Toward single particle reconstruction without particle picking: Breaking the detection limit

Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method for biological macromolecules. In a cryo-EM experiment, the microscope produces images called micrographs. Projections of the molecule of interest are embedded in the micrographs at unknown locations, and under unknown viewing directions. Standard imaging techniques first locate these projections (detection) and then reconstruct the 3-D structure from them. Unfortunately, high noise levels hinder detection. When reliable detection is rendered impossible, the standard techniques fail. This is a problem especially for small molecules, which can be particularly hard to detect. In this paper, we propose a radically different approach: we contend that the structure could, in principle, be reconstructed directly from the micrographs, without intermediate detection. As a result, even small molecules should be within reach for cryo-EM. To support this claim, we setup a simplified mathematical model and demonstrate how our autocorrelation analysis technique allows to go directly from the micrographs to the sought signals. This involves only one pass over the micrographs, which is desirable for large experiments. We show numerical results and discuss challenges that lay ahead to turn this proof-of-concept into a competitive alternative to state-of-the-art algorithms

Statistical Image Recovery from Laser Speckle Patterns with Polarization Diversity

This research extends the theory and understanding of the laser speckle imaging technique. This non-traditional imaging technique may be employed to improve space situational awareness and image deep space objects from a ground-based sensor system. The use of this technique is motivated by the ability to overcome aperture size limitations and the distortion effects from Earth’s atmosphere. Laser speckle imaging is a lensless, coherent method for forming two-dimensional images from their autocorrelation functions. Phase retrieval from autocorrelation data is an ill-posed problem where multiple solutions exist. This research introduces polarization diversity as a method for obtaining additional information so the structure of the object being reconstructed can be improved. Results show that in some cases the images restored using polarization diversity are superior to those reconstructed without it. This research presents statistical analysis of the observed data, two distinct image recovery algorithms, and a Cramer-Rao Lower Bound on resolution. A mathematical proof is provided to demonstrate the statistical properties of the observed, noisy autocorrelation data. The algorithms are constructed using the Expectation-Maximization approach and a polarization parameter that relates two independently observed data channels. The algorithms are validated with computer simulation and laboratory experiment. Comparison is made to an existing phase-retrieval technique. The theoretical lower bound is developed for comparing theoretical performance with and without polarization diversity. The results demonstrate the laser speckle imaging technique is improved with polarization diversity

Final Research Report on Auto-Tagging of Music

The deliverable D4.7 concerns the work achieved by IRCAM until M36 for the “auto-tagging of music”. The deliverable is a research report. The software libraries resulting from the research have been integrated into Fincons/HearDis! Music Library Manager or are used by TU Berlin. The final software libraries are described in D4.5. The research work on auto-tagging has concentrated on four aspects: 1) Further improving IRCAM’s machine-learning system ircamclass. This has been done by developing the new MASSS audio features, including audio augmentation and audio segmentation into ircamclass. The system has then been applied to train HearDis! “soft” features (Vocals-1, Vocals-2, Pop-Appeal, Intensity, Instrumentation, Timbre, Genre, Style). This is described in Part 3. 2) Developing two sets of “hard” features (i.e. related to musical or musicological concepts) as specified by HearDis! (for integration into Fincons/HearDis! Music Library Manager) and TU Berlin (as input for the prediction model of the GMBI attributes). Such features are either derived from previously estimated higher-level concepts (such as structure, key or succession of chords) or by developing new signal processing algorithm (such as HPSS) or main melody estimation. This is described in Part 4. 3) Developing audio features to characterize the audio quality of a music track. The goal is to describe the quality of the audio independently of its apparent encoding. This is then used to estimate audio degradation or music decade. This is to be used to ensure that playlists contain tracks with similar audio quality. This is described in Part 5. 4) Developing innovative algorithms to extract specific audio features to improve music mixes. So far, innovative techniques (based on various Blind Audio Source Separation algorithms and Convolutional Neural Network) have been developed for singing voice separation, singing voice segmentation, music structure boundaries estimation, and DJ cue-region estimation. This is described in Part 6.EC/H2020/688122/EU/Artist-to-Business-to-Business-to-Consumer Audio Branding System/ABC D

Automatic Drum Transcription and Source Separation

While research has been carried out on automated polyphonic music transcription, to-date the problem of automated polyphonic percussion transcription has not received the same degree of attention. A related problem is that of sound source separation, which attempts to separate a mixture signal into its constituent sources. This thesis focuses on the task of polyphonic percussion transcription and sound source separation of a limited set of drum instruments, namely the drums found in the standard rock/pop drum kit. As there was little previous research on polyphonic percussion transcription a broad review of music information retrieval methods, including previous polyphonic percussion systems, was also carried out to determine if there were any methods which were of potential use in the area of polyphonic drum transcription. Following on from this a review was conducted of general source separation and redundancy reduction techniques, such as Independent Component Analysis and Independent Subspace Analysis, as these techniques have shown potential in separating mixtures of sources. Upon completion of the review it was decided that a combination of the blind separation approach, Independent Subspace Analysis (ISA), with the use of prior knowledge as used in music information retrieval methods, was the best approach to tackling the problem of polyphonic percussion transcription as well as that of sound source separation. A number of new algorithms which combine the use of prior knowledge with the source separation abilities of techniques such as ISA are presented. These include sub-band ISA, Prior Subspace Analysis (PSA), and an automatic modelling and grouping technique which is used in conjunction with PSA to perform polyphonic percussion transcription. These approaches are demonstrated to be effective in the task of polyphonic percussion transcription, and PSA is also demonstrated to be capable of transcribing drums in the presence of pitched instruments