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ORCIDDavid K. Gifford
David Gifford 0001
Person information
- affiliation: MIT, Cambridge, USA
Other persons with the same name
- David Gifford 0002 — RIKEN, Wako, Japan
- David Gifford 0003 — San Joaquin Delta College, Stockton, CA, USA
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Journal Articles
- 2021
[j46]Zheng Dai, Brooke D. Huisman, Haoyang Zeng, Brandon Carter, Siddhartha Jain, Michael E. Birnbaum
, David K. Gifford:
Machine learning optimization of peptides for presentation by class II MHCs. Bioinform. 37(19): 3160-3167 (2021)- [j45]Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang, Daniel Worstell, Christopher A. Cassa, Richard I. Sherwood, David K. Gifford:
Machine learning based CRISPR gRNA design for therapeutic exon skipping. PLoS Comput. Biol. 17(1) (2021) - [j44]Grace Hui Ting Yeo, Oscar Juez, Qing Chen, Budhaditya Banerjee, Lendy Chu, Max W. Shen, May Sabry, Ive Logister, Richard I. Sherwood, David K. Gifford:
Detection of gene cis-regulatory element perturbations in single-cell transcriptomes. PLoS Comput. Biol. 17(3) (2021) - [j43]Jennifer Hammelman, David K. Gifford:
Discovering differential genome sequence activity with interpretable and efficient deep learning. PLoS Comput. Biol. 17(8) (2021) - 2020
- [j42]Ge Liu, Haoyang Zeng, Jonas Mueller, Brandon Carter, Ziheng Wang, Jonas Schilz, Geraldine Horny, Michael E. Birnbaum, Stefan Ewert, David K. Gifford:
Antibody complementarity determining region design using high-capacity machine learning. Bioinform. 36(7): 2126-2133 (2020) - 2019
- [j41]Haoyang Zeng, David K. Gifford:
DeepLigand: accurate prediction of MHC class I ligands using peptide embedding. Bioinform. 35(14): i278-i283 (2019) - [j40]Ge Liu, Haoyang Zeng, David K. Gifford:
Visualizing complex feature interactions and feature sharing in genomic deep neural networks. BMC Bioinform. 20(1): 401:1-401:14 (2019) - 2018
- [j39]Max W. Shen, Mandana Arbab, Jonathan Y. Hsu, Daniel Worstell, Sannie J. Culbertson, Olga Krabbe, Christopher A. Cassa, David R. Liu, David K. Gifford, Richard I. Sherwood:
Predictable and precise template-free CRISPR editing of pathogenic variants. Nat. 563(7733): 646-651 (2018) - 2016
- [j38]Haoyang Zeng, Tatsunori B. Hashimoto, Daniel D. Kang, David K. Gifford:
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding. Bioinform. 32(4): 490-496 (2016) - [j37]Haoyang Zeng, Matthew D. Edwards, Ge Liu, David K. Gifford:
Convolutional neural network architectures for predicting DNA-protein binding. Bioinform. 32(12): 121-127 (2016) - 2014
- [j36]Tatsunori B. Hashimoto, Matthew D. Edwards, David K. Gifford:
Universal Count Correction for High-Throughput Sequencing. PLoS Comput. Biol. 10(3) (2014) - [j35]Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford:
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding. PLoS Comput. Biol. 10(3) (2014) - 2012
- [j34]Tatsunori B. Hashimoto, Tommi S. Jaakkola, Richard Sherwood, Esteban O. Mazzoni, Hynek Wichterle, David K. Gifford:
Lineage-based identification of cellular states and expression programs. Bioinform. 28(12): 250-257 (2012) - [j33]Matthew D. Edwards, David K. Gifford:
High-resolution genetic mapping with pooled sequencing. BMC Bioinform. 13(S-6): S8 (2012) - [j32]Yuchun Guo, Shaun Mahony, David K. Gifford:
High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints. PLoS Comput. Biol. 8(8) (2012) - 2011
- [j31]P. Alexander Rolfe, David K. Gifford:
ReadDB Provides Efficient Storage for Mapped Short Reads. BMC Bioinform. 12: 278 (2011) - [j30]Sejoon Lim, Hari Balakrishnan, David Gifford, Samuel Madden, Daniela Rus:
