Mary Wootters
Associate Professor of Computer Science and of Electrical Engineering
Academic Appointments
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Associate Professor, Computer Science
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Associate Professor, Electrical Engineering
2024-25 Courses
- Algebraic Error Correcting Codes
CS 250, EE 387 (Win) - Randomized Algorithms and Probabilistic Analysis
CME 309, CS 265 (Win) -
Independent Studies (20)
- Advanced Reading and Research
CS 499 (Aut, Win, Spr, Sum) - Advanced Reading and Research
CS 499P (Aut, Win, Spr, Sum) - Curricular Practical Training
CS 390A (Aut, Win, Spr, Sum) - Curricular Practical Training
CS 390B (Aut, Win, Spr, Sum) - Directed Studies in Applied Physics
APPPHYS 290 (Aut, Sum) - Independent Project
CS 399 (Aut, Win, Spr, Sum) - Independent Work
CS 199 (Aut, Win, Spr, Sum) - Independent Work
CS 199P (Aut, Win, Spr, Sum) - Master's Research
CME 291 (Aut, Win, Spr, Sum) - Master's Thesis and Thesis Research
EE 300 (Aut, Win, Spr, Sum) - Part-time Curricular Practical Training
CS 390D (Aut, Win, Spr, Sum) - Research
PHYSICS 490 (Aut, Win, Spr, Sum) - Senior Project
CS 191 (Aut, Win, Spr, Sum) - Special Studies and Reports in Electrical Engineering
EE 191 (Aut, Win, Spr, Sum) - Special Studies and Reports in Electrical Engineering
EE 191A (Aut, Win, Spr) - Special Studies and Reports in Electrical Engineering
EE 391 (Aut, Win, Spr, Sum) - Special Studies and Reports in Electrical Engineering (WIM)
EE 191W (Aut, Win, Spr, Sum) - Special Studies or Projects in Electrical Engineering
EE 190 (Aut, Win, Spr, Sum) - Special Studies or Projects in Electrical Engineering
EE 390 (Aut, Win, Spr, Sum) - Writing Intensive Senior Research Project
CS 191W (Aut, Win, Spr)
- Advanced Reading and Research
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Prior Year Courses
2023-24 Courses
- Dealing with Data
OSPISTAN 20 (Aut)
2022-23 Courses
- Citizenship in the 21st Century
COLLEGE 102 (Win) - Design and Analysis of Algorithms
CS 161 (Spr) - Randomized Algorithms and Probabilistic Analysis
CME 309, CS 265 (Aut)
2021-22 Courses
- Algebraic Error Correcting Codes
CS 250, EE 387 (Win) - Randomized Algorithms and Probabilistic Analysis
CME 309, CS 265 (Win) - Randomness: Computational and Philosophical Approaches
CS 57N, PHIL 3N (Win)
- Dealing with Data
Stanford Advisees
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Doctoral Dissertation Reader (AC)
Shaun Datta -
Postdoctoral Faculty Sponsor
Tushant Mittal -
Doctoral Dissertation Advisor (AC)
Dorsa Fathollahi -
Master's Program Advisor
Jason Chen, Michael Cho, Noor Fakih, Chenchen Gu, Meiqing Huo, Yash Kadadi, Andrei Mandelshtam, Annika Mauro, Hlumelo Notshe, Vikram Sivashankar, Vicky Wu -
Doctoral (Program)
Keller Blackwell, Kamilla Nazirkhanova, Joachim Neu
All Publications
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IMPROVED LIST-DECODABILITY AND LIST-RECOVERABILITY OF REED-SOLOMON CODES VIA TREE PACKINGS
SIAM JOURNAL ON COMPUTING
2024; 53 (2): 389-430
View details for DOI 10.1137/21M1463707
View details for Web of Science ID 001189705300001
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A Characterization of Optimal-Rate Linear Homomorphic Secret Sharing Schemes, and Applications
SCHLOSS DAGSTUHL, LEIBNIZ CENTER INFORMATICS. 2024
View details for DOI 10.4230/LIPIcs.ITCS.2024.16
View details for Web of Science ID 001300389400016
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Viderman's algorithm for quantum LDPC codes
SIAM. 2024: 2481-2507
View details for Web of Science ID 001267398705004
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Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing.
