JabRef references

Quinn TP, Nguyen T, Lee SC and Venkatesh S (2019), "Cancer as a Tissue Anomaly: Classifying Tumor Transcriptomes Based Only on Healthy Data", Frontiers in Genetics. Vol. 10, pp. 599.

[Abstract] [BibTeX] [DOI] [URL]

Abstract: Since the turn of the century, researchers have sought to diagnose cancer based on gene expression signatures measured from the blood or biopsy as biomarkers. This task, known as classification, is typically solved using a suite of algorithms that learn a mathematical rule capable of discriminating one group (``cases'') from another (``controls''). However, discriminatory methods can only identify cancerous samples that resemble those that the algorithm already saw during training. As such, discriminatory methods may be ill-suited for the classification of cancer: because the possibility space of cancer is definitively large, the existence of a one-of-a-kind gene expression signature is likely. Instead, we propose using an established surveillance method that detects anomalous samples based on their deviation from a learned normal steady-state structure. By transferring this method to transcriptomic data, we can create an anomaly detector for tissue transcriptomes, a ``tissue detector'', that is capable of identifying cancer without ever seeing a single cancer example. As a proof-of-concept, we train a ``tissue detector'' on normal GTEx samples that can classify TCGA samples with >90% AUC for 3 out of 6 tissues. Importantly, we find that the classification accuracy is improved simply by adding more healthy samples. We conclude this report by emphasizing the conceptual advantages of anomaly detection and by highlighting future directions for this field of study.

BibTeX:

@article{10.3389/fgene.2019.00599,
  author = {Quinn, Thomas P. and Nguyen, Thin and Lee, Samuel C. and Venkatesh, Svetha},
  title = {Cancer as a Tissue Anomaly: Classifying Tumor Transcriptomes Based Only on Healthy Data},
  journal = {Frontiers in Genetics},
  year = {2019},
  volume = {10},
  pages = {599},
  url = {https://www.frontiersin.org/article/10.3389/fgene.2019.00599},
  doi = {10.3389/fgene.2019.00599}
}

Ramachandran A, Gupta S, Rana S and Venkatesh S (2019), "Information-Theoretic Multi-task Learning Framework for Bayesian Optimisation", In AI 2019: Advances in Artificial Intelligence. , pp. 497-509. Springer International Publishing.

BibTeX:

@inproceedings{anil2019multitask,
  author = {Ramachandran, Anil and Gupta, Sunil and Rana, Santu and Venkatesh, Svetha},
  title = {Information-Theoretic Multi-task Learning Framework for Bayesian Optimisation},
  booktitle = {AI 2019: Advances in Artificial Intelligence},
  publisher = {Springer International Publishing},
  year = {2019},
  pages = {497--509}
}

Arun Kumar AV, Rana S, Li C, Gupta S, Shilton A and Venkatesh S (2019), "Bayesian Optimisation for Objective Functions with Varying Smoothness", In AI 2019: Advances in Artificial Intelligence. , pp. 460-472. Springer International Publishing.

BibTeX:

@inproceedings{arun2019smoothness,
  author = {Arun Kumar, A. V. and Rana, Santu and Li, Cheng and Gupta, Sunil and Shilton, Alistair and Venkatesh, Svetha},
  title = {Bayesian Optimisation for Objective Functions with Varying Smoothness},
  booktitle = {AI 2019: Advances in Artificial Intelligence},
  publisher = {Springer International Publishing},
  year = {2019},
  pages = {460--472}
}

Barnett S, Huckvale K, Christensen H, Venkatesh S, Mouzakis K and Vasa R (2019), "Intelligent Sensing to Inform and Learn (InSTIL): A Scalable and Governance-Aware Platform for Universal, Smartphone-Based Digital Phenotyping for Research and Clinical Applications", Journal of medical Internet research. Vol. 21(11), pp. e16399. JMIR Publications Inc., Toronto, Canada.

