In the field of robotics, researches have sought to control robots capable of dealing with a variety of environments and tasks generically, through the use of foundation models. Among these, the systems for robot behavior planning utilizing video have also been proposed. The system enables the generation of robot behaviors that are not dependent on specific environments or tasks. This is achieved by generating videos based on text input, which utilizes the vast knowledge inherent in the foundation models. Also, by using a visual interface such as video, it is possible to confirm the behavioral indicators on which the robot is operating. Although, there are few examples of research on robot behavior planning utilizing video. Previous studies have emphasized the verification of behavior generation utilizing video, with simplified object manipulation for testing on simulations. This is not enough to demonstrate the usefulness of robot behavior planning utilizing video in real-world environments. In addition, the systems from previous studies are not open, and such systems have not been sufficiently discussed. This paper attempts to construct robot behavior planning utilizing video as an open system, and to verify the validity of the behavior planning using actual machines. In this paper, we first focus on using Robotis's TURTLEBOT3 Waffle Pi and Mobile Manipulator(referred to as "Waffle") to construct robot behavior planning system utilizing video. Second, we create planning videos targeting the pick-and-place motion using the proposed system, and control the arm part of Waffle in the actual machine verification. Finally, by comparing the target coordinates from the planning video with the coordinates observed from the actual machine, we can confirm whether it is possible to control Waffle as planned. Errors are calculated from the coordinate comparison, and the control is performed again. Based on the results, we verify whether the proposed system is useful for controlling robots in real-world environments.

A system is expected to facilitate coordination among multiple construction machines or robots, enabling them to adaptively perform various tasks in disaster sites and unknown environments. Prior research has generally adopted a model-based approach to designing cooperative behavior. However, it is difficult to adapt to environments and scenarios that cannot be predicted by the model. In recent years, it has been reported that a robot equipped with foundation models can adapt to unknown (open) environments and unpredictable situations. However, there has been little discussion on foundation models for multiple robot systems; a flow that cooperatively handles unexpected events does not exist. In this paper, we propose the system flow that enables multiple robots to adaptively coordinate to unforeseen scenarios based on the functional expressions of each other and environment understanding utilizing GPT-4 and GPT-4V. Through experimentation, we verify that the proposed flow is able to adapt to an unforeseen environment, particularly path obstruction via robot experiments. Furthermore, we examine the validity of the proposed flow by varying the robots’ functional expressions and sensor information for the environment.

RNA structural elements called pseudoknots are involved in various biological phenomena including ribosomal frameshifts. Because it is infeasible to construct an efficiently computable secondary structure model including pseudoknots, secondary structure prediction methods considering pseudoknots are not yet widely available. We developed IPknot, which uses heuristics to speed up computations, but it has remained difficult to apply it to long sequences, such as messenger RNA and viral RNA, because it requires cubic computational time with respect to sequence length and has threshold parameters that need to be manually adjusted. Here, we propose an improvement of IPknot that enables calculation in linear time by employing the LinearPartition model and automatically selects the optimal threshold parameters based on the pseudo-expected accuracy. In addition, IPknot showed favorable prediction accuracy across a wide range of conditions in our exhaustive benchmarking, not only for single sequences but also for multiple alignments.

The control performance of a propeller propulsion system depends on its rotor thrust control performance. When a rotor thrust controller that includes a constant-thrust-coefficient model is utilized, rotor thrust response sometimes does not track rotor thrust command. This paper, therefore, proposes a novel rotor thrust controller whose thrust coefficient is a function of airspeed and rotor angular velocity. The validity of the proposed controller is verified by simulation and experiment.

MOTIVATION: Genetic variant calling with high-throughput sequencing data has been recognized as a useful tool for better understanding of disease mechanism and detection of potential off-target sites in genome editing. Since most of the variant calling algorithms rely on initial mapping onto a reference genome and tend to predict many variant candidates, variant calling remains challenging in terms of predicting variants with low false positives. RESULTS: Here we present Bivartect, a simple yet versatile variant caller based on direct comparison of short sequence reads between normal and mutated samples. Bivartect can detect not only single nucleotide variants but also insertions/deletions, inversions and their complexes. Bivartect achieves high predictive performance with an elaborate memory-saving mechanism, which allows Bivartect to run on a computer with a single node for analyzing small omics data. Tests with simulated benchmark and real genome-editing data indicate that Bivartect was comparable to state-of-the-art variant callers in positive predictive value for detection of single nucleotide variants, even though it yielded a substantially small number of candidates. These results suggest that Bivartect, a reference-free approach, will contribute to the identification of germline mutations as well as off-target sites introduced during genome editing with high accuracy. AVAILABILITY AND IMPLEMENTATION: Bivartect is implemented in C++ and available along with in silico simulated data at https://github.com/ykat0/bivartect. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: RNA-RNA interactions via base pairing play a vital role in the post-transcriptional regulation of gene expression. Efficient identification of targets for such regulatory RNAs needs not only discriminative power for positive and negative RNA-RNA interacting sequence data but also accurate prediction of interaction sites from positive data. Recently, a few studies have incorporated interaction site accessibility into their prediction methods, indicating the enhancement of predictive performance on limited positive data. RESULTS: Here we show the efficacy of our accessibility-based prediction model RactIPAce on newly compiled datasets. The first experiment in interaction site prediction shows that RactIPAce achieves the best predictive performance on the newly compiled dataset of experimentally verified interactions in the literature as compared with the state-of-the-art methods. In addition, the second experiment in discrimination between positive and negative interacting pairs reveals that the combination of accessibility-based methods including our approach can be effective to discern real interacting RNAs. Taking these into account, our prediction model can be effective to predict interaction sites after screening for real interacting RNAs, which will boost the functional analysis of regulatory RNAs. AVAILABILITY AND IMPLEMENTATION: The program RactIPAce along with data used in this work is available at https://github.com/satoken/ractip/releases/tag/v1.0.1 CONTACT: : [email protected] or [email protected] information: Supplementary data are available at Bioinformatics online.