Stochastic motion planning and applications to traffic. Int. J. Robotics Res. 30(6): 699-712 (2011) - [j29]Timothy Danford, Robin D. Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David K. Gifford:
Discovering Regulatory Overlapping RNA Transcripts. J. Comput. Biol. 18(3): 295-303 (2011) - 2010
- [j28]Yuchun Guo, Georgios Papachristoudis, Robert C. Altshuler, Georg K. Gerber, Tommi S. Jaakkola, David K. Gifford, Shaun Mahony:
Discovering homotypic binding events at high spatial resolution. Bioinform. 26(24): 3028-3034 (2010) - 2007
- [j27]Georg K. Gerber, Robin D. Dowell, Tommi S. Jaakkola, David K. Gifford:
Automated Discovery of Functional Generality of Human Gene Expression Programs. PLoS Comput. Biol. 3(8) (2007) - 2006
- [j26]Kenzie D. MacIsaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, Richard A. Young, Ernest Fraenkel:
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinform. 22(4): 423-429 (2006) - [j25]Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel:
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinform. 7: 113 (2006) - 2003
- [j24]Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Nathan Srebro, Angèle M. Hamel, Tommi S. Jaakkola:
K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. Bioinform. 19(9): 1070-1078 (2003) - [j23]Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon:
Continuous Representations of Time-Series Gene Expression Data. J. Comput. Biol. 10(3/4): 341-356 (2003) - 2002
- [j22]Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young:
Bayesian Methods for Elucidating Genetic Regulatory Networks. IEEE Intell. Syst. 17(2): 37-43 (2002) - [j21]Julia Khodor, David K. Gifford:
Programmed Mutagenesis Is Universal. Theory Comput. Syst. 35(5): 483-500 (2002) - [j20]Julia Khodor, David K. Gifford:
Experimental Efficiency of Programmed Mutagenesis. New Gener. Comput. 20(3): 307-315 (2002) - 1995
- [j19]Mark A. Sheldon, Andrzej Duda, David K. Gifford:
Discover: A Resource Discovery System Based on Content Routing. Comput. Networks ISDN Syst. 27(6): 953-972 (1995) - [j18]Ron Weiss, Andrzej Duda, David K. Gifford:
Composition and Search with a Video Algebra. IEEE Multim. 2(1): 12-25 (1995) - 1992
- [j17]Vincent Dornic, Pierre Jouvelot, David K. Gifford:
Polymorphic Time Systems for Estimating Program Complexity. LOPLAS 1(1): 33-45 (1992) - [j16]David K. Gifford:
Five Forces Shaping Experimental Computer Science. ACM SIGOPS Oper. Syst. Rev. 26(1): 6 (1992) - 1990
- [j15]David K. Gifford:
Polychannel Systems for Mass Digital Communications. Commun. ACM 33(2): 141-151 (1990) - [j14]James W. Stamos, David K. Gifford:
Remote Evaluation. ACM Trans. Program. Lang. Syst. 12(4): 537-565 (1990) - [j13]James W. Stamos, David K. Gifford:
Implementing Remote Evaluation. IEEE Trans. Software Eng. 16(7): 710-722 (1990) - 1988
- [j12]David K. Gifford, Roger M. Needham, Michael D. Schroeder:
The Cedar System. Commun. ACM 31(3): 288-298 (1988) - [j11]David K. Gifford, Nathan Glasser:
Remote Pipes and Procedures for Efficient Distributed Communication. ACM Trans. Comput. Syst. 6(3): 258-283 (1988) - 1987
- [j10]Alfred Z. Spector, David K. Gifford:
Case Study: IBM's System/360-370 Architecture. Commun. ACM 30(4): 291-307 (1987) - 1986
- [j9]Alfred Z. Spector, David K. Gifford:
A Computer Science Perspective of Bridge Design. Commun. ACM 29(4): 267-283 (1986) - 1985
- [j8]David K. Gifford, Alfred Z. Spector:
The Cirrus Banking Network. Commun. ACM 28(8): 797-807 (1985) - [j7]David K. Gifford, John M. Lucassen, Stephen T. Berlin:
The Application of Digital Broadcast Communication to Large Scale Information Systems. IEEE J. Sel. Areas Commun. 3(3): 457-467 (1985) - 1984
- [j6]David K. Gifford, Alfred Z. Spector:
The TWA Reservation System. Commun. ACM 27(7): 649-665 (1984) - [j5]David K. Gifford, Alfred Z. Spector:
