Literature DB >> 31466916

Looking beyond the hype: Applied AI and machine learning in translational medicine.

Tzen S Toh1, Frank Dondelinger2, Dennis Wang3.   

Abstract

Big data problems are becoming more prevalent for laboratory scientists who look to make clinical impact. A large part of this is due to increased computing power, in parallel with new technologies for high quality data generation. Both new and old techniques of artificial intelligence (AI) and machine learning (ML) can now help increase the success of translational studies in three areas: drug discovery, imaging, and genomic medicine. However, ML technologies do not come without their limitations and shortcomings. Current technical limitations and other limitations including governance, reproducibility, and interpretation will be discussed in this article. Overcoming these limitations will enable ML methods to be more powerful for discovery and reduce ambiguity within translational medicine, allowing data-informed decision-making to deliver the next generation of diagnostics and therapeutics to patients quicker, at lowered costs, and at scale.
Copyright © 2019. Published by Elsevier B.V.

Entities:  

Keywords:  Artificial intelligence; Drug discovery; Genomic medicine; Imaging; Machine learning; Translational medicine

Year:  2019        PMID: 31466916      PMCID: PMC6796516          DOI: 10.1016/j.ebiom.2019.08.027

Source DB:  PubMed          Journal:  EBioMedicine        ISSN: 2352-3964            Impact factor:   8.143


  56 in total

1.  Accurate Prediction of Biological Assays with High-Throughput Microscopy Images and Convolutional Networks.

Authors:  Markus Hofmarcher; Elisabeth Rumetshofer; Djork-Arné Clevert; Sepp Hochreiter; Günter Klambauer
Journal:  J Chem Inf Model       Date:  2019-03-06       Impact factor: 4.956

2.  Improved survival with ipilimumab in patients with metastatic melanoma.

Authors:  F Stephen Hodi; Steven J O'Day; David F McDermott; Robert W Weber; Jeffrey A Sosman; John B Haanen; Rene Gonzalez; Caroline Robert; Dirk Schadendorf; Jessica C Hassel; Wallace Akerley; Alfons J M van den Eertwegh; Jose Lutzky; Paul Lorigan; Julia M Vaubel; Gerald P Linette; David Hogg; Christian H Ottensmeier; Celeste Lebbé; Christian Peschel; Ian Quirt; Joseph I Clark; Jedd D Wolchok; Jeffrey S Weber; Jason Tian; Michael J Yellin; Geoffrey M Nichol; Axel Hoos; Walter J Urba
Journal:  N Engl J Med       Date:  2010-06-05       Impact factor: 91.245

3.  Affinity network fusion and semi-supervised learning for cancer patient clustering.

Authors:  Tianle Ma; Aidong Zhang
Journal:  Methods       Date:  2018-05-26       Impact factor: 3.608

4.  Intertumoral Heterogeneity within Medulloblastoma Subgroups.

Authors:  Florence M G Cavalli; Marc Remke; Ladislav Rampasek; John Peacock; David J H Shih; Betty Luu; Livia Garzia; Jonathon Torchia; Carolina Nor; A Sorana Morrissy; Sameer Agnihotri; Yuan Yao Thompson; Claudia M Kuzan-Fischer; Hamza Farooq; Keren Isaev; Craig Daniels; Byung-Kyu Cho; Seung-Ki Kim; Kyu-Chang Wang; Ji Yeoun Lee; Wieslawa A Grajkowska; Marta Perek-Polnik; Alexandre Vasiljevic; Cecile Faure-Conter; Anne Jouvet; Caterina Giannini; Amulya A Nageswara Rao; Kay Ka Wai Li; Ho-Keung Ng; Charles G Eberhart; Ian F Pollack; Ronald L Hamilton; G Yancey Gillespie; James M Olson; Sarah Leary; William A Weiss; Boleslaw Lach; Lola B Chambless; Reid C Thompson; Michael K Cooper; Rajeev Vibhakar; Peter Hauser; Marie-Lise C van Veelen; Johan M Kros; Pim J French; Young Shin Ra; Toshihiro Kumabe; Enrique López-Aguilar; Karel Zitterbart; Jaroslav Sterba; Gaetano Finocchiaro; Maura Massimino; Erwin G Van Meir; Satoru Osuka; Tomoko Shofuda; Almos Klekner; Massimo Zollo; Jeffrey R Leonard; Joshua B Rubin; Nada Jabado; Steffen Albrecht; Jaume Mora; Timothy E Van Meter; Shin Jung; Andrew S Moore; Andrew R Hallahan; Jennifer A Chan; Daniela P C Tirapelli; Carlos G Carlotti; Maryam Fouladi; José Pimentel; Claudia C Faria; Ali G Saad; Luca Massimi; Linda M Liau; Helen Wheeler; Hideo Nakamura; Samer K Elbabaa; Mario Perezpeña-Diazconti; Fernando Chico Ponce de León; Shenandoah Robinson; Michal Zapotocky; Alvaro Lassaletta; Annie Huang; Cynthia E Hawkins; Uri Tabori; Eric Bouffet; Ute Bartels; Peter B Dirks; James T Rutka; Gary D Bader; Jüri Reimand; Anna Goldenberg; Vijay Ramaswamy; Michael D Taylor
Journal:  Cancer Cell       Date:  2017-06-12       Impact factor: 31.743

