Avanti Shrikumar

发表

Kipoi: accelerating the community exchange and reuse of predictive models for genomics

Jun Cheng, Oliver Stegle, Ziga Avsec, 2018, bioRxiv.

fastISM: Performant in-silico saturation mutagenesis for convolutional neural networks

Avanti Shrikumar, Anshul Kundaje, Surag Nair, 2020, bioRxiv.

Gkmexplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer SVMs Using Integrated Gradients

Avanti Shrikumar, Anshul Kundaje, Eva Prakash, 2018, bioRxiv.

Technical Note on Transcription Factor Motif Discovery from Importance Scores (TF-MoDISco) version 0.4.2.2

Avanti Shrikumar, Abhimanyu Banerjee, Anshul Kundaje, 2019 .

Base-resolution models of transcription factor binding reveal soft motif syntax

Avanti Shrikumar, Anshul Kundaje, Julien Gagneur, 2019, Nature Genetics.

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

Jun Cheng, Oliver Stegle, Roman Kreuzhuber, 2019, Nature Biotechnology.

Not Just a Black Box: Learning Important Features Through Propagating Activation Differences pdf

Anna Shcherbina, Avanti Shrikumar, Anshul Kundaje, 2016, ArXiv.

Avanti Shrikumar, 2019, AAAI Spring Symposium: Interpretable AI for Well-being.

Learning to Abstain via Curve Optimization pdf

Avanti Shrikumar, Anshul Kundaje, Amr Alexandari, 2018, ArXiv.

Benchmarking Reverse-Complement Strategies for Deep Learning Models in Genomics

Avanti Shrikumar, Anshul Kundaje, Hannah Zhou, 2020, bioRxiv.

GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs

Avanti Shrikumar, Anshul Kundaje, Eva Prakash, 2019, Bioinform..

Opportunities and obstacles for deep learning in biology and medicine

Yifan Peng, Wei Xie, Yanjun Qi, 2017 .

Maximum Likelihood with Bias-Corrected Calibration is Hard-To-Beat at Label Shift Adaptation

Avanti Shrikumar, Anshul Kundaje, Amr Alexandari, 2020, ICML.

Separable Fully Connected Layers Improve Deep Learning Models For Genomics

Avanti Shrikumar, Anshul Kundaje, Amr Alexandari, 2017, bioRxiv.

Reverse-complement parameter sharing improves deep learning models for genomics

Avanti Shrikumar, Anshul Kundaje, Peyton Greenside, 2017, bioRxiv.

Learning Important Features Through Propagating Activation Differences pdf

Avanti Shrikumar, Anshul Kundaje, Peyton Greenside, 2017, ICML.

EM with Bias-Corrected Calibration is Hard-To-Beat at Label Shift Adaptation

Avanti Shrikumar, Anshul Kundaje, Amr Alexandari, 2019 .

Fourier-transform-based attribution priors improve the interpretability and stability of deep learning models for genomics

Avanti Shrikumar, Anshul Kundaje, Alex M. Tseng, 2020, bioRxiv.

Adapting to Label Shift with Bias-Corrected Calibration

Avanti Shrikumar, Anshul Kundaje, Amr Alexandari, 2019 .

TF-MoDISco v0.4.4.2-alpha: Technical Note pdf

Anna Shcherbina, Avanti Shrikumar, Abhimanyu Banerjee, 2018, ArXiv.

Computationally Efficient Measures of Internal Neuron Importance pdf

Avanti Shrikumar, Anshul Kundaje, Jocelin Su, 2018, ArXiv.

Calibration with Bias-Corrected Temperature Scaling Improves Domain Adaptation Under Label Shift in Modern Neural Networks pdf

Avanti Shrikumar, Anshul Kundaje, A. Kundaje, 2019, ArXiv.

PYOMPA version 0.3: Technical Note

Avanti Shrikumar, Rian Lawrence, Karen L Casciotti, 2021 .

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding

Avanti Shrikumar, Anshul Kundaje, Shaun Mahony, 2021, bioRxiv.

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays

Avanti Shrikumar, Anshul Kundaje, Surag Nair, 2019, PloS one.

Maximum Likelihood with Bias-Corrected Calibration is Hard-To-Beat at Label Shift Adaptation

Avanti Shrikumar, Anshul Kundaje, Amr Alexandari, 2020, ICML.

A multi-modal neural network for learning cis and trans regulation of stress response in yeast.

Avanti Shrikumar, Anshul Kundaje, Stephen B. Montgomery, 2019 .

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays

Avanti Shrikumar, Anshul Kundaje, Peyton Greenside, 2018, bioRxiv.