More Like this

1. Discovery and Utilization of Jazz Motifs for Computer-Generated Solos

   Yaconelli, Joseph; Keller, Robert M. (August 2018, Computer Simulation of Musical Creativity)

   Building on previous work in computer generated jazz solos using probabilistic grammars, this paper describes research extending the capabilities of the current learning process and grammar representation used in the Impro-Visor educational music software with the concepts of motifs and motif patterns. An approach has been developed using clustering, best match search techniques, and probabilistic grammar rules to identify motifs and incorporate them into computer generated solos. The abilities of this technique are further expanded through the use of motif patterns. Motif patterns are used to induce coherence in generated solos by learning the patterns in which motifs were used in a given set of transcriptions. This approach is implemented as a feature of the Impro- Visor software. 

   more » « less
2. Fast and exact quantification of motif occurrences in biological sequences

   https://doi.org/10.1186/s12859-021-04355-6  

   Prosperi, Mattia; Marini, Simone; Boucher, Christina (December 2021, BMC Bioinformatics)

   null (Ed.)

   Abstract Background Identification of motifs and quantification of their occurrences are important for the study of genetic diseases, gene evolution, transcription sites, and other biological mechanisms. Exact formulae for estimating count distributions of motifs under Markovian assumptions have high computational complexity and are impractical to be used on large motif sets. Approximated formulae, e.g. based on compound Poisson, are faster, but reliable p value calculation remains challenging. Here, we introduce ‘motif_prob’, a fast implementation of an exact formula for motif count distribution through progressive approximation with arbitrary precision. Our implementation speeds up the exact calculation, usually impractical, making it feasible and posit to substitute currently employed heuristics. Results We implement motif_prob in both Perl and C+ + languages, using an efficient error-bound iterative process for the exact formula, providing comparison with state-of-the-art tools (e.g. MoSDi) in terms of precision, run time benchmarks, along with a real-world use case on bacterial motif characterization. Our software is able to process a million of motifs (13–31 bases) over genome lengths of 5 million bases within the minute on a regular laptop, and the run times for both the Perl and C+ + code are several orders of magnitude smaller (50–1000× faster) than MoSDi, even when using their fast compound Poisson approximation (60–120× faster). In the real-world use cases, we first show the consistency of motif_prob with MoSDi, and then how the p-value quantification is crucial for enrichment quantification when bacteria have different GC content, using motifs found in antimicrobial resistance genes. The software and the code sources are available under the MIT license at https://github.com/DataIntellSystLab/motif_prob . Conclusions The motif_prob software is a multi-platform and efficient open source solution for calculating exact frequency distributions of motifs. It can be integrated with motif discovery/characterization tools for quantifying enrichment and deviation from expected frequency ranges with exact p values, without loss in data processing efficiency. 

   more » « less
3. Binding peptide generation for MHC Class I proteins with deep reinforcement learning

   https://doi.org/10.1093/bioinformatics/btad055  

   Chen, Ziqi; Zhang, Baoyi; Guo, Hongyu; Emani, Prashant; Clancy, Trevor; Jiang, Chongming; Gerstein, Mark; Ning, Xia; Cheng, Chao; Min, Martin Renqiang; et al (January 2023, Bioinformatics)

   Abstract MotivationMHC Class I protein plays an important role in immunotherapy by presenting immunogenic peptides to anti-tumor immune cells. The repertoires of peptides for various MHC Class I proteins are distinct, which can be reflected by their diverse binding motifs. To characterize binding motifs for MHC Class I proteins, in vitro experiments have been conducted to screen peptides with high binding affinities to hundreds of given MHC Class I proteins. However, considering tens of thousands of known MHC Class I proteins, conducting in vitro experiments for extensive MHC proteins is infeasible, and thus a more efficient and scalable way to characterize binding motifs is needed. ResultsWe presented a de novo generation framework, coined PepPPO, to characterize binding motif for any given MHC Class I proteins via generating repertoires of peptides presented by them. PepPPO leverages a reinforcement learning agent with a mutation policy to mutate random input peptides into positive presented ones. Using PepPPO, we characterized binding motifs for around 10 000 known human MHC Class I proteins with and without experimental data. These computed motifs demonstrated high similarities with those derived from experimental data. In addition, we found that the motifs could be used for the rapid screening of neoantigens at a much lower time cost than previous deep-learning methods. Availability and implementationThe software can be found in https://github.com/minrq/pMHC. Supplementary informationSupplementary data are available at Bioinformatics online. 

   more » « less
4. Vimo: Visual Analysis of Neuronal Connectivity Motifs

   https://doi.org/10.1101/2022.12.09.519772  

   Troidl, J.; Warchol, S.; Choi, J.; Matelsky, J.; Dhanysai, N.; Wang, X.; Wester, B.; Wei, D.; Lichtman, J.W.; Pfister, H.; et al (January 2023, IEEE transactions on visualization and computer graphics)

   Recent advances in high-resolution connectomics provide researchers access to accurate reconstructions of vast neuronal circuits and brain networks for the first time. Neuroscientists anticipate analyzing these networks to gain a better understanding of information processing in the brain. In particular, scientists are interested in identifying specific network motifs, i.e., repeating subgraphs of the larger brain network that are believed to be neuronal building blocks. To analyze these motifs, it is crucial to review instances of a motif in the brain network and then map the graph structure to the detailed 3D reconstructions of the involved neurons and synapses. We present Vimo, an interactive visual approach to analyze neuronal motifs and motif chains in large brain networks. Experts can sketch network motifs intuitively in a visual interface and specify structural properties of the involved neurons and synapses to query large connectomics datasets. Motif instances (MIs) can be explored in high-resolution 3D renderings of the involved neurons and synapses. To reduce visual clutter and simplify the analysis of MIs, we designed a continuous focus&context metaphor inspired by continuous visual abstractions [MAAB∗18] that allows the user to transition from the highly-detailed rendering of the anatomical structure to views that emphasize the underlying motif structure and synaptic connectivity. Furthermore, Vimo supports the identification of motif chains where a motif is used repeatedly to form a longer synaptic chain. We evaluate Vimo in a user study with seven domain experts and an in-depth case study on motifs in the central complex (CX) of the fruit fly brain. 

   more » « less
5. Using Sequence Analysis to Identify Conversational Motifs in Supportive Interactions

   https://doi.org/10.1177/02654075211066618  

   Solomon, Denise Haunani; Jones, Susanne; Brinberg, Miriam; Bodie, Graham D.; Ram, Nilam (January 2022, Journal of Social and Personal Relationships)

   This study demonstrates how sequence analysis, which is a method for identifying common patterns in categorical time series data, illuminates the nonlinear dynamics of dyadic conversations by describing chains of behavior that shift categorically, rather than incrementally. When applied to interpersonal interactions, sequence analysis supports the identification of conversational motifs, which can be used to test hypotheses linking patterns of interaction to conversational antecedents or outcomes. As an illustrative example, this study evaluated 285 conversations involving stranger, friend, and dating dyads in which one partner, the discloser, communicated about a source of stress to a partner in the role of listener. Using sequence analysis, we identified three five-turn supportive conversational motifs that had also emerged in a previous study of stranger dyads: discloser problem description, discloser problem processing, and listener-focused dialogue. We also observed a new, fourth motif: listener-focused, discloser questioning. Tests of hypotheses linking the prevalence and timing of particular motifs to the problem discloser’s emotional improvement and perceptions of support quality, as moderated by the discloser’s pre-interaction stress, offered a partial replication of previous findings. The discussion highlights the value of using sequence analysis to illuminate dynamic patterns in dyadic interactions. 

   more » « less