DVMark: A Deep Multiscale Framework for Video Watermarking.

Video watermarking embeds a message into a cover video in an imperceptible manner, which can be retrieved even if the video undergoes certain modifications or distortions. Traditional watermarking methods are often manually designed for particular types of distortions and thus cannot simultaneously handle a broad spectrum of distortions. To this end, we propose a robust deep learning-based solution for video watermarking that is end-to-end trainable. Our model consists of a novel multiscale design where the watermarks are distributed across multiple spatial-temporal scales. Extensive evaluations on a wide variety of distortions show that our method outperforms traditional video watermarking methods as well as deep image watermarking models by a large margin. We further demonstrate the practicality of our method on a realistic video-editing application.

A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics.

Spectrum clustering is a powerful strategy to minimize redundant mass spectra by grouping them based on similarity, with the aim of forming groups of mass spectra from the same repeatedly measured analytes. Each such group of near-identical spectra can be represented by its so-called consensus spectrum for downstream processing. Although several algorithms for spectrum clustering have been adequately benchmarked and tested, the influence of the consensus spectrum generation step is rarely evaluated. Here, we present an implementation and benchmark of common consensus spectrum algorithms, including spectrum averaging, spectrum binning, the most similar spectrum, and the best-identified spectrum. We have analyzed diverse public data sets using two different clustering algorithms (spectra-cluster and MaRaCluster) to evaluate how the consensus spectrum generation procedure influences downstream peptide identification. The BEST and BIN methods were found the most reliable methods for consensus spectrum generation, including for data sets with post-translational modifications (PTM) such as phosphorylation. All source code and data of the present study are freely available on GitHub at https://github.com/statisticalbiotechnology/representative-spectra-benchmark.

Better Compression With Deep Pre-Editing.

Could we compress images via standard codecs while avoiding visible artifacts? The answer is obvious - this is doable as long as the bit budget is generous enough. What if the allocated bit-rate for compression is insufficient? Then unfortunately, artifacts are a fact of life. Many attempts were made over the years to fight this phenomenon, with various degrees of success. In this work we aim to break the unholy connection between bit-rate and image quality, and propose a way to circumvent compression artifacts by pre-editing the incoming image and modifying its content to fit the given bits. We design this editing operation as a learned convolutional neural network, and formulate an optimization problem for its training. Our loss takes into account a proximity between the original image and the edited one, a bit-budget penalty over the proposed image, and a no-reference image quality measure for forcing the outcome to be visually pleasing. The proposed approach is demonstrated on the popular JPEG compression, showing savings in bits and/or improvements in visual quality, obtained with intricate editing effects.

Deep learning embedder method and tool for mass spectra similarity search.

Spectral similarity calculation is widely used in protein identification tools and mass spectra clustering algorithms while comparing theoretical or experimental spectra. The performance of the spectral similarity calculation plays an important role in these tools and algorithms especially in the analysis of large-scale datasets. Recently, deep learning methods have been proposed to improve the performance of clustering algorithms and protein identification by training the algorithms with existing data and the use of multiple spectra and identified peptide features. While the efficiency of these algorithms is still under study in comparison with traditional approaches, their application in proteomics data analysis is becoming more common. Here, we propose the use of deep learning to improve spectral similarity comparison. We assessed the performance of deep learning for spectral similarity, with GLEAMS and a newly trained embedder model (DLEAMSE), which uses high-quality spectra from PRIDE Cluster. Also, we developed a new bioinformatics tool (mslookup - https://github.com/bigbio/DLEAMSE/) that allows users to quickly search for spectra in previously identified mass spectra publish in public repositories and spectral libraries. Finally, we released a human database to enable bioinformaticians and biologists to search for identified spectra in their machines. SIGNIFICANCE STATEMENT: Spectral similarity calculation plays an important role in proteomics data analysis. With deep learning's ability to learn the implicit and effective features from large-scale training datasets, deep learning-based MS/MS spectra embedding models has emerged as a solution to improve mass spectral clustering similarity calculation algorithms. We compare multiple similarity scoring and deep learning methods in terms of accuracy (compute the similarity for a pair of the mass spectrum) and computing-time performance. The benchmark results showed no major differences in accuracy between DLEAMSE and normalized dot product for spectrum similarity calculations. The DLEAMSE GPU implementation is faster than NDP in preprocessing on the GPU server and the similarity calculation of DLEAMSE (Euclidean distance on 32-D vectors) takes about 1/3 of dot product calculations. The deep learning model (DLEAMSE) encoding and embedding steps needed to run once for each spectrum and the embedded 32-D points can be persisted in the repository for future comparison, which is faster for future comparisons and large-scale data. Based on these, we proposed a new tool mslookup that enables the researcher to find spectra previously identified in public data. The tool can be also used to generate in-house databases of previously identified spectra to share with other laboratories and consortiums.