David K. Gifford

107 papers A* 19A 1B 7C 1Misc 4Journal 55Unranked 19
YearRankTypeTitle / Venue / Authors
2024 J jnl
Ablation Based Counterfactuals.
CoRR
Zheng Dai, David K. Gifford
2023 A* conf
Constrained Submodular Optimization for Vaccine Design.
AAAI
Zheng Dai, David K. Gifford
2023 J jnl
Training Data Attribution for Diffusion Models.
CoRR
Zheng Dai, David K. Gifford
2022 J jnl
Constrained Submodular Optimization for Vaccine Design.
CoRR
Zheng Dai, David K. Gifford
2022 A* conf
Maximum n-times Coverage for Vaccine Design.
ICLR
Ge Liu, Alexander Dimitrakakis, Brandon Carter, David K. Gifford
2022 B conf
Ultra High Diversity Factorizable Libraries for Efficient Therapeutic Discovery.
RECOMB
Zheng Dai, Sachit D. Saksena, Geraldine Horny, Christine Banholzer, Stefan Ewert, David K. Gifford
2022 J jnl
seqgra: principled selection of neural network architectures for genomics prediction tasks.
Bioinform.
Konstantin Krismer, Jennifer Hammelman, David K. Gifford
2021 J jnl
Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
PLoS Comput. Biol.
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
2021 J jnl
Discovering differential genome sequence activity with interpretable and efficient deep learning.
PLoS Comput. Biol.
Jennifer Hammelman, David K. Gifford
2021 J jnl
Image classifiers can not be made robust to small perturbations.
CoRR
Zheng Dai, David K. Gifford
2021 J jnl
Machine learning based CRISPR gRNA design for therapeutic exon skipping.
PLoS Comput. Biol.
Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang, Daniel Worstell, Christopher A. Cassa, Richard I. Sherwood, David K. Gifford
2021 J jnl
Machine learning optimization of peptides for presentation by class II MHCs.
Bioinform.
Zheng Dai, Brooke D. Huisman, Haoyang Zeng, Brandon Carter, Siddhartha Jain, Michael E. Birnbaum, David K. Gifford
2021 J jnl
Maximum n-times Coverage for COVID-19 Vaccine Design.
CoRR
Ge Liu, Brandon Carter, David K. Gifford
2020 J jnl
Antibody complementarity determining region design using high-capacity machine learning.
Bioinform.
Ge Liu, Haoyang Zeng, Jonas Mueller, Brandon Carter, Ziheng Wang, Jonas Schilz, Geraldine Horny, Michael E. Birnbaum, Stefan Ewert, David K. Gifford
2020 J jnl
Information Condensing Active Learning.
CoRR
Siddhartha Jain, Ge Liu, David K. Gifford
2020 J jnl
Overinterpretation reveals image classification model pathologies.
CoRR
Brandon Carter, Siddhartha Jain, Jonas Mueller, David K. Gifford
2019 J jnl
DeepLigand: accurate prediction of MHC class I ligands using peptide embedding.
Bioinform.
Haoyang Zeng, David K. Gifford
2019 J jnl
Maximizing Overall Diversity for Improved Uncertainty Estimates in Deep Ensembles.
CoRR
Siddhartha Jain, Ge Liu, Jonas Mueller, David K. Gifford
2019 J jnl
Visualizing complex feature interactions and feature sharing in genomic deep neural networks.
BMC Bioinform.
Ge Liu, Haoyang Zeng, David K. Gifford
2019 A conf
What made you do this? Understanding black-box decisions with sufficient input subsets.
AISTATS
Brandon Carter, Jonas Mueller, Siddhartha Jain, David K. Gifford
2018 J jnl
Predictable and precise template-free CRISPR editing of pathogenic variants.
Nat.
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
2018 J jnl
What made you do this? Understanding black-box decisions with sufficient input subsets.
CoRR
Brandon Carter, Jonas Mueller, Siddhartha Jain, David K. Gifford
2017 B conf
K-mer Set Memory (KSM) Motif Representation Enables Accurate Prediction of the Impact of Regulatory Variants.
RECOMB
Yuchun Guo, Kevin Tian, Haoyang Zeng, David K. Gifford
2017 A* conf
Sequence to Better Sequence: Continuous Revision of Combinatorial Structures.
