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  1. Free, publicly-accessible full text available June 13, 2023
  2. Projection algorithms such as t-SNE or UMAP are useful for the visualization of high dimensional data, but depend on hyperpa- rameters which must be tuned carefully. Unfortunately, iteratively recomputing projections to find the optimal hyperparameter values is computationally intensive and unintuitive due to the stochastic nature of such methods. In this paper we propose Hy- perNP, a scalable method that allows for real-time interactive hyperparameter exploration of projection methods by training neural network approximations. A HyperNP model can be trained on a fraction of the total data instances and hyperparameter configurations that one would like to investigate and can compute projections for new data and hyperparameters at interactive speeds. HyperNP models are compact in size and fast to compute, thus allowing them to be embedded in lightweight visualiza- tion systems. We evaluate the performance of HyperNP across three datasets in terms of performance and speed. The results suggest that HyperNP models are accurate, scalable, interactive, and appropriate for use in real-world settings.
    Free, publicly-accessible full text available June 13, 2023
  3. Free, publicly-accessible full text available June 1, 2023
  4. Photoswitches are molecules that undergo a reversible, structural isomerization after exposure to different wavelengths of light. The dynamic control offered by molecular photoswitches is favorable for applications in materials chemistry, photopharmacology, and catalysis. Ideal photoswitches absorb visible light and have long-lived metastable isomers. We used high throughput virtual screening to predict the absorption maxima (λmax) of the E-isomer and half-lives (t1/2) of the Z-isomer. However, computing the photophysical and kinetic properties of each entry of a virtual molecular library containing 103–106 entries with density functional theory is prohibitively time-consuming. We applied active search, a machine learning technique to intelligently search a chemical search space of 255991 photoswitches based on 29 known azoarenes and their derivatives. We iteratively trained the active search algorithm based on whether a candidate absorbed visible light (λmax > 450 nm). Active search was found to triple the discovery rate compared to random search. Further, we projected 1962 photoswitches to 2D using the Uniform Manifold Approximation and Projection (umap) algorithm and found that λmax depends on the core, which is tunable with substituents. We then incorporated a second stage of screening with to predict the stabilities of the Z-isomers for the top 1% of candidates. We identifiedmore »four ideal photoswitches that concurrently satisfy λmax > 450 nm and t1/2 > 2 hours; the range of λmax and t1/2 range from 465 to 531 nm and hours to years, respectively.« less
  5. We analyze the Secure Remote Password (SRP) protocol for structural weaknesses using the Cryptographic Protocol Shapes Analyzer (CPSA) in the first formal analysis of SRP (specifically, Version 3). SRP is a widely deployed Password Authenticated Key Exchange (PAKE) protocol used in 1Password, iCloud Keychain, and other products. As with many PAKE protocols, two participants use knowledge of a pre-shared password to authenticate each other and establish a session key. SRP aims to resist dictionary attacks, not store plaintext-equivalent passwords on the server, avoid patent infringement, and avoid export controls by not using encryption. Formal analysis of SRP is challenging in part because existing tools provide no simple way to reason about its use of the mathematical expression “v + g b mod q”. Modeling v + g b as encryption, we complete an exhaustive study of all possible execution sequences of SRP. Ignoring possible algebraic attacks, this analysis detects no major structural weakness, and in particular no leakage of any secrets. We do uncover one notable weakness of SRP, which follows from its design constraints. It is possible for a malicious server to fake an authentication session with a client, without the client’s participation. This action might facilitate an escalationmore »of privilege attack, if the client has higher privileges than does the server. We conceived of this attack before we used CPSA and confirmed it by generating corresponding execution shapes using CPSA.« less