MOTIVATION: It is well known that the accuracy of RNA secondary structure prediction from a single sequence is limited, and thus a comparative approach that predicts a common secondary structure from aligned sequences is a better choice if homologous sequences with reliable alignments are available. However, correct secondary structure information is needed to produce reliable alignments of RNA sequences. To tackle this dilemma, we require a fast and accurate aligner that takes structural information into consideration to yield reliable structural alignments, which are suitable for common secondary structure prediction. RESULTS: We develop DAFS, a novel algorithm that simultaneously aligns and folds RNA sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment. DAFS decomposes the pairwise structural alignment problem into two independent secondary structure prediction problems and one pairwise (non-structural) alignment problem by the dual decomposition technique, and maintains the consistency of a pairwise structural alignment by imposing penalties on inconsistent base pairs and alignment columns that are iteratively updated. Furthermore, we extend DAFS to consider pseudoknots in RNA structural alignments by integrating IPknot for predicting a pseudoknotted structure. The experiments on publicly available datasets showed that DAFS can produce reliable structural alignments from unaligned sequences in terms of accuracy of common secondary structure prediction.

MOTIVATION: Pseudoknots found in secondary structures of a number of functional RNAs play various roles in biological processes. Recent methods for predicting RNA secondary structures cover certain classes of pseudoknotted structures, but only a few of them achieve satisfying predictions in terms of both speed and accuracy. RESULTS: We propose IPknot, a novel computational method for predicting RNA secondary structures with pseudoknots based on maximizing expected accuracy of a predicted structure. IPknot decomposes a pseudoknotted structure into a set of pseudoknot-free substructures and approximates a base-pairing probability distribution that considers pseudoknots, leading to the capability of modeling a wide class of pseudoknots and running quite fast. In addition, we propose a heuristic algorithm for refining base-paring probabilities to improve the prediction accuracy of IPknot. The problem of maximizing expected accuracy is solved by using integer programming with threshold cut. We also extend IPknot so that it can predict the consensus secondary structure with pseudoknots when a multiple sequence alignment is given. IPknot is validated through extensive experiments on various datasets, showing that IPknot achieves better prediction accuracy and faster running time as compared with several competitive prediction methods. AVAILABILITY: The program of IPknot is available at http://www.ncrna.org/software/ipknot/. IPknot is also available as a web server at http://rna.naist.jp/ipknot/. CONTACT: [email protected]; [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets of non-coding small RNAs that regulate gene expression post-transcriptionally. A number of computational studies have so far been devoted to predicting joint secondary structures or binding sites under a specific class of interactions. In general, there is a trade-off between range of interaction type and efficiency of a prediction algorithm, and thus efficient computational methods for predicting comprehensive type of interaction are still awaited. RESULTS: We present RactIP, a fast and accurate prediction method for RNA-RNA interaction of general type using integer programming. RactIP can integrate approximate information on an ensemble of equilibrium joint structures into the objective function of integer programming using posterior internal and external base-paring probabilities. Experimental results on real interaction data show that prediction accuracy of RactIP is at least comparable to that of several state-of-the-art methods for RNA-RNA interaction prediction. Moreover, we demonstrate that RactIP can run incomparably faster than competitive methods for predicting joint secondary structures. AVAILABILITY: RactIP is implemented in C++, and the source code is available at http://www.ncrna.org/software/ractip/.

BACKGROUND: RNA secondary structure prediction is one major task in bioinformatics, and various computational methods have been proposed so far. Pseudoknot is one of the typical substructures appearing in several RNAs, and plays an important role in some biological processes. Prediction of RNA secondary structure with pseudoknots is still challenging since the problem is NP-hard when arbitrary pseudoknots are taken into consideration. RESULTS: We introduce a new method of predicting RNA secondary structure with pseudoknots based on integer programming. In our formulation, we aim at minimizing the value of the objective function that reflects free energy of a folding structure of an input RNA sequence. We focus on a practical class of pseudoknots by setting constraints appropriately. Experimental results for a set of real RNA sequences show that our proposed method outperforms several existing methods in sensitivity. Furthermore, for a set of sequences of small length, our approach achieved good performance in both sensitivity and specificity. CONCLUSION: Our integer programming-based approach for RNA structure prediction is flexible and extensible.