ICML
Jonas Mueller, David K. Gifford, Tommi S. Jaakkola
2016 J jnl
Convolutional neural network architectures for predicting DNA-protein binding.
Bioinform.
Haoyang Zeng, Matthew D. Edwards, Ge Liu, David K. Gifford
2016 J jnl
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding.
Bioinform.
Haoyang Zeng, Tatsunori B. Hashimoto, Daniel D. Kang, David K. Gifford
2016 A* conf
Learning Population-Level Diffusions with Generative RNNs.
ICML
Tatsunori B. Hashimoto, David K. Gifford, Tommi S. Jaakkola
2014 B conf
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding.
RECOMB
Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
2014 J jnl
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding.
PLoS Comput. Biol.
Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
2014 J jnl
Universal Count Correction for High-Throughput Sequencing.
PLoS Comput. Biol.
Tatsunori B. Hashimoto, Matthew D. Edwards, David K. Gifford
2012 J jnl
High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints.
PLoS Comput. Biol.
Yuchun Guo, Shaun Mahony, David K. Gifford
2012 J jnl
High-resolution genetic mapping with pooled sequencing.
BMC Bioinform.
Matthew D. Edwards, David K. Gifford
2012 J jnl
Lineage-based identification of cellular states and expression programs.
Bioinform.
Tatsunori B. Hashimoto, Tommi S. Jaakkola, Richard Sherwood, Esteban O. Mazzoni, Hynek Wichterle, David K. Gifford
2011 J jnl
Discovering Regulatory Overlapping RNA Transcripts.
J. Comput. Biol.
Timothy Danford, Robin D. Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David K. Gifford
2011 J jnl
ReadDB Provides Efficient Storage for Mapped Short Reads.
BMC Bioinform.
P. Alexander Rolfe, David K. Gifford
2010 B conf
Discovering Regulatory Overlapping RNA Transcripts.
RECOMB
Timothy Danford, Robin D. Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David K. Gifford
2010 J jnl
Discovering homotypic binding events at high spatial resolution.
Bioinform.
Yuchun Guo, Georgios Papachristoudis, Robert C. Altshuler, Georg K. Gerber, Tommi S. Jaakkola, David K. Gifford, Shaun Mahony
2008 Misc conf
GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data.
Pacific Symposium on Biocomputing
Timothy Danford, P. Alexander Rolfe, David K. Gifford
2007 J jnl
Automated Discovery of Functional Generality of Human Gene Expression Programs.
PLoS Comput. Biol.
Georg K. Gerber, Robin D. Dowell, Tommi S. Jaakkola, David K. Gifford
2006 J jnl
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.
Bioinform.
Kenzie D. MacIsaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, Richard A. Young, Ernest Fraenkel
2006 J jnl
An improved map of conserved regulatory sites for
BMC Bioinform.
Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel
2006 — conf
Semi-supervised analysis of gene expression profiles for lineage-specific development in the
ISMB (Supplement of Bioinformatics)
Yuan (Alan) Qi, Patrycja E. Missiuro, Ashish Kapoor, Craig P. Hunter, Tommi S. Jaakkola, David K. Gifford, Hui Ge
2005 A* conf
Active learning for sampling in time-series experiments with application to gene expression analysis.
ICML
Rohit Singh, Nathan P. Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph
2004 — conf
Analysis of Signaling Pathways in Human T-Cells Using Bayesian Network Modeling of Single Cell Data.
CSB
Karen Sachs, Omar D. Perez, Dana Pe'er, Garry P. Nolan, David K. Gifford, Tommi S. Jaakkola, Douglas A. Lauffenburger
2004 — conf
Deconvolving cell cycle expression data with complementary information.
ISMB/ECCB (Supplement of Bioinformatics)
Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, Roni Rosenfeld
2004 Misc conf
Negative Information for Motif Discovery.
Pacific Symposium on Biocomputing
Ken T. Takusagawa, David K. Gifford
2003 J jnl
Continuous Representations of Time-Series Gene Expression Data.
J. Comput. Biol.
Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon
2003 J jnl
K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data.
Bioinform.
Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Nathan Srebro, Angèle M. Hamel, Tommi S. Jaakkola
2002 B conf
A new approach to analyzing gene expression time series data.