The Space Shuttle Primary Computer System. Commun. ACM 27(9): 872-900 (1984) - 1982
- [j4]David K. Gifford:
Cryptographic Sealing for Information Secrecy and Authentication. Commun. ACM 25(4): 274-286 (1982) - [j3]David K. Gifford:
Surveyor's Forum: Technical Transactions. ACM Comput. Surv. 14(2): 316 (1982) - 1981
- [j2]David K. Gifford:
Violet, an Experimental Decentralized System. Comput. Networks 5: 423-433 (1981) - 1977
- [j1]David K. Gifford:
Hardware Estimation of Process' Primary Memory Requirements. Commun. ACM 20(9): 655-663 (1977)
Conference and Workshop Papers
- 2023
- [c58]Zheng Dai, David K. Gifford:
Constrained Submodular Optimization for Vaccine Design. AAAI 2023: 5045-5053 - [c57]Zheng Dai, David Gifford:
Fundamental limits on the robustness of image classifiers. ICLR 2023 - 2022
- [c56]Ge Liu, Alexander Dimitrakakis, Brandon Carter, David K. Gifford:
Maximum n-times Coverage for Vaccine Design. ICLR 2022 - [c55]Zheng Dai, Sachit D. Saksena, Geraldine Horny, Christine Banholzer, Stefan Ewert, David K. Gifford:
Ultra High Diversity Factorizable Libraries for Efficient Therapeutic Discovery. RECOMB 2022: 390-392 - 2021
- [c54]Lucas Liebenwein, Cenk Baykal, Brandon Carter, David Gifford, Daniela Rus:
Lost in Pruning: The Effects of Pruning Neural Networks beyond Test Accuracy. MLSys 2021 - [c53]Brandon Carter, Siddhartha Jain, Jonas Mueller, David Gifford:
Overinterpretation reveals image classification model pathologies. NeurIPS 2021: 15395-15407 - 2020
- [c52]Siddhartha Jain, Ge Liu, Jonas Mueller, David Gifford:
Maximizing Overall Diversity for Improved Uncertainty Estimates in Deep Ensembles. AAAI 2020: 4264-4271 - 2019
- [c51]Brandon Carter, Jonas Mueller, Siddhartha Jain, David K. Gifford:
What made you do this? Understanding black-box decisions with sufficient input subsets. AISTATS 2019: 567-576 - [c50]Ziheng Wang, Grace H. T. Yeo, Richard Sherwood, David Gifford:
Disentangled Representations of Cellular Identity. RECOMB 2019: 256-271 - 2017
- [c49]Jonas Mueller, David K. Gifford, Tommi S. Jaakkola:
Sequence to Better Sequence: Continuous Revision of Combinatorial Structures. ICML 2017: 2536-2544 - [c48]Yuchun Guo, Kevin Tian, Haoyang Zeng, David K. Gifford:
K-mer Set Memory (KSM) Motif Representation Enables Accurate Prediction of the Impact of Regulatory Variants. RECOMB 2017: 372-374 - 2016
- [c47]Tatsunori B. Hashimoto, David K. Gifford, Tommi S. Jaakkola:
Learning Population-Level Diffusions with Generative RNNs. ICML 2016: 2417-2426 - 2014
- [c46]Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford:
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding. RECOMB 2014: 175-176 - 2013
- [c45]Christopher Reeder, David Gifford:
High Resolution Modeling of Chromatin Interactions. RECOMB 2013: 186-198 - 2010
- [c44]Timothy Danford, Robin D. Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David K. Gifford:
Discovering Regulatory Overlapping RNA Transcripts. RECOMB 2010: 110-122 - 2008
- [c43]Timothy Danford, P. Alexander Rolfe, David K. Gifford:
GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data. Pacific Symposium on Biocomputing 2008: 539-550 - [c42]Sejoon Lim, Hari Balakrishnan, David Gifford, Samuel Madden, Daniela Rus:
Stochastic Motion Planning and Applications to Traffic. WAFR 2008: 483-500 - 2006
- [c41]Yuan (Alan) Qi, Patrycja E. Missiuro, Ashish Kapoor, Craig P. Hunter, Tommi S. Jaakkola, David K. Gifford, Hui Ge:
Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo. ISMB (Supplement of Bioinformatics) 2006: 417-423 - 2005
- [c40]Rohit Singh, Nathan P. Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph:
Active learning for sampling in time-series experiments with application to gene expression analysis. ICML 2005: 832-839 - 2004