Scientific reports
2023; 13 (1): 8514
Abstract
The storage of data in DNA typically involves encoding and synthesizing data into short oligonucleotides, followed by reading with a sequencing instrument. Major challenges include the molecular consumption of synthesized DNA, basecalling errors, and limitations with scaling up read operations for individual data elements. Addressing these challenges, we describe a DNA storage system called MDRAM (Magnetic DNA-based Random Access Memory) that enables repetitive and efficient readouts of targeted files with nanopore-based sequencing. By conjugating synthesized DNA to magnetic agarose beads, we enabled repeated data readouts while preserving the original DNA analyte and maintaining data readout quality. MDRAM utilizes an efficient convolutional coding scheme that leverages soft information in raw nanopore sequencing signals to achieve information reading costs comparable to Illumina sequencing despite higher error rates. Finally, we demonstrate a proof-of-concept DNA-based proto-filesystem that enables an exponentially-scalable data address space using only small numbers of targeting primers for assembly and readout.
View details for DOI 10.1038/s41598-023-29575-z
View details for PubMedID 37231057
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IMPROVED LIST DECODING OF FOLDED REED-SOLOMON AND MULTIPLICITY CODES
SIAM JOURNAL ON COMPUTING
2023; 52 (3): 794-840
View details for DOI 10.1137/20M1370215
View details for Web of Science ID 001082560700002
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Bounds for List-Decoding and List-Recovery of Random Linear Codes
IEEE TRANSACTIONS ON INFORMATION THEORY
2022; 68 (2): 923-939
View details for DOI 10.1109/TIT.2021.3127126
View details for Web of Science ID 000745528100017
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Threshold Rates for Properties of Random Codes
IEEE TRANSACTIONS ON INFORMATION THEORY
2022; 68 (2): 905-922
View details for DOI 10.1109/TIT.2021.3123497
View details for Web of Science ID 000745528100016
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Asynchronous Distributed Optimization with Stochastic Delays
JMLR-JOURNAL MACHINE LEARNING RESEARCH. 2022
View details for Web of Science ID 000841852303028
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Improved List-Decodability and List-Recoverability of Reed-Solomon Codes via Tree Packings
IEEE COMPUTER SOC. 2022: 708-719
View details for DOI 10.1109/FOCS52979.2021.00074
View details for Web of Science ID 000802209600064
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Linear-Time Erasure List-Decoding of Expander Codes
IEEE TRANSACTIONS ON INFORMATION THEORY
2021; 67 (9): 5827-5839
View details for DOI 10.1109/TIT.2021.3086805
View details for Web of Science ID 000690440100015
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Improved List-Decodability of Random Linear Binary Codes
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. 2021: 1522–36
View details for DOI 10.1109/TIT.2020.3041650
View details for Web of Science ID 000619322300009
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Embedded Index Coding
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. 2021: 1461–77
View details for DOI 10.1109/TIT.2020.3043767
View details for Web of Science ID 000619322300006
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Lifted Multiplicity Codes and the Disjoint Repair Group Property
IEEE TRANSACTIONS ON INFORMATION THEORY
2021; 67 (2): 716–25
View details for DOI 10.1109/TIT.2020.3034962
View details for Web of Science ID 000612137400004
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Superbridge and bridge indices for knots
JOURNAL OF KNOT THEORY AND ITS RAMIFICATIONS
2021; 30 (2)
View details for DOI 10.1142/S0218216521500097
View details for Web of Science ID 000641745600003
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Weighted Matrix Completion From Non-Random, Non-Uniform Sampling Patterns
IEEE TRANSACTIONS ON INFORMATION THEORY
2021; 67 (2): 1264–90
View details for DOI 10.1109/TIT.2020.3039308
View details for Web of Science ID 000613330500001
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Hermitian-lifted codes
DESIGNS CODES AND CRYPTOGRAPHY
2021
View details for DOI 10.1007/s10623-020-00836-6
View details for Web of Science ID 000607364600001
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Illusion of large on-chip memory by networked computing chips for neural network inference
NATURE ELECTRONICS
2021
View details for DOI 10.1038/s41928-020-00515-3
View details for Web of Science ID 000607033100001
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Wedge-Lifted Codes
IEEE. 2021: 2990-2995
View details for DOI 10.1109/ISIT45174.2021.9518246
View details for Web of Science ID 000701502203015
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Approximate Gradient Coding with Optimal Decoding
IEEE. 2021: 2280-2285
View details for DOI 10.1109/ISIT45174.2021.9517990
View details for Web of Science ID 000701502202063
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On Greedy Approaches to Hierarchical Aggregation
IEEE. 2021: 2649-2654
View details for DOI 10.1109/ISIT45174.2021.9517814