RECOMB
Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon
2002 J jnl
Bayesian Methods for Elucidating Genetic Regulatory Networks.
IEEE Intell. Syst.
Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young
2002 Misc conf
Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models.
Pacific Symposium on Biocomputing
Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young
2002 J jnl
Experimental Efficiency of Programmed Mutagenesis.
New Gener. Comput.
Julia Khodor, David K. Gifford
2002 C conf
K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data.
WABI
Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi S. Jaakkola, Nathan Srebro
2002 J jnl
Programmed Mutagenesis Is Universal.
Theory Comput. Syst.
Julia Khodor, David K. Gifford
2001 — conf
Fast optimal leaf ordering for hierarchical clustering.
ISMB (Supplement of Bioinformatics)
Ziv Bar-Joseph, David K. Gifford, Tommi S. Jaakkola
2001 A* conf
Mesh Based Content Routing using XML.
SOSP
Alex C. Snoeren, Kenneth Conley, David K. Gifford
2001 B conf
Programmed Mutagenesis Is a Universal Model of Computation.
DNA
Julia Khodor, David K. Gifford
2001 Misc conf
Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks.
Pacific Symposium on Biocomputing
Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young
2000 — ed.
DNA Based Computers, Proceedings of a DIMACS Workshop, New Brunswick, New Jersey, USA, June 14-15, 1999
DNA Based Computers
Erik Winfree, David K. Gifford
2000 A* conf
Overcast: Reliable Multicasting with an Overlay Network.
OSDI
John Jannotti, David K. Gifford, Kirk L. Johnson, M. Frans Kaashoek, James W. O'Toole Jr.
1999 — conf
Simulating biological reactions: A modular approach.
DNA Based Computers
Alexander J. Hartemink, Tarjei S. Mikkelsen, David K. Gifford
1997 A* conf
Fast and Effective Query Refinement.
SIGIR
Bienvenido Vélez, Ron Weiss, Mark A. Sheldon, David K. Gifford
1997 — conf
The efficiency of sequence-specific separation of DNA mixtures for biological computing.
DNA Based Computers
Julia Khodor, David K. Gifford
1997 — conf
Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation.
DNA Based Computers
Alexander J. Hartemink, David K. Gifford
1996 — conf
HyPursuit: A Hierarchical Network Search Engine that Exploits Content-Link Hypertext Clustering.
Hypertext
Ron Weiss, Bienvenido Vélez, Mark A. Sheldon, Chanathip Namprempre, Péter Szilágyi, Andrzej Duda, David K. Gifford
1995 J jnl
Composition and Search with a Video Algebra.
IEEE Multim.
Ron Weiss, Andrzej Duda, David K. Gifford
1995 J jnl
Discover: A Resource Discovery System Based on Content Routing.
Comput. Networks ISDN Syst.
Mark A. Sheldon, Andrzej Duda, David K. Gifford
1995 — conf
Payment Switches for Open Networks.
USENIX Workshop on Electronic Commerce
David K. Gifford, Lawrence C. Stewart, Andrew C. Payne, G. Winfield Treese
1995 — conf
Payment for Open Networks.
COMPCON
David K. Gifford, Lawrence C. Stewart, Andrew C. Payne, G. Winfield Treese
1995 A* conf
Rover: A Toolkit for Mobile Information Access.
SOSP
Anthony D. Joseph, Alan F. deLespinasse, Joshua A. Tauber, David K. Gifford, M. Frans Kaashoek
1994 B conf
Content Routing for Distributed Information Servers.
EDBT
Mark A. Sheldon, Andrzej Duda, Ron Weiss, James W. O'Toole Jr., David K. Gifford
1994 — conf
Content-Based Access to Algebraic Video.
ICMCS
Ron Weiss, Andrzej Duda, David K. Gifford
1994 — conf
Static Dependent Costs for Estimating Execution Time.
LISP and Functional Programming
Brian Reistad, David K. Gifford
1993 A* conf
Concurrent Compacting Garbage Collection of a Persistent Heap.
SOSP
James W. O'Toole Jr., Scott Nettles, David K. Gifford
1992 J jnl
Five Forces Shaping Experimental Computer Science.
ACM SIGOPS Oper. Syst. Rev.
David K. Gifford
1992 — conf
Names should mean what, not where.
