care physician perspective.. Computer methods and programs in biomedicine, 2015.
54. Hollada J, Speier W, Oshiro T, Marzan-McGill R, Ruehm SG, Bassett LW, Wells C. Patients' Perceptions of Radiation Exposure Associated With Mammography.. AJR. American journal of roentgenology, 2015.
55. Speier W, Arnold CW, Deshpande A, Knall J, Pouratian N. Incorporating advanced language models into the P300 speller using particle filtering.. Journal of neural engineering, 2015.
56. Mostafavi L, Marfori W, Arellano C, Tognolini A, Speier W, Adibi A, Ruehm SG. Prevalence of coronary artery disease evaluated by coronary CT angiography in women with mammographically detected breast arterial calcifications.. PloS one, 2015.
57. Singleton KW, Speier W, Bui AA, Hsu W. Motivating the additional use of external validity: examining transportability in a model of glioblastoma multiforme.. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2014.
58. Ho KC, Speier W, El-Saden S, Liebeskind DS, Saver JL, Bui AA, Arnold CW. Predicting discharge mortality after acute ischemic stroke using balanced data.. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2014.
59. Speier W, Deshpande A, Pouratian N. A method for optimizing EEG electrode number and configuration for signal acquisition in P300 speller systems.. Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology, 2014.
60. Speier W, Arnold C, Lu J, Deshpande A, Pouratian N. Integrating language information with a hidden Markov model to improve communication rate in the P300 speller.. IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society, 2014.
61. Hollada J, Marfori W, Tognolini A, Speier W, Ristow L, Ruehm SG. Successful patient recruitment in CT imaging clinical trials: what factors influence patient participation?. Academic radiology, 2014.
62. Speier W, Arnold C, Pouratian N. Evaluating true BCI communication rate through mutual information and language models.. PloS one, 2013.
63. Speier W, Fried I, Pouratian N. Improved P300 speller performance using electrocorticography, spectral features, and natural language processing.. Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology, 2013.
64. Hsu W, Speier W, Taira RK. Automated extraction of reported statistical analyses: towards a logical representation of clinical trial literature.. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2012.
65. Speier W, Ochs MF. Updating annotations with the distributed annotation system and the automated sequence annotation pipeline.. Bioinformatics (Oxford, England), 2012.
66. Lu J, Speier W, Hu X, Pouratian N. The effects of stimulus timing features on P300 speller performance.. Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology, 2012.
67. Speier W, Arnold C, Lu J, Taira RK, Pouratian N. Natural language processing with dynamic classification improves P300 speller accuracy and bit rate.. Journal of neural engineering, 2011.
68. Favorov A, Lvovs D, Speier W, Parmigiani G, Ochs MF. OnionTree XML: a format to exchange gene-related probabilities.. Journal of biomolecular structure & dynamics, 2011.
69. Speier W, Iglesias JE, El-Kara L, Tu Z, Arnold C. Robust skull stripping of clinical glioblastoma multiforme data.. Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention, 2011.
70. Wong YN, Meropol NJ, Speier W, Sargent D, Goldberg RM, Beck JR. Cost implications of new treatments for advanced colorectal cancer.. Cancer, 2009.
71. Konski A, Speier W, Hanlon A, Beck JR, Pollack A. Is proton beam therapy cost effective in the treatment of adenocarcinoma of the prostate?. Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 2007.
72. Yu Z, Weinberger PM, Sasaki C, Egleston BL, Speier WF, Haffty B, Kowalski D, Camp R, Rimm D, Vairaktaris E, Burtness B, Psyrri A. Phosphorylation of Akt (Ser473) predicts poor clinical outcome in oropharyngeal squamous cell cancer.. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2007.
73. Moloshok TD, Klevecz RR, Grant JD, Manion FJ, Speier WF, Ochs MF. Application of Bayesian decomposition for analysing microarray data.. Bioinformatics (Oxford, England), 2002.