BibTeX:

@article{barnett2019intelligent,
  author = {Barnett, Scott and Huckvale, Kit and Christensen, Helen and Venkatesh, Svetha and Mouzakis, Kon and Vasa, Rajesh},
  title = {Intelligent Sensing to Inform and Learn (InSTIL): A Scalable and Governance-Aware Platform for Universal, Smartphone-Based Digital Phenotyping for Research and Clinical Applications},
  journal = {Journal of medical Internet research},
  publisher = {JMIR Publications Inc., Toronto, Canada},
  year = {2019},
  volume = {21},
  number = {11},
  pages = {e16399}
}

Kuttichira DP, Gupta S, Nguyen D, Rana S and Venkatesh S (2019), "Detection of Compromised Models Using Bayesian Optimization", In AI 2019: Advances in Artificial Intelligence. , pp. 485-496. Springer International Publishing.

BibTeX:

@inproceedings{deepthi2019detection,
  author = {Kuttichira, Deepthi Praveenlal and Gupta, Sunil and Nguyen, Dang and Rana, Santu and Venkatesh, Svetha},
  title = {Detection of Compromised Models Using Bayesian Optimization},
  booktitle = {AI 2019: Advances in Artificial Intelligence},
  publisher = {Springer International Publishing},
  year = {2019},
  pages = {485--496}
}

Do K, Tran T, Nguyen T and Venkatesh S (2019), "Attentional multilabel learning over graphs: a message passing approach", Machine Learning. Vol. 108(10), pp. 1757-1781. Springer.

BibTeX:

@article{do2019attentional,
  author = {Do, Kien and Tran, Truyen and Nguyen, Thin and Venkatesh, Svetha},
  title = {Attentional multilabel learning over graphs: a message passing approach},
  journal = {Machine Learning},
  publisher = {Springer},
  year = {2019},
  volume = {108},
  number = {10},
  pages = {1757--1781}
}

Do K, Tran T and Venkatesh S (2019), "Graph Transformation Policy Network for Chemical Reaction Prediction", In Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD). , pp. 750-760.

BibTeX:

@inproceedings{do2019graph,
  author = {Do, Kien and Tran, Truyen and Venkatesh, Svetha},
  title = {Graph Transformation Policy Network for Chemical Reaction Prediction},
  booktitle = {Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD)},
  year = {2019},
  pages = {750--760}
}

Ha H, Rana S, Gupta S, Nguyen T, Venkatesh S and others (2019), "Bayesian Optimization with Unknown Search Space", In Advances in Neural Information Processing Systems. , pp. 11772-11781.

BibTeX:

@inproceedings{ha2019bayesian,
  author = {Ha, Huong and Rana, Santu and Gupta, Sunil and Nguyen, Thanh and Venkatesh, Svetha and others},
  title = {Bayesian Optimization with Unknown Search Space},
  booktitle = {Advances in Neural Information Processing Systems},
  year = {2019},
  pages = {11772--11781},
  url = {http://papers.nips.cc/paper/9350-bayesian-optimization-with-unknown-search-space.pdf}
}

Huckvale K, Venkatesh S and Christensen H (2019), "Toward clinical digital phenotyping: a timely opportunity to consider purpose, quality, and safety", NPJ Digital Medicine. Vol. 2(1), pp. 1-11. Nature Publishing Group.

BibTeX:

@article{huckvale2019toward,
  author = {Huckvale, Kit and Venkatesh, Svetha and Christensen, Helen},
  title = {Toward clinical digital phenotyping: a timely opportunity to consider purpose, quality, and safety},
  journal = {NPJ Digital Medicine},
  publisher = {Nature Publishing Group},
  year = {2019},
  volume = {2},
  number = {1},
  pages = {1--11}
}

Joy TT, Rana S, Gupta S and Venkatesh S (2019), "Batch Bayesian optimization using multi-scale search", Knowledge-Based Systems. , pp. 104818. Elsevier.

BibTeX:

@article{joy2019batch,
  author = {Joy, Tinu Theckel and Rana, Santu and Gupta, Sunil and Venkatesh, Svetha},
  title = {Batch Bayesian optimization using multi-scale search},
  journal = {Knowledge-Based Systems},
  publisher = {Elsevier},
  year = {2019},
  pages = {104818}
}

Joy T, Rana S, Gupta S and Venkatesh S (2019), "A flexible transfer learning framework for Bayesian optimization with convergence guarantee", Expert Systems with Applications. Vol. 115, pp. 656-672. Elsevier.