ACM SIGOPS European Workshop
James W. O'Toole Jr., David K. Gifford
1992 J jnl
Polymorphic Time Systems for Estimating Program Complexity.
LOPLAS
Vincent Dornic, Pierre Jouvelot, David K. Gifford
1991 A* conf
Algebraic Reconstruction of Types and Effects.
POPL
Pierre Jouvelot, David K. Gifford
1991 — conf
Intelligent File Systems for Object Repositories.
Operating Systems of the 90s and Beyond
David K. Gifford, James W. O'Toole Jr.
1991 — conf
Polymorphic Time Systems for Estimating Program Complexity.
JTASPEFT/WSA
Vincent Dornic, Pierre Jouvelot, David K. Gifford
1991 A* conf
Semantic File Systems.
SOSP
David K. Gifford, Pierre Jouvelot, Mark A. Sheldon, James W. O'Toole Jr.
1990 J jnl
Implementing Remote Evaluation.
IEEE Trans. Software Eng.
James W. Stamos, David K. Gifford
1990 J jnl
Polychannel Systems for Mass Digital Communications.
Commun. ACM
David K. Gifford
1990 J jnl
Remote Evaluation.
ACM Trans. Program. Lang. Syst.
James W. Stamos, David K. Gifford
1990 — conf
Static Dependent Types for First Class Modules.
LISP and Functional Programming
Mark A. Sheldon, David K. Gifford
1989 A* conf
Reasoning about Continuations with Control Effects.
PLDI
Pierre Jouvelot, David K. Gifford
1989 A* conf
Type Reconstruction with First-Class Polymorphic Values.
PLDI
James W. O'Toole Jr., David K. Gifford
1988 A* conf
Polymorphic Effect Systems.
POPL
John M. Lucassen, David K. Gifford
1988 J jnl
Remote Pipes and Procedures for Efficient Distributed Communication.
ACM Trans. Comput. Syst.
David K. Gifford, Nathan Glasser
1988 J jnl
The Cedar System.
Commun. ACM
David K. Gifford, Roger M. Needham, Michael D. Schroeder
1988 — conf
The FX-87 Interpreter.
ICCL
Pierre Jouvelot, David K. Gifford
1987 J jnl
Case Study: IBM's System/360-370 Architecture.
Commun. ACM
Alfred Z. Spector, David K. Gifford
1986 J jnl
A Computer Science Perspective of Bridge Design.
Commun. ACM
Alfred Z. Spector, David K. Gifford
1986 — conf
Integrating Functional and Imperative Programming.
LISP and Functional Programming
David K. Gifford, John M. Lucassen
1985 A* conf
A Caching File System For a Programmer's Workstation.
SOSP
Michael D. Schroeder, David K. Gifford, Roger M. Needham
1985 A* conf
An Architecture for Large Scale Information Systems.
SOSP
David K. Gifford, Robert W. Baldwin, Stephen T. Berlin, John M. Lucassen
1985 — conf
Coordinating Independent Atomic Actions.
COMPCON
David K. Gifford, James E. Donahue
1985 J jnl
The Application of Digital Broadcast Communication to Large Scale Information Systems.
IEEE J. Sel. Areas Commun.
David K. Gifford, John M. Lucassen, Stephen T. Berlin
1985 J jnl
The Cirrus Banking Network.
Commun. ACM
David K. Gifford, Alfred Z. Spector
1984 J jnl
The Space Shuttle Primary Computer System.
Commun. ACM
David K. Gifford, Alfred Z. Spector
1984 J jnl
The TWA Reservation System.
Commun. ACM
David K. Gifford, Alfred Z. Spector
1982 J jnl
Cryptographic Sealing for Information Secrecy and Authentication.
Commun. ACM
David K. Gifford
1982 J jnl
Surveyor's Forum: Technical Transactions.
ACM Comput. Surv.
David K. Gifford
1981 A* conf
Cryptographic Sealing for Information Secrecy and Authentication (Summary).
SOSP
David K. Gifford
1981 J jnl
Violet, an Experimental Decentralized System.
Comput. Networks
David K. Gifford
1979 A* conf
Weighted Voting for Replicated Data.
SOSP
David K. Gifford
1977 J jnl
Hardware Estimation of Process' Primary Memory Requirements.
Commun. ACM
David K. Gifford