FUnc-SNE: A flexible, Fast, and Unconstrained algorithm for neighbour embeddings

Neighbour embeddings (NE) allow the representation of high dimensional datasets into lower dimensional spaces and are often used in data visualisation. In practice, accelerated approximations are employed to handle very large datasets. Accelerating NE is challenging, and two main directions have been explored: very coarse approximations based on negative sampling (as in UMAP) achieve high effective speed but may lack quality in the extracted structures; less coarse approximations, as used in FIt-SNE or BH-t-SNE, offer better structure preservation at the cost of speed, while also restricting the target dimensionality to 2 or 3, limiting NE to visualisation. In some variants, the precision of these costlier accelerations also enables finer-grained control on the extracted structures through dedicated hyperparameters. This paper proposes to bridge the gab between both approaches by introducing a novel way to accelerate NE, requiring a small number of computations per iteration while maintaining good fine-grained structure preservation and flexibility through hyperparameter tuning, without limiting the dimensionality of the embedding space. The method was designed for interactive exploration of data; as such, it abandons the traditional two-phased approach of other NE methods, allowing instantaneous visual feedback when changing hyperparameters, even when these control processes happening on the high-dimensional side of the computations. Experiments using a publicly available, GPU accelerated GUI integration of the method show promising results in terms of speed, flexibility in the structures getting extracted, and show potential uses in broader machine learning contexts with minimal algorithmic modifications. Central to this algorithm is a novel approach to iterative approximate nearest neighbour search, which shows promising results compared to nearest neighbour descent.

Compressive lensless endoscopy with partial speckle scanning

The lensless endoscope (LE) is a promising device to acquire in vivo images at a cellular scale. The tiny size of the probe enables a deep exploration of the tissues. Lensless endoscopy with a multicore fiber (MCF) commonly uses a spatial light modulator (SLM) to coherently combine, at the output of the MCF, few hundreds of beamlets into a focus spot. This spot is subsequently scanned across the sample to generate a fluorescent image. We propose here a novel scanning scheme, partial speckle scanning (PSS), inspired by compressive sensing theory, that avoids the use of an SLM to perform fluorescent imaging in LE with reduced acquisition time. Such a strategy avoids photo-bleaching while keeping high reconstruction quality. We develop our approach on two key properties of the LE: (i) the ability to easily generate speckles, and (ii) the memory effect in MCF that allows to use fast scan mirrors to shift light patterns. First, we show that speckles are sub-exponential random fields. Despite their granular structure, an appropriate choice of the reconstruction parameters makes them good candidates to build efficient sensing matrices. Then, we numerically validate our approach and apply it on experimental data. The proposed sensing technique outperforms conventional raster scanning: higher reconstruction quality is achieved with far fewer observations. For a fixed reconstruction quality, our speckle scanning approach is faster than compressive sensing schemes which require to change the speckle pattern for each observation.