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Publications

The latest publications from the Molecular Programming Project.

Force Spectroscopy and Beyond: Innovations and Opportunities

Life operates at the intersection of chemistry and mechanics. Over the years, we have made remarkable progress in understanding life from a biochemical perspective and the mechanics of life at the single-molecule scale. Yet the full integration of physical and mechanical models into mainstream...
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A Content-Addressable DNA Database with Learned Sequence Encodings

We present strand and codeword design schemes for a DNA database capable of approximate similarity search over a multidimensional dataset of content-rich media. Our strand designs address cross-talk in associative DNA databases, and we demonstrate a novel method for learning DNA sequence encod...
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Layering Assume-Guarantee Contracts for Hierarchical System Design

Specifications for complex engineering systems are typically decomposed into specifications for individual subsystems in a manner that ensures they are implementable and simpler to develop further. We describe a method to algorithmically construct component specifications that implement a give...
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On Coding over Sliced Information

The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes for this channel under substitution errors, and provid...
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On the Uncertainty of Information Retrieval in Associative Memories

We (people) are memory machines. Our decision processes, emotions, and interactions with the world around us are based on and driven by associations to our memories. This natural association paradigm will become critical in future memory systems, namely, the key question will not be “How do I ...
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Erratum: Random access in large-scale DNA data storage

In the version of this article initially published, the references in the reference list were in the wrong order; the references have been renumbered as follows: 3 as 2; 5 as 3; 6 as 8; 7 as 9; 8 as 11; 9 as 6; 10 as 12; 11 as 5; 12 as 13; 13 as 7; 16 as 10; and no. 2, “Hoch, J.A. & Losick...
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A molecular multi-gene classifier for disease diagnostics

Despite its early promise as a diagnostic and prognostic tool, gene expression profiling remains cost-prohibitive and challenging to implement in a clinical setting. Here, we introduce a molecular computation strategy for analysing the information contained in complex gene expression signature...
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How to Best Share a Big Secret

When sensitive data is stored in the cloud, the only way to ensure its secrecy is by encrypting it before it is uploaded. The emerging multi-cloud model, in which data is stored redundantly in two or more independent clouds, provides an opportunity to protect sensitive data with secret-sharing...
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Two Deletion Correcting Codes from Indicator Vectors

Construction of capacity achieving deletion correcting codes has been a baffling challenge for decades. A recent breakthrough by Brakensiek et al., alongside novel applications in DNA storage, have reignited the interest in this longstanding open problem. In spite of recent advances, the amoun...
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Proving properties of a minimal covering algorithm

Proving properties of a minimal covering algorithm … Control & Dynamical Systems California Institute of Technology … Filippidis and Murray ( Caltech ) Proving properties of a minimal covering algorithm July 18, 2018 1 / 27 … Motivation: Converting binary decision diagrams to minimal …

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Detecting Adversarial Examples via Neural Fingerprinting

Deep neural networks are vulnerable to adversarial examples, which dramatically alter model output using small input changes. We propose Neural Fingerprinting, a simple, yet effective method to detect adversarial examples by verifying whether model behavior is consistent with a set of secret f...
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