We used data sets consisting of miRNA-target gene binding information and expression profiles of miRNAs and mRNAs on human cancer samples. Our method allowed us to detect functionally correlated miRNA-mRNA modules involved in specific biological processes from multiple data sources by using a balanced fitness function and efficient searching over multiple populations. The proposed algorithm found two miRNA-mRNA modules, highly correlated with respect to their expression and biological function. Moreover, the mRNAs included in the same module showed much higher correlations when the related miRNAs were highly expressed, demonstrating our method's ability for finding coherent miRNA-mRNA modules. Most members of these modules have been reported to be closely related with cancer. Consequently, our method can provide a primary source of miRNA and target sets presumed to constitute closely related parts of gene regulatory pathways.

Genetic programming is distinguished from other evolutionary algorithms in that it uses tree representations of variable size instead of linear strings of fixed length. The flexible representation scheme is very important because it allows the underlying structure of the data to be discovered automatically. One primary difficulty, however, is that the solutions may grow too big without any improvement of their generalization ability. In this article we investigate the fundamental relationship between the performance and complexity of the evolved structures. The essence of the parsimony problem is demonstrated empirically by analyzing error landscapes of programs evolved for neural network synthesis. We consider genetic programming as a statistical inference problem and apply the Bayesian model-comparison framework to introduce a class of fitness functions with error and complexity terms. An adaptive learning method is then presented that automatically balances the model-complexity factor to evolve parsimonious programs without losing the diversity of the population needed for achieving the desired training accuracy. The effectiveness of this approach is empirically shown on the induction of sigma-pi neural networks for solving a real-world medical diagnosis problem as well as benchmark tasks.

Question-answering (QA) on video contents is a significant challenge for achieving human-level intelligence as it involves both vision and language in real-world settings. Here we demonstrate the possibility of an AI agent performing video story QA by learning from a large amount of cartoon videos. We develop a video-story learning model, i.e. Deep Embedded Memory Networks (DEMN), to reconstruct stories from a joint scene-dialogue video stream using a latent embedding space of observed data. The video stories are stored in a long-term memory component. For a given question, an LSTM-based attention model uses the long-term memory to recall the best question-story-answer triplet by focusing on specific words containing key information. We trained the DEMN on a novel QA dataset of children's cartoon video series, Pororo. The dataset contains 16,066 scene-dialogue pairs of 20.5-hour videos, 27,328 fine-grained sentences for scene description, and 8,913 story-related QA pairs. Our experimental results show that the DEMN outperforms other QA models. This is mainly due to 1) the reconstruction of video stories in a scene-dialogue combined form that utilize the latent embedding and 2) attention. DEMN also achieved state-of-the-art results on the MovieQA benchmark.

Abstract-DNA computing relies on biochemical reactions of DNA molecules and may result in incorrect or undesirable computations. Therefore, much work has focused on designing the DNA sequences to make the molecular computation more reliable. Sequence design involves with a number of heterogeneous and conflicting design criteria and traditional optimization methods may face difficulties. In this paper, we formulate the DNA sequence design as a multiobjective optimization problem and solve it using a constrained multiobjective evolutionary algorithm (EA). The method is implemented into the DNA sequence design system, NACST/Seq, with a suite of sequence-analysis tools to help choose the best solutions among many alternatives. The performance of NACST/Seq is compared with other sequence design methods, and analyzed on