David K. Gifford

Orcid: 0000-0003-1709-4034

Affiliations:
  • MIT, Cambridge, USA


According to our database1, David K. Gifford authored at least 103 papers between 1977 and 2023.

Collaborative distances:

Awards

ACM Fellow

ACM Fellow 2011, "For contributions to distributed systems, e-commerce and content distribution.".

Timeline

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Bibliography

2023
Training Data Attribution for Diffusion Models.
CoRR, 2023

Fundamental limits on the robustness of image classifiers.
Proceedings of the Eleventh International Conference on Learning Representations, 2023

Constrained Submodular Optimization for Vaccine Design.
Proceedings of the Thirty-Seventh AAAI Conference on Artificial Intelligence, 2023

2022
Ultra High Diversity Factorizable Libraries for Efficient Therapeutic Discovery.
Proceedings of the Research in Computational Molecular Biology, 2022

Maximum n-times Coverage for Vaccine Design.
Proceedings of the Tenth International Conference on Learning Representations, 2022

2021
Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
PLoS Comput. Biol., 2021

Machine learning based CRISPR gRNA design for therapeutic exon skipping.
PLoS Comput. Biol., 2021

Discovering differential genome sequence activity with interpretable and efficient deep learning.
PLoS Comput. Biol., 2021

Image classifiers can not be made robust to small perturbations.
CoRR, 2021

Maximum n-times Coverage for COVID-19 Vaccine Design.
CoRR, 2021

Machine learning optimization of peptides for presentation by class II MHCs.
Bioinform., 2021

Overinterpretation reveals image classification model pathologies.
Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021

Lost in Pruning: The Effects of Pruning Neural Networks beyond Test Accuracy.
Proceedings of Machine Learning and Systems 2021, 2021

2020
Information Condensing Active Learning.
CoRR, 2020

Antibody complementarity determining region design using high-capacity machine learning.
Bioinform., 2020

Maximizing Overall Diversity for Improved Uncertainty Estimates in Deep Ensembles.
Proceedings of the Thirty-Fourth AAAI Conference on Artificial Intelligence, 2020

2019
Visualizing complex feature interactions and feature sharing in genomic deep neural networks.
BMC Bioinform., 2019

DeepLigand: accurate prediction of MHC class I ligands using peptide embedding.
Bioinform., 2019

Disentangled Representations of Cellular Identity.
Proceedings of the Research in Computational Molecular Biology, 2019

What made you do this? Understanding black-box decisions with sufficient input subsets.
Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, 2019

2018
Predictable and precise template-free CRISPR editing of pathogenic variants.
Nat., 2018

2017
K-mer Set Memory (KSM) Motif Representation Enables Accurate Prediction of the Impact of Regulatory Variants.
Proceedings of the Research in Computational Molecular Biology, 2017

Sequence to Better Sequence: Continuous Revision of Combinatorial Structures.
Proceedings of the 34th International Conference on Machine Learning, 2017

2016
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding.
Bioinform., 2016

Convolutional neural network architectures for predicting DNA-protein binding.
Bioinform., 2016

Learning Population-Level Diffusions with Generative RNNs.
Proceedings of the 33nd International Conference on Machine Learning, 2016

2014
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding.
PLoS Comput. Biol., 2014

Universal Count Correction for High-Throughput Sequencing.
PLoS Comput. Biol., 2014

2013
High Resolution Modeling of Chromatin Interactions.
Proceedings of the Research in Computational Molecular Biology, 2013

2012
High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints.
PLoS Comput. Biol., 2012

High-resolution genetic mapping with pooled sequencing.
BMC Bioinform., 2012

Lineage-based identification of cellular states and expression programs.
Bioinform., 2012

2011
Discovering Regulatory Overlapping RNA Transcripts.
J. Comput. Biol., 2011

Stochastic motion planning and applications to traffic.
Int. J. Robotics Res., 2011

ReadDB Provides Efficient Storage for Mapped Short Reads.
BMC Bioinform., 2011

2010
Discovering homotypic binding events at high spatial resolution.
Bioinform., 2010

2008
GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data.
Proceedings of the Biocomputing 2008, 2008

2007
Automated Discovery of Functional Generality of Human Gene Expression Programs.
PLoS Comput. Biol., 2007

2006
An improved map of conserved regulatory sites for <i>Saccharomyces cerevisiae</i>.
BMC Bioinform., 2006

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.
Bioinform., 2006

Semi-supervised analysis of gene expression profiles for lineage-specific development in the <i>Caenorhabditis elegans</i> embryo.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005
Active learning for sampling in time-series experiments with application to gene expression analysis.
Proceedings of the Machine Learning, 2005

2004
Negative Information for Motif Discovery.
Proceedings of the Biocomputing 2004, 2004

Deconvolving cell cycle expression data with complementary information.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Analysis of Signaling Pathways in Human T-Cells Using Bayesian Network Modeling of Single Cell Data.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003
Continuous Representations of Time-Series Gene Expression Data.
J. Comput. Biol., 2003

K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data.
Bioinform., 2003

2002
Experimental Efficiency of Programmed Mutagenesis.
New Gener. Comput., 2002

Programmed Mutagenesis Is Universal.
Theory Comput. Syst., 2002

Bayesian Methods for Elucidating Genetic Regulatory Networks.
IEEE Intell. Syst., 2002

A new approach to analyzing gene expression time series data.
Proceedings of the Sixth Annual International Conference on Computational Biology, 2002

Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001
Mesh Based Content Routing using XML.
Proceedings of the 18th ACM Symposium on Operating System Principles, 2001

Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

Fast optimal leaf ordering for hierarchical clustering.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

Programmed Mutagenesis Is a Universal Model of Computation.
Proceedings of the DNA Computing, 7th International Workshop on DNA-Based Computers, 2001

2000
Overcast: Reliable Multicasting with an Overlay Network.
Proceedings of the 4th Symposium on Operating System Design and Implementation (OSDI 2000), 2000

1999
Simulating biological reactions: A modular approach.
Proceedings of the DNA Based Computers, 1999

1997
Fast and Effective Query Refinement.
Proceedings of the SIGIR '97: Proceedings of the 20th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, 1997

The efficiency of sequence-specific separation of DNA mixtures for biological computing.
Proceedings of the DNA Based Computers, 1997

Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation.
Proceedings of the DNA Based Computers, 1997

1996
HyPursuit: A Hierarchical Network Search Engine that Exploits Content-Link Hypertext Clustering.
Proceedings of the Hypertext '96, 1996

1995
Composition and Search with a Video Algebra.
IEEE Multim., 1995

Discover: A Resource Discovery System Based on Content Routing.
Comput. Networks ISDN Syst., 1995

Payment Switches for Open Networks.
Proceedings of the First USENIX Workshop on Electronic Commerce, 1995

Rover: A Toolkit for Mobile Information Access.
Proceedings of the Fifteenth ACM Symposium on Operating System Principles, 1995

Payment for Open Networks.
Proceedings of the COMPCON '95: Technologies for the Information Superhighway, 1995

1994
Static Dependent Costs for Estimating Execution Time.
Proceedings of the 1994 ACM Conference on LISP and Functional Programming, 1994

Content-Based Access to Algebraic Video.
Proceedings of the International Conference on Multimedia Computing and Systems, 1994

Content Routing for Distributed Information Servers.
Proceedings of the Advances in Database Technology, 1994

1993
Concurrent Compacting Garbage Collection of a Persistent Heap.
Proceedings of the Fourteenth ACM Symposium on Operating System Principles, 1993

1992
Five Forces Shaping Experimental Computer Science.
ACM SIGOPS Oper. Syst. Rev., 1992

Polymorphic Time Systems for Estimating Program Complexity.
LOPLAS, 1992

Names should mean what, not where.
Proceedings of the 5th ACM SIGOPS European Workshop: Models and Paradigms for Distributed Systems Structuring, 1992

1991
Semantic File Systems.
Proceedings of the Thirteenth ACM Symposium on Operating System Principles, 1991

Algebraic Reconstruction of Types and Effects.
Proceedings of the Conference Record of the Eighteenth Annual ACM Symposium on Principles of Programming Languages, 1991

Intelligent File Systems for Object Repositories.
Proceedings of the Operating Systems of the 90s and Beyond, International Workshop, 1991

1990
Implementing Remote Evaluation.
IEEE Trans. Software Eng., 1990

Remote Evaluation.
ACM Trans. Program. Lang. Syst., 1990

Polychannel Systems for Mass Digital Communications.
Commun. ACM, 1990

Static Dependent Types for First Class Modules.
Proceedings of the 1990 ACM Conference on LISP and Functional Programming, 1990

1989
Type Reconstruction with First-Class Polymorphic Values.
Proceedings of the ACM SIGPLAN'89 Conference on Programming Language Design and Implementation (PLDI), 1989

Reasoning about Continuations with Control Effects.
Proceedings of the ACM SIGPLAN'89 Conference on Programming Language Design and Implementation (PLDI), 1989

1988
Remote Pipes and Procedures for Efficient Distributed Communication.
ACM Trans. Comput. Syst., 1988

The Cedar System.
Commun. ACM, 1988

Polymorphic Effect Systems.
Proceedings of the Conference Record of the Fifteenth Annual ACM Symposium on Principles of Programming Languages, 1988

The FX-87 Interpreter.
Proceedings of the 1988 Internation Conference on Computer Languages, 1988

1987
Case Study: IBM's System/360-370 Architecture.
Commun. ACM, 1987

1986
A Computer Science Perspective of Bridge Design.
Commun. ACM, 1986

Integrating Functional and Imperative Programming.
Proceedings of the 1986 ACM Conference on LISP and Functional Programming, 1986

1985
The Application of Digital Broadcast Communication to Large Scale Information Systems.
IEEE J. Sel. Areas Commun., 1985

The Cirrus Banking Network.
Commun. ACM, 1985

A Caching File System For a Programmer's Workstation.
Proceedings of the Tenth ACM Symposium on Operating System Principles, 1985

An Architecture for Large Scale Information Systems.
Proceedings of the Tenth ACM Symposium on Operating System Principles, 1985

Coordinating Independent Atomic Actions.
Proceedings of the Spring COMPCON'85, 1985

1984
The Space Shuttle Primary Computer System.
Commun. ACM, 1984

The TWA Reservation System.
Commun. ACM, 1984

1982
Surveyor's Forum: Technical Transactions.
ACM Comput. Surv., 1982

Cryptographic Sealing for Information Secrecy and Authentication.
Commun. ACM, 1982

1981
Violet, an Experimental Decentralized System.
Comput. Networks, 1981

Cryptographic Sealing for Information Secrecy and Authentication (Summary).
Proceedings of the Eighth Symposium on Operating System Principles, 1981

1979
Weighted Voting for Replicated Data.
Proceedings of the Seventh Symposium on Operating System Principles, 1979

1977
Hardware Estimation of Process' Primary Memory Requirements.
Commun. ACM, 1977


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