View details for Web of Science ID 000701502202125
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On Coding for an Abstracted Nanopore Channel for DNA Storage
IEEE. 2021: 2465-2470
View details for DOI 10.1109/ISIT45174.2021.9518236
View details for Web of Science ID 000701502202094
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LOCAL LIST RECOVERY OF HIGH-RATE TENSOR CODES AND APPLICATIONS
SIAM JOURNAL ON COMPUTING
2020; 49 (4)
View details for DOI 10.1137/17M116149X
View details for Web of Science ID 000568207500005
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Linear-time Erasure List-decoding of Expander Codes
IEEE. 2020: 379-383
View details for Web of Science ID 000714963400065
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LDPC Codes Achieve List Decoding Capacity
IEEE. 2020: 458-469
View details for DOI 10.1109/FOCS46700.2020.00050
View details for Web of Science ID 000652333400042
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Tight Limits on Nonlocality from Nontrivial Communication Complexity; a.k.a. Reliable Computation with Asymmetric Gate Noise
IEEE. 2020: 206-217
View details for DOI 10.1109/FOCS46700.2020.00028
View details for Web of Science ID 000652333400020
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OVERCOMING HIGH NANOPORE BASECALLER ERROR RATES FOR DNA STORAGE VIA BASECALLER-DECODER INTEGRATION AND CONVOLUTIONAL CODES
IEEE. 2020: 8822–26
View details for Web of Science ID 000615970409020
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A Data-Compressive Wired-OR Readout for Massively Parallel Neural Recording
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. 2019: 1128–40
Abstract
Neural interfaces of the future will be used to help restore lost sensory, motor, and other capabilities. However, realizing this futuristic promise requires a major leap forward in how electronic devices interface with the nervous system. Next generation neural interfaces must support parallel recording from tens of thousands of electrodes within the form factor and power budget of a fully implanted device, posing a number of significant engineering challenges. In this paper, we exploit sparsity and diversity of neural signals to achieve simultaneous data compression and channel multiplexing for neural recordings. The architecture uses wired-OR interactions within an array of single-slope A/D converters to obtain massively parallel digitization of neural action potentials. The achieved compression is lossy but effective at retaining the critical samples belonging to action potentials, enabling efficient spike sorting and cell type identification. Simulation results of the architecture using data obtained from primate retina ex-vivo with a 512-channel electrode array show average compression rates up to ∼ 40× while missing less than 5% of cells. In principle, the techniques presented here could be used to design interfaces to other parts of the nervous system.
View details for DOI 10.1109/TBCAS.2019.2935468
View details for Web of Science ID 000507321400002
View details for PubMedID 31425051
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On the Optimality of the Kautz-Singleton Construction in Probabilistic Group Testing
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. 2019: 5592–5603
View details for DOI 10.1109/TIT.2019.2902397
View details for Web of Science ID 000481981000022
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Fast Blind MIMO Decoding Through Vertex Hopping
IEEE TRANSACTIONS ON WIRELESS COMMUNICATIONS
2019; 18 (7): 3669–82
View details for DOI 10.1109/TWC.2019.2917002
View details for Web of Science ID 000475339700024
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Repairing Multiple Failures for Scalar MDS Codes
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. 2019: 2661–72
View details for DOI 10.1109/TIT.2018.2876542
View details for Web of Science ID 000466029900003
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Blind Joint MIMO Channel Estimation and Decoding
IEEE TRANSACTIONS ON INFORMATION THEORY
2019; 65 (4): 2507–24
View details for DOI 10.1109/TIT.2018.2878016
View details for Web of Science ID 000461840600035
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Resistive RAM Endurance: Array-Level Characterization and Correction Techniques Targeting Deep Learning Applications
IEEE TRANSACTIONS ON ELECTRON DEVICES
2019; 66 (3): 1281–88
View details for DOI 10.1109/TED.2019.2894387
View details for Web of Science ID 000460970400022
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A 43pJ/Cycle Non-Volatile Microcontroller with 4.7 mu s Shutdown/Wake-up Integrating 2.3-bit/Cell Resistive RAM and Resilience Techniques
IEEE. 2019: 226-+
View details for Web of Science ID 000463153600071
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A Data-Compressive Wired-OR Readout for Massively Parallel Neural Recording
IEEE. 2019
View details for Web of Science ID 000483076401065
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Stochastic Gradient Coding for Flexible Straggler Mitigation in Distributed Learning
IEEE. 2019: 394–98
View details for Web of Science ID 000540384500080
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Embedded Index Coding