- [c39]Karen Sachs, Omar D. Perez, Dana Pe'er, Garry P. Nolan, David K. Gifford, Tommi S. Jaakkola, Douglas A. Lauffenburger:
Analysis of Signaling Pathways in Human T-Cells Using Bayesian Network Modeling of Single Cell Data. CSB 2004: 644 - [c38]Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, Roni Rosenfeld:
Deconvolving cell cycle expression data with complementary information. ISMB/ECCB (Supplement of Bioinformatics) 2004: 23-30 - [c37]Ken T. Takusagawa, David K. Gifford:
Negative Information for Motif Discovery. Pacific Symposium on Biocomputing 2004: 360-371 - 2002
- [c36]Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young:
Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models. Pacific Symposium on Biocomputing 2002: 437-449 - [c35]Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon:
A new approach to analyzing gene expression time series data. RECOMB 2002: 39-48 - [c34]Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi S. Jaakkola, Nathan Srebro:
K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. WABI 2002: 506-520 - 2001
- [c33]Julia Khodor, David K. Gifford:
Programmed Mutagenesis Is a Universal Model of Computation. DNA 2001: 300-307 - [c32]Ziv Bar-Joseph, David K. Gifford, Tommi S. Jaakkola:
Fast optimal leaf ordering for hierarchical clustering. ISMB (Supplement of Bioinformatics) 2001: 22-29 - [c31]Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young:
Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks. Pacific Symposium on Biocomputing 2001: 422-433 - [c30]Alex C. Snoeren, Kenneth Conley, David K. Gifford:
Mesh Based Content Routing using XML. SOSP 2001: 160-173 - 2000
- [c29]John Jannotti, David K. Gifford, Kirk L. Johnson, M. Frans Kaashoek, James W. O'Toole Jr.:
Overcast: Reliable Multicasting with an Overlay Network. OSDI 2000: 197-212 - 1999
- [c28]Alexander J. Hartemink, Tarjei S. Mikkelsen, David K. Gifford:
Simulating biological reactions: A modular approach. DNA Based Computers 1999: 111-121 - 1997
- [c27]Alexander J. Hartemink, David K. Gifford:
Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation. DNA Based Computers 1997: 25-37 - [c26]Julia Khodor, David K. Gifford:
The efficiency of sequence-specific separation of DNA mixtures for biological computing. DNA Based Computers 1997: 39-46 - [c25]Bienvenido Vélez, Ron Weiss, Mark A. Sheldon, David K. Gifford:
Fast and Effective Query Refinement. SIGIR 1997: 6-15 - 1996
- [c24]Ron Weiss, Bienvenido Vélez, Mark A. Sheldon, Chanathip Namprempre, Péter Szilágyi, Andrzej Duda, David K. Gifford:
HyPursuit: A Hierarchical Network Search Engine that Exploits Content-Link Hypertext Clustering. Hypertext 1996: 180-193 - 1995
- [c23]David K. Gifford, Lawrence C. Stewart, Andrew C. Payne, G. Winfield Treese:
Payment for Open Networks. COMPCON 1995: 26-31 - [c22]Anthony D. Joseph, Alan F. deLespinasse, Joshua A. Tauber, David K. Gifford, M. Frans Kaashoek:
Rover: A Toolkit for Mobile Information Access. SOSP 1995: 156-171 - [c21]David K. Gifford, Lawrence C. Stewart, Andrew C. Payne, G. Winfield Treese:
Payment Switches for Open Networks. USENIX Workshop on Electronic Commerce 1995 - 1994
- [c20]Mark A. Sheldon, Andrzej Duda, Ron Weiss, James W. O'Toole Jr., David K. Gifford:
Content Routing for Distributed Information Servers. EDBT 1994: 109-122 - [c19]Ron Weiss, Andrzej Duda, David K. Gifford:
Content-Based Access to Algebraic Video. ICMCS 1994: 140-151 - [c18]Brian Reistad, David K. Gifford:
Static Dependent Costs for Estimating Execution Time. LISP and Functional Programming 1994: 65-78 - 1993
- [c17]James W. O'Toole Jr., Scott Nettles, David K. Gifford:
Concurrent Compacting Garbage Collection of a Persistent Heap. SOSP 1993: 161-174 - 1992
- [c16]James W. O'Toole Jr., David K. Gifford:
