Maximum-likelihood decoding of device-specific multi-bit symbols for reliable key generation

We present a PUF key generation scheme that uses the provably optimal method of maximum-likelihood (ML) detection on symbols derived from PUF response bits. Each device forms a noisy, device-specific symbol constellation, based on manufacturing variation. Each detected symbol is a letter in a codeword of an error correction code, resulting in non-binary codewords. We present a three-pronged validation strategy: i. mathematical (deriving an optimal symbol decoder), ii. simulation (comparing against prior approaches), and iii. empirical (using implementation data). We present simulation results demonstrating that for a given PUF noise level and block size (an estimate of helper data size), our new symbol-based ML approach can have orders of magnitude better bit error rates compared to prior schemes such as block coding, repetition coding, and threshold-based pattern matching, especially under high levels of noise due to extreme environmental variation. We demonstrate environmental reliability of a ML symbol-based soft-decision error correction approach in 28nm FPGA silicon, covering -65°C to 105°C ambient (and including 125°C junction), and with 128bit key regeneration error probability ≤ 1 ppm.Bavaria California Technology Center (Grant 2014-1/9

Non-EST based prediction of exon skipping and intron retention events using Pfam information

Most of the known alternative splice events have been detected by the comparison of expressed sequence tags (ESTs) and cDNAs. However, not all splice events are represented in EST databases since ESTs have several biases. Therefore, non-EST based approaches are needed to extend our view of a transcriptome. Here, we describe a novel method for the ab initio prediction of alternative splice events that is solely based on the annotation of Pfam domains. Furthermore, we applied this approach in a genome-wide manner to all human RefSeq transcripts and predicted a total of 321 exon skipping and intron retention events. We show that this method is very reliable as 78% (250 of 321) of our predictions are confirmed by ESTs or cDNAs. Subsequent analyses of splice events within Pfam domains revealed a significant preference of alternative exon junctions to be located at the protein surface and to avoid secondary structure elements. Thus, splice events within Pfams are probable to alter the structure and function of a domain which makes them highly interesting for detailed biological investigation. As Pfam domains are annotated in many other species, our strategy to predict exon skipping and intron retention events might be important for species with a lower number of ESTs

Improved identification of conserved cassette exons using Bayesian networks

<p>Abstract</p> <p>Background</p> <p>Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microarrays does not capture all alternative splicing events. Moreover, for many species genomic data is being produced at a far greater rate than corresponding transcript data, hence <it>in silico </it>methods of predicting alternative splicing have to be improved.</p> <p>Results</p> <p>Here, we show that the use of Bayesian networks (BNs) allows accurate prediction of evolutionary conserved exon skipping events. At a stringent false positive rate of 0.5%, our BN achieves an improved true positive rate of 61%, compared to a previously reported 50% on the same dataset using support vector machines (SVMs). Incorporating several novel discriminative features such as intronic splicing regulatory elements leads to the improvement. Features related to mRNA secondary structure increase the prediction performance, corroborating previous findings that secondary structures are important for exon recognition. Random labelling tests rule out overfitting. Cross-validation on another dataset confirms the increased performance. When using the same dataset and the same set of features, the BN matches the performance of an SVM in earlier literature. Remarkably, we could show that about half of the exons which are labelled constitutive but receive a high probability of being alternative by the BN, are in fact alternative exons according to the latest EST data. Finally, we predict exon skipping without using conservation-based features, and achieve a true positive rate of 29% at a false positive rate of 0.5%.</p> <p>Conclusion</p> <p>BNs can be used to achieve accurate identification of alternative exons and provide clues about possible dependencies between relevant features. The near-identical performance of the BN and SVM when using the same features shows that good classification depends more on features than on the choice of classifier. Conservation based features continue to be the most informative, and hence distinguishing alternative exons from constitutive ones without using conservation based features remains a challenging problem.</p

A Lockdown Technique to Prevent Machine Learning on PUFs for Lightweight Authentication

We present a lightweight PUF-based authentication approach that is practical in settings where a server authenticates a device, and for use cases where the number of authentications is limited over a device's lifetime. Our scheme uses a server-managed challenge/response pair (CRP) lockdown protocol: unlike prior approaches, an adaptive chosen-challenge adversary with machine learning capabilities cannot obtain new CRPs without the server's implicit permission. The adversary is faced with the problem of deriving a PUF model with a limited amount of machine learning training data. Our system-level approach allows a so-called strong PUF to be used for lightweight authentication in a manner that is heuristically secure against today's best machine learning methods through a worst-case CRP exposure algorithmic validation. We also present a degenerate instantiation using a weak PUF that is secure against computationally unrestricted adversaries, which includes any learning adversary, for practical device lifetimes and read-out rates. We validate our approach using silicon PUF data, and demonstrate the feasibility of supporting 10, 1,000, and 1M authentications, including practical configurations that are not learnable with polynomial resources, e.g., the number of CRPs and the attack runtime, using recent results based on the probably-approximately-correct (PAC) complexity-theoretic framework