IEEE. 2019: 354–58
View details for Web of Science ID 000540384500072
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Improved read/write cost tradeoff in DNA-based data storage using LDPC codes
IEEE. 2019: 147–56
View details for Web of Science ID 000535355700022
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The N3XT Approach to Energy-Efficient Abundant-Data Computing
PROCEEDINGS OF THE IEEE
2019; 107 (1): 19–48
View details for DOI 10.1109/JPROC.2018.2882603
View details for Web of Science ID 000454770800004
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Linear-time list recovery of high-rate expander codes
ACADEMIC PRESS INC ELSEVIER SCIENCE. 2018: 202–18
View details for DOI 10.1016/j.ic.2018.02.004
View details for Web of Science ID 000436490400004
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Fast Blind MIMO Decoding through Vertex Hopping
IEEE. 2018: 148–49
View details for Web of Science ID 000467845100025
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Average-radius list-recoverability of random linear codes
ASSOC COMPUTING MACHINERY. 2018: 644–62
View details for Web of Science ID 000483921200043
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On the Optimality of the Kautz-Singleton Construction in Probabilistic Group Testing
IEEE. 2018: 188–95
View details for Web of Science ID 000461021200028
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On taking advantage of multiple requests in error correcting codes
IEEE. 2018: 1340–44
View details for Web of Science ID 000448139300269
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Load-Balanced Fractional Repetition Codes
IEEE. 2018: 2072–76
View details for Web of Science ID 000448139300416
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Improved decoding of Folded Reed-Solomon and Multiplicity Codes
IEEE COMPUTER SOC. 2018: 212–23
View details for DOI 10.1109/FOCS.2018.00029
View details for Web of Science ID 000455014500020
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Repairing Reed-Solomon Codes
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. 2017: 5684–98
View details for DOI 10.1109/TIT.2017.2702660
View details for Web of Science ID 000411016000017
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Exponential Decay of Reconstruction Error From Binary Measurements of Sparse Signals
IEEE TRANSACTIONS ON INFORMATION THEORY
2017; 63 (6): 3368–85
View details for DOI 10.1109/TIT.2017.2688381
View details for Web of Science ID 000402058900003
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De-biasing low-rank projection for matrix completion
SPIE-INT SOC OPTICAL ENGINEERING. 2017
View details for DOI 10.1117/12.2275004
View details for Web of Science ID 000416302900033
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Repairing multiple failures for scalar MDS codes
IEEE. 2017: 1145–52
View details for Web of Science ID 000428047800156
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Blind Joint MIMO Channel Estimation and Decoding
IEEE. 2017
View details for Web of Science ID 000428054301082
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Limitations of Piggybacking Codes with Low Substriping
IEEE. 2017: 1131–38
View details for Web of Science ID 000428047800154
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SPECIAL ISSUE: APPROX-RANDOM 2015 Foreword
THEORY OF COMPUTING
2016; 12
View details for DOI 10.4086/toc.2016.v012a013
View details for Web of Science ID 000433607300004
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Local correctability of expander codes
ACADEMIC PRESS INC ELSEVIER SCIENCE. 2015: 178–90
View details for DOI 10.1016/j.ic.2014.12.013
View details for Web of Science ID 000355665500012
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Linear-Time List Recovery of High-Rate Expander Codes
SPRINGER-VERLAG BERLIN. 2015: 701–12
View details for DOI 10.1007/978-3-662-47672-7_57
View details for Web of Science ID 000364317700057
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Configuration spaces of convex and embedded polygons in the plane
GEOMETRIAE DEDICATA
2014; 172 (1): 121–34
View details for DOI 10.1007/s10711-013-9910-x
View details for Web of Science ID 000341500400005
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1-Bit matrix completion
INFORMATION AND INFERENCE-A JOURNAL OF THE IMA
2014; 3 (3): 189–223
View details for DOI 10.1093/imaiai/iau006
View details for Web of Science ID 000218926400001
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Optimal entanglement-assisted one-shot classical communication
PHYSICAL REVIEW A
2013; 87 (6)
View details for DOI 10.1103/PhysRevA.87.062301
View details for Web of Science ID 000319909500001
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Lower Bounds for Quantized Matrix Completion
IEEE. 2013: 296-+
View details for Web of Science ID 000348913400060
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Local Correctability of Expander Codes
SPRINGER-VERLAG BERLIN. 2013: 540–51
View details for Web of Science ID 000342686600046
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REUSABLE LOW-ERROR COMPRESSIVE SAMPLING SCHEMES THROUGH PRIVACY
IEEE. 2012: 536–39
View details for Web of Science ID 000309943200135