David K. Gifford

ORCID

Publication Activity (10 Years)

Years Active: 1977-2024
Publications (10 Years): 26

Top Venues

Publications

Zheng Dai, David K. Gifford
Ablation Based Counterfactuals. CoRR (2024)
Zheng Dai, David K. Gifford
Constrained Submodular Optimization for Vaccine Design. AAAI (2023)
Zheng Dai, David K. Gifford
Training Data Attribution for Diffusion Models. CoRR (2023)
Ge Liu, Alexander Dimitrakakis, Brandon Carter, David K. Gifford
Maximum n-times Coverage for Vaccine Design. ICLR (2022)
Zheng Dai, David K. Gifford
Constrained Submodular Optimization for Vaccine Design. CoRR (2022)
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)
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)
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)
Ge Liu, Brandon Carter, David K. Gifford
Maximum n-times Coverage for COVID-19 Vaccine Design. CoRR (2021)
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) (2021)
Zheng Dai, David K. Gifford
Image classifiers can not be made robust to small perturbations. CoRR (2021)
Jennifer Hammelman, David K. Gifford
Discovering differential genome sequence activity with interpretable and efficient deep learning. PLoS Comput. Biol. 17 (8) (2021)
Brandon Carter, Siddhartha Jain, Jonas Mueller, David K. Gifford
Overinterpretation reveals image classification model pathologies. CoRR (2020)
Siddhartha Jain, Ge Liu, David K. Gifford
Information Condensing Active Learning. CoRR (2020)
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) (2020)
Brandon Carter, Jonas Mueller, Siddhartha Jain, David K. Gifford
What made you do this? Understanding black-box decisions with sufficient input subsets. AISTATS (2019)
Haoyang Zeng, David K. Gifford
DeepLigand: accurate prediction of MHC class I ligands using peptide embedding. Bioinform. 35 (14) (2019)
Siddhartha Jain, Ge Liu, Jonas Mueller, David K. Gifford
Maximizing Overall Diversity for Improved Uncertainty Estimates in Deep Ensembles. CoRR (2019)
Ge Liu, Haoyang Zeng, David K. Gifford
Visualizing complex feature interactions and feature sharing in genomic deep neural networks. BMC Bioinform. 20 (1) (2019)
Brandon Carter, Jonas Mueller, Siddhartha Jain, David K. Gifford
What made you do this? Understanding black-box decisions with sufficient input subsets. CoRR (2018)
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) (2018)
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)
Jonas Mueller, David K. Gifford, Tommi S. Jaakkola
Sequence to Better Sequence: Continuous Revision of Combinatorial Structures. ICML (2017)
Tatsunori B. Hashimoto, David K. Gifford, Tommi S. Jaakkola
Learning Population-Level Diffusions with Generative RNNs. ICML (2016)
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) (2016)
Haoyang Zeng, Matthew D. Edwards, Ge Liu, David K. Gifford
Convolutional neural network architectures for predicting DNA-protein binding. Bioinform. 32 (12) (2016)
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)
Tatsunori B. Hashimoto, Matthew D. Edwards, David K. Gifford
Universal Count Correction for High-Throughput Sequencing. PLoS Comput. Biol. 10 (3) (2014)
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)
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)
Matthew D. Edwards, David K. Gifford
High-resolution genetic mapping with pooled sequencing. BMC Bioinform. 13 (S-6) (2012)
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) (2012)
P. Alexander Rolfe, David K. Gifford
ReadDB Provides Efficient Storage for Mapped Short Reads. BMC Bioinform. 12 (2011)
Timothy Danford, Robin D. Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David K. Gifford
Discovering Regulatory Overlapping RNA Transcripts. J. Comput. Biol. 18 (3) (2011)
Timothy Danford, Robin D. Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David K. Gifford
Discovering Regulatory Overlapping RNA Transcripts. RECOMB (2010)
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) (2010)
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)
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)
Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel
. BMC Bioinform. 7 (2006)
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) (2006)
Yuan (Alan) Qi, Patrycja E. Missiuro, Ashish Kapoor, Craig P. Hunter, Tommi S. Jaakkola, David K. Gifford, Hui Ge
embryo. ISMB (Supplement of Bioinformatics) (2006)
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)
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)
Ken T. Takusagawa, David K. Gifford
Negative Information for Motif Discovery. Pacific Symposium on Biocomputing (2004)
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)
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) (2003)
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) (2003)
Julia Khodor, David K. Gifford
Experimental Efficiency of Programmed Mutagenesis. New Gener. Comput. 20 (3) (2002)
Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young
Bayesian Methods for Elucidating Genetic Regulatory Networks. IEEE Intell. Syst. 17 (2) (2002)
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)
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)
Julia Khodor, David K. Gifford
Programmed Mutagenesis Is Universal. Theory Comput. Syst. 35 (5) (2002)
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)