BibTeX:

@article{joy2019flexible,
  author = {Joy, Tinu and Rana, Santu and Gupta, Sunil and Venkatesh, Svetha},
  title = {A flexible transfer learning framework for Bayesian optimization with convergence guarantee},
  journal = {Expert Systems with Applications},
  publisher = {Elsevier},
  year = {2019},
  volume = {115},
  pages = {656--672}
}

Kuttichira DP, Gupta S, Li C, Rana S and Venkatesh S (2019), "Explaining Black-Box Models Using Interpretable Surrogates", In Pacific Rim International Conference on Artificial Intelligence. , pp. 3-15.

BibTeX:

@inproceedings{kuttichira2019explaining,
  author = {Kuttichira, Deepthi Praveenlal and Gupta, Sunil and Li, Cheng and Rana, Santu and Venkatesh, Svetha},
  title = {Explaining Black-Box Models Using Interpretable Surrogates},
  booktitle = {Pacific Rim International Conference on Artificial Intelligence},
  year = {2019},
  pages = {3--15}
}

Le H, Tran T and Venkatesh S (2019), "Learning to Remember More with Less Memorization", In International Conference on Learning Representations (ICLR). , pp. 1-20.

BibTeX:

@inproceedings{le2019learning,
  author = {Le, Hung and Tran, Truyen and Venkatesh, Svetha},
  title = {Learning to Remember More with Less Memorization},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2019},
  pages = {1--20},
  url = {https://openreview.net/forum?id=r1xlvi0qYm}
}

Luong P, Gupta S, Nguyen D, Rana S and Venkatesh S (2019), "Bayesian Optimization with Discrete Variables", In AI 2019: Advances in Artificial Intelligence. , pp. 473-484. Springer International Publishing.

BibTeX:

@inproceedings{luong2019discrete,
  author = {Luong, Phuc and Gupta, Sunil and Nguyen, Dang and Rana, Santu and Venkatesh, Svetha},
  title = {Bayesian Optimization with Discrete Variables},
  booktitle = {AI 2019: Advances in Artificial Intelligence},
  publisher = {Springer International Publishing},
  year = {2019},
  pages = {473--484}
}

Abdolshah M, Shilton A, Rana S, Gupta S and Venkatesh S (2019), "Multi-objective Bayesian optimisation with preferences over objectives", In Conference on Neural Information Processing Systems (NeurIPS 2019). , pp. 12214-12224.

BibTeX:

@inproceedings{MajidPreference2019,
  author = {Abdolshah, Majid and Shilton, Alistair and Rana, Santu and Gupta, Sunil and Venkatesh, Svetha},
  title = {Multi-objective Bayesian optimisation with preferences over objectives},
  booktitle = {Conference on Neural Information Processing Systems (NeurIPS 2019)},
  year = {2019},
  pages = {12214--12224},
  url = {http://papers.nips.cc/paper/9390-multi-objective-bayesian-optimisation-with-preferences-over-objectives.pdf}
}

Morais R, Le V, Tran T, Saha B, Mansour M and Venkatesh S (2019), "Learning Regularity in Skeleton Trajectories for Anomaly Detection in Videos", In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. , pp. 11996-12004.

BibTeX:

@inproceedings{morais2019learning,
  author = {Morais, Romero and Le, Vuong and Tran, Truyen and Saha, Budhaditya and Mansour, Moussa and Venkatesh, Svetha},
  title = {Learning Regularity in Skeleton Trajectories for Anomaly Detection in Videos},
  booktitle = {Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  year = {2019},
  pages = {11996--12004}
}

Nguyen V, Gupta S, Rana S, Li C and Venkatesh S (2019), "Filtering Bayesian optimization approach in weakly specified search space", Knowledge and Information Systems. Vol. 60(1), pp. 385-413. Springer.

BibTeX:

@article{nguyen2019filtering,
  author = {Nguyen, Vu and Gupta, Sunil and Rana, Santu and Li, Cheng and Venkatesh, Svetha},
  title = {Filtering Bayesian optimization approach in weakly specified search space},
  journal = {Knowledge and Information Systems},
  publisher = {Springer},
  year = {2019},
  volume = {60},
  number = {1},
  pages = {385--413}
}

Nguyen P, Tran T, Gupta S, Rana S and Venkatesh S (2019), "Incomplete Conditional Density Estimation for Fast Materials Discovery", In SIAM International Conference on Data Mining (SDM). , pp. 549-557.