5.  Next-generation characterization of the Cancer Cell Line Encyclopedia.

Authors:  Mahmoud Ghandi; Franklin W Huang; Judit Jané-Valbuena; Gregory V Kryukov; Christopher C Lo; E Robert McDonald; Jordi Barretina; Ellen T Gelfand; Craig M Bielski; Haoxin Li; Kevin Hu; Alexander Y Andreev-Drakhlin; Jaegil Kim; Julian M Hess; Brian J Haas; François Aguet; Barbara A Weir; Michael V Rothberg; Brenton R Paolella; Michael S Lawrence; Rehan Akbani; Yiling Lu; Hong L Tiv; Prafulla C Gokhale; Antoine de Weck; Ali Amin Mansour; Coyin Oh; Juliann Shih; Kevin Hadi; Yanay Rosen; Jonathan Bistline; Kavitha Venkatesan; Anupama Reddy; Dmitriy Sonkin; Manway Liu; Joseph Lehar; Joshua M Korn; Dale A Porter; Michael D Jones; Javad Golji; Giordano Caponigro; Jordan E Taylor; Caitlin M Dunning; Amanda L Creech; Allison C Warren; James M McFarland; Mahdi Zamanighomi; Audrey Kauffmann; Nicolas Stransky; Marcin Imielinski; Yosef E Maruvka; Andrew D Cherniack; Aviad Tsherniak; Francisca Vazquez; Jacob D Jaffe; Andrew A Lane; David M Weinstock; Cory M Johannessen; Michael P Morrissey; Frank Stegmeier; Robert Schlegel; William C Hahn; Gad Getz; Gordon B Mills; Jesse S Boehm; Todd R Golub; Levi A Garraway; William R Sellers
Journal:  Nature       Date:  2019-05-08       Impact factor: 49.962

6.  The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Authors:  Jordi Barretina; Giordano Caponigro; Nicolas Stransky; Kavitha Venkatesan; Adam A Margolin; Sungjoon Kim; Christopher J Wilson; Joseph Lehár; Gregory V Kryukov; Dmitriy Sonkin; Anupama Reddy; Manway Liu; Lauren Murray; Michael F Berger; John E Monahan; Paula Morais; Jodi Meltzer; Adam Korejwa; Judit Jané-Valbuena; Felipa A Mapa; Joseph Thibault; Eva Bric-Furlong; Pichai Raman; Aaron Shipway; Ingo H Engels; Jill Cheng; Guoying K Yu; Jianjun Yu; Peter Aspesi; Melanie de Silva; Kalpana Jagtap; Michael D Jones; Li Wang; Charles Hatton; Emanuele Palescandolo; Supriya Gupta; Scott Mahan; Carrie Sougnez; Robert C Onofrio; Ted Liefeld; Laura MacConaill; Wendy Winckler; Michael Reich; Nanxin Li; Jill P Mesirov; Stacey B Gabriel; Gad Getz; Kristin Ardlie; Vivien Chan; Vic E Myer; Barbara L Weber; Jeff Porter; Markus Warmuth; Peter Finan; Jennifer L Harris; Matthew Meyerson; Todd R Golub; Michael P Morrissey; William R Sellers; Robert Schlegel; Levi A Garraway
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

7.  Clusternomics: Integrative context-dependent clustering for heterogeneous datasets.

Authors:  Evelina Gabasova; John Reid; Lorenz Wernisch
Journal:  PLoS Comput Biol       Date:  2017-10-16       Impact factor: 4.475

8.  High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines.

Authors:  Channing Yu; Aristotle M Mannan; Griselda Metta Yvone; Kenneth N Ross; Yan-Ling Zhang; Melissa A Marton; Bradley R Taylor; Andrew Crenshaw; Joshua Z Gould; Pablo Tamayo; Barbara A Weir; Aviad Tsherniak; Bang Wong; Levi A Garraway; Alykhan F Shamji; Michelle A Palmer; Michael A Foley; Wendy Winckler; Stuart L Schreiber; Andrew L Kung; Todd R Golub
Journal:  Nat Biotechnol       Date:  2016-02-29       Impact factor: 54.908

9.  Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning.