Names should mean what, not where. ACM SIGOPS European Workshop 1992 - 1991
- [c15]David K. Gifford, James W. O'Toole Jr.:
Intelligent File Systems for Object Repositories. Operating Systems of the 90s and Beyond 1991: 20-24 - [c14]Pierre Jouvelot, David K. Gifford:
Algebraic Reconstruction of Types and Effects. POPL 1991: 303-310 - [c13]Vincent Dornic, Pierre Jouvelot, David K. Gifford:
Polymorphic Time Systems for Estimating Program Complexity. JTASPEFT/WSA 1991: 9-17 - [c12]David K. Gifford, Pierre Jouvelot, Mark A. Sheldon, James W. O'Toole Jr.:
Semantic File Systems. SOSP 1991: 16-25 - 1990
- [c11]Mark A. Sheldon, David K. Gifford:
Static Dependent Types for First Class Modules. LISP and Functional Programming 1990: 20-29 - 1989
- [c10]James W. O'Toole Jr., David K. Gifford:
Type Reconstruction with First-Class Polymorphic Values. PLDI 1989: 207-217 - [c9]Pierre Jouvelot, David K. Gifford:
Reasoning about Continuations with Control Effects. PLDI 1989: 218-226 - 1988
- [c8]Pierre Jouvelot, David K. Gifford:
The FX-87 Interpreter. ICCL 1988: 65-72 - [c7]John M. Lucassen, David K. Gifford:
Polymorphic Effect Systems. POPL 1988: 47-57 - 1986
- [c6]David K. Gifford, John M. Lucassen:
Integrating Functional and Imperative Programming. LISP and Functional Programming 1986: 28-38 - 1985
- [c5]David K. Gifford, James E. Donahue:
Coordinating Independent Atomic Actions. COMPCON 1985: 92-95 - [c4]Michael D. Schroeder, David K. Gifford, Roger M. Needham:
A Caching File System For a Programmer's Workstation. SOSP 1985: 25-34 - [c3]David K. Gifford, Robert W. Baldwin, Stephen T. Berlin, John M. Lucassen:
An Architecture for Large Scale Information Systems. SOSP 1985: 161-170 - 1981
- [c2]David K. Gifford:
Cryptographic Sealing for Information Secrecy and Authentication (Summary). SOSP 1981: 123-124 - 1979
- [c1]David K. Gifford:
Weighted Voting for Replicated Data. SOSP 1979: 150-162
Editorship
- 2000
- [e1]Erik Winfree, David K. Gifford:
DNA Based Computers, Proceedings of a DIMACS Workshop, New Brunswick, New Jersey, USA, June 14-15, 1999. DIMACS Series in Discrete Mathematics and Theoretical Computer Science 54, DIMACS/AMS 2000, ISBN 978-0-8218-2053-7 [contents]
Informal and Other Publications
- 2024
- [i10]Zheng Dai, David K. Gifford:
Ablation Based Counterfactuals. CoRR abs/2406.07908 (2024) - 2023
- [i9]Zheng Dai, David K. Gifford:
Training Data Attribution for Diffusion Models. CoRR abs/2306.02174 (2023) - 2022
- [i8]Zheng Dai, David K. Gifford:
Constrained Submodular Optimization for Vaccine Design. CoRR abs/2206.08336 (2022) - 2021
- [i7]Ge Liu, Brandon Carter, David K. Gifford:
Maximum n-times Coverage for COVID-19 Vaccine Design. CoRR abs/2101.10902 (2021) - [i6]Lucas Liebenwein, Cenk Baykal, Brandon Carter, David Gifford, Daniela Rus:
Lost in Pruning: The Effects of Pruning Neural Networks beyond Test Accuracy. CoRR abs/2103.03014 (2021) - [i5]Zheng Dai, David K. Gifford:
Image classifiers can not be made robust to small perturbations. CoRR abs/2112.04033 (2021) - 2020
- [i4]Siddhartha Jain, Ge Liu, David K. Gifford:
Information Condensing Active Learning. CoRR abs/2002.07916 (2020) - [i3]Brandon Carter, Siddhartha Jain, Jonas Mueller, David K. Gifford:
Overinterpretation reveals image classification model pathologies. CoRR abs/2003.08907 (2020) - 2019
- [i2]Siddhartha Jain, Ge Liu, Jonas Mueller, David K. Gifford:
Maximizing Overall Diversity for Improved Uncertainty Estimates in Deep Ensembles. CoRR abs/1906.07380 (2019) - 2018
- [i1]Brandon Carter, Jonas Mueller, Siddhartha Jain, David K. Gifford:
What made you do this? Understanding black-box decisions with sufficient input subsets. CoRR abs/1810.03805 (2018)
Coauthor Index
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