BibTeX:

@inproceedings{nguyen2019incomplete,
  author = {Nguyen, Phuoc and Tran, Truyen and Gupta, Sunil and Rana, Santu and Venkatesh, Svetha},
  title = {Incomplete Conditional Density Estimation for Fast Materials Discovery},
  booktitle = {SIAM International Conference on Data Mining (SDM)},
  year = {2019},
  pages = {549--557}
}

Quinn TP, Lee SC, Venkatesh S and Nguyen T (2019), "Improving the classification of neuropsychiatric conditions using gene ontology terms as features", American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. Vol. 180(7), pp. 508-518. Wiley Online Library.

BibTeX:

@article{quinn2019improving,
  author = {Quinn, Thomas P and Lee, Samuel C and Venkatesh, Svetha and Nguyen, Thin},
  title = {Improving the classification of neuropsychiatric conditions using gene ontology terms as features},
  journal = {American Journal of Medical Genetics Part B: Neuropsychiatric Genetics},
  publisher = {Wiley Online Library},
  year = {2019},
  volume = {180},
  number = {7},
  pages = {508--518}
}

Rubin de Celis Leal D, Nguyen D, Vellanki P, Li C, Rana S, Thompson N, Gupta S, Pringle K, Subianto S, Venkatesh S and others (2019), "Efficient Bayesian Function Optimization of Evolving Material Manufacturing Processes", ACS omega. Vol. 4(24), pp. 20571-20578. ACS Publications.

BibTeX:

@article{rubi?n2019efficient,
  author = {Rubin de Celis Leal, David and Nguyen, Dang and Vellanki, Pratibha and Li, Cheng and Rana, Santu and Thompson, Nathan and Gupta, Sunil and Pringle, Keiran and Subianto, Surya and Venkatesh, Svetha and others},
  title = {Efficient Bayesian Function Optimization of Evolving Material Manufacturing Processes},
  journal = {ACS omega},
  publisher = {ACS Publications},
  year = {2019},
  volume = {4},
  number = {24},
  pages = {20571--20578}
}

Subianto S, Li C, Rubin de Celis Leal D, Rana S, Gupta S, He R, Venkatesh S and Sutti A (2019), "Optimizing a High-Entropy System: Software-Assisted Development of Highly Hydrophobic Surfaces using an Amphiphilic Polymer", ACS omega. Vol. 4(14), pp. 15912-15922. ACS Publications.

BibTeX:

@article{subianto2019optimizing,
  author = {Subianto, Surya and Li, Cheng and Rubin de Celis Leal, David and Rana, Santu and Gupta, Sunil and He, Rongliang and Venkatesh, Svetha and Sutti, Alessandra},
  title = {Optimizing a High-Entropy System: Software-Assisted Development of Highly Hydrophobic Surfaces using an Amphiphilic Polymer},
  journal = {ACS omega},
  publisher = {ACS Publications},
  year = {2019},
  volume = {4},
  number = {14},
  pages = {15912--15922}
}

Thanh-Tung H, Tran T and Venkatesh S (2019), "Improving Generalization and Stability of Generative Adversarial Networks", In International Conference on Learning Representations (ICLR). , pp. 1-18.

BibTeX:

@inproceedings{tung2019improving,
  author = {Thanh-Tung, Hoang and Tran, Truyen and Venkatesh, Svetha},
  title = {Improving Generalization and Stability of Generative Adversarial Networks},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2019},
  pages = {1--18},
  url = {https://openreview.net/pdf?id=ByxPYjC5KQ}
}

Vellanki P, Rana S, Gupta S, de Celis Leal DR, Sutti A, Height M and Venkatesh S (2019), "Bayesian functional optimisation with shape prior", In Proceedings of the AAAI Conference on Artificial Intelligence. Vol. 33, pp. 1617-1624.

BibTeX:

@inproceedings{vellanki2019bayesian,
  author = {Vellanki, Pratibha and Rana, Santu and Gupta, Sunil and de Celis Leal, David Rubin and Sutti, Alessandra and Height, Murray and Venkatesh, Svetha},
  title = {Bayesian functional optimisation with shape prior},
  booktitle = {Proceedings of the AAAI Conference on Artificial Intelligence},
  year = {2019},
  volume = {33},
  pages = {1617--1624}
}