Authors:  Nicolas Coudray; Paolo Santiago Ocampo; Theodore Sakellaropoulos; Navneet Narula; Matija Snuderl; David Fenyö; Andre L Moreira; Narges Razavian; Aristotelis Tsirigos
Journal:  Nat Med       Date:  2018-09-17       Impact factor: 53.440

10.  Predicting non-small cell lung cancer prognosis by fully automated microscopic pathology image features.

Authors:  Kun-Hsing Yu; Ce Zhang; Gerald J Berry; Russ B Altman; Christopher Ré; Daniel L Rubin; Michael Snyder
Journal:  Nat Commun       Date:  2016-08-16       Impact factor: 14.919

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  17 in total

1.  Using Machine Learning Methods to Predict Bone Metastases in Breast Infiltrating Ductal Carcinoma Patients.

Authors:  Wen-Cai Liu; Ming-Xuan Li; Shi-Nan Wu; Wei-Lai Tong; An-An Li; Bo-Lin Sun; Zhi-Li Liu; Jia-Ming Liu
Journal:  Front Public Health       Date:  2022-07-06

Review 2.  High-dimensional role of AI and machine learning in cancer research.

Authors:  Enrico Capobianco
Journal:  Br J Cancer       Date:  2022-01-10       Impact factor: 9.075

3.  Detecting premature departure in online text-based counseling using logic-based pattern matching.

Authors:  Yucan Xu; Christian S Chan; Christy Tsang; Florence Cheung; Evangeline Chan; Jerry Fung; James Chow; Lihong He; Zhongzhi Xu; Paul S F Yip
Journal:  Internet Interv       Date:  2021-11-23

Review 4.  Understanding Mosquito Surveillance Data for Analytic Efforts: A Case Study.

Authors:  Heidi E Brown; Luigi Sedda; Chris Sumner; Elene Stefanakos; Irene Ruberto; Matthew Roach
Journal:  J Med Entomol       Date:  2021-07-16       Impact factor: 2.278

Review 5.  Artificial intelligence to deep learning: machine intelligence approach for drug discovery.

Authors:  Rohan Gupta; Devesh Srivastava; Mehar Sahu; Swati Tiwari; Rashmi K Ambasta; Pravir Kumar
Journal:  Mol Divers       Date:  2021-04-12       Impact factor: 3.364

6.  Automated Enteropathy: Discovering the Potential of Machine Learning in Environmental Enteropathy.

Authors:  Thomas Wallach
Journal:  J Pediatr Gastroenterol Nutr       Date:  2021-06-01       Impact factor: 3.288

7.  Ontologies, Knowledge Representation, and Machine Learning for Translational Research: Recent Contributions.

Authors:  Peter N Robinson; Melissa A Haendel
Journal:  Yearb Med Inform       Date:  2020-08-21

8.  Use of a community advisory board to build equitable algorithms for participation in clinical trials: a protocol paper for HoPeNET.

Authors:  Nicole Farmer; Foster Osei Baah; Faustine Williams; Erika Ortiz-Chapparo; Valerie M Mitchell; Latifa Jackson; Billy Collins; Lennox Graham; Gwenyth R Wallen; Tiffany M Powell-Wiley; Allan Johnson
Journal:  BMJ Health Care Inform       Date:  2022-02

Review 9.  Artificial Intelligence (AI) in Rare Diseases: Is the Future Brighter?

Authors:  Sandra Brasil; Carlota Pascoal; Rita Francisco; Vanessa Dos Reis Ferreira; Paula A Videira; And Gonçalo Valadão
Journal:  Genes (Basel)       Date:  2019-11-27       Impact factor: 4.096

Review 10.  Artificial intelligence in orthopaedics: false hope or not? A narrative review along the line of Gartner's hype cycle.

Authors:  Jacobien H F Oosterhoff; Job N Doornberg
Journal:  EFORT Open Rev       Date:  2020-10-26
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