Alex C. Snoeren, Kenneth Conley, David K. Gifford
Mesh Based Content Routing using XML. SOSP (2001)
Ziv Bar-Joseph, David K. Gifford, Tommi S. Jaakkola
Fast optimal leaf ordering for hierarchical clustering. ISMB (Supplement of Bioinformatics) (2001)
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)
Julia Khodor, David K. Gifford
Programmed Mutagenesis Is a Universal Model of Computation. DNA (2001)
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)
Alexander J. Hartemink, Tarjei S. Mikkelsen, David K. Gifford
Simulating biological reactions: A modular approach. DNA Based Computers (1999)
Alexander J. Hartemink, David K. Gifford
Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation. DNA Based Computers (1997)
Bienvenido Vélez, Ron Weiss, Mark A. Sheldon, David K. Gifford
Fast and Effective Query Refinement. SIGIR (1997)
Julia Khodor, David K. Gifford
The efficiency of sequence-specific separation of DNA mixtures for biological computing. DNA Based Computers (1997)
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)
Mark A. Sheldon, Andrzej Duda, David K. Gifford
Discover: A Resource Discovery System Based on Content Routing. Comput. Networks ISDN Syst. 27 (6) (1995)
David K. Gifford, Lawrence C. Stewart, Andrew C. Payne, G. Winfield Treese
Payment for Open Networks. COMPCON (1995)
David K. Gifford, Lawrence C. Stewart, Andrew C. Payne, G. Winfield Treese
Payment Switches for Open Networks. USENIX Workshop on Electronic Commerce (1995)
Anthony D. Joseph, Alan F. deLespinasse, Joshua A. Tauber, David K. Gifford, M. Frans Kaashoek
Rover: A Toolkit for Mobile Information Access. SOSP (1995)
Ron Weiss, Andrzej Duda, David K. Gifford
Composition and Search with a Video Algebra. IEEE Multim. 2 (1) (1995)
Mark A. Sheldon, Andrzej Duda, Ron Weiss, James W. O'Toole Jr., David K. Gifford
Content Routing for Distributed Information Servers. EDBT (1994)
Brian Reistad, David K. Gifford
Static Dependent Costs for Estimating Execution Time. LISP and Functional Programming (1994)
Ron Weiss, Andrzej Duda, David K. Gifford
Content-Based Access to Algebraic Video. ICMCS (1994)
James W. O'Toole Jr., Scott Nettles, David K. Gifford
Concurrent Compacting Garbage Collection of a Persistent Heap. SOSP (1993)
David K. Gifford
Five Forces Shaping Experimental Computer Science. ACM SIGOPS Oper. Syst. Rev. 26 (1) (1992)
Vincent Dornic, Pierre Jouvelot, David K. Gifford
Polymorphic Time Systems for Estimating Program Complexity. LOPLAS 1 (1) (1992)
James W. O'Toole Jr., David K. Gifford
Names should mean what, not where. ACM SIGOPS European Workshop (1992)
David K. Gifford, Pierre Jouvelot, Mark A. Sheldon, James W. O'Toole Jr.
Semantic File Systems. SOSP (1991)
David K. Gifford, James W. O'Toole Jr.
Intelligent File Systems for Object Repositories. Operating Systems of the 90s and Beyond (1991)
Pierre Jouvelot, David K. Gifford
Algebraic Reconstruction of Types and Effects. POPL (1991)
Vincent Dornic, Pierre Jouvelot, David K. Gifford
Polymorphic Time Systems for Estimating Program Complexity. JTASPEFT/WSA (1991)
David K. Gifford
Polychannel Systems for Mass Digital Communications. Commun. ACM 33 (2) (1990)
James W. Stamos, David K. Gifford
Remote Evaluation. ACM Trans. Program. Lang. Syst. 12 (4) (1990)
Mark A. Sheldon, David K. Gifford
Static Dependent Types for First Class Modules. LISP and Functional Programming (1990)
James W. Stamos, David K. Gifford
Implementing Remote Evaluation. IEEE Trans. Software Eng. 16 (7) (1990)
Pierre Jouvelot, David K. Gifford
Reasoning about Continuations with Control Effects. PLDI (1989)
James W. O'Toole Jr., David K. Gifford
Type Reconstruction with First-Class Polymorphic Values. PLDI (1989)
David K. Gifford, Nathan Glasser
Remote Pipes and Procedures for Efficient Distributed Communication. ACM Trans. Comput. Syst. 6 (3) (1988)
David K. Gifford, Roger M. Needham, Michael D. Schroeder
The Cedar System. Commun. ACM 31 (3) (1988)
Pierre Jouvelot, David K. Gifford
The FX-87 Interpreter. ICCL (1988)
John M. Lucassen, David K. Gifford
Polymorphic Effect Systems. POPL (1988)
Alfred Z. Spector, David K. Gifford
Case Study: IBM's System/360-370 Architecture. Commun. ACM 30 (4) (1987)
Alfred Z. Spector, David K. Gifford
A Computer Science Perspective of Bridge Design. Commun. ACM 29 (4) (1986)
David K. Gifford, John M. Lucassen
Integrating Functional and Imperative Programming. LISP and Functional Programming (1986)
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) (1985)
David K. Gifford, Alfred Z. Spector
The Cirrus Banking Network. Commun. ACM 28 (8) (1985)
David K. Gifford, Robert W. Baldwin, Stephen T. Berlin, John M. Lucassen
An Architecture for Large Scale Information Systems. SOSP (1985)
Michael D. Schroeder, David K. Gifford, Roger M. Needham
A Caching File System For a Programmer's Workstation. SOSP (1985)
David K. Gifford, James E. Donahue
Coordinating Independent Atomic Actions. COMPCON (1985)
David K. Gifford, Alfred Z. Spector
The Space Shuttle Primary Computer System. Commun. ACM 27 (9) (1984)
David K. Gifford, Alfred Z. Spector
The TWA Reservation System. Commun. ACM 27 (7) (1984)
David K. Gifford
Surveyor's Forum: Technical Transactions. ACM Comput. Surv. 14 (2) (1982)

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Publication Activity (10 Years)

Top Topics

Top Venues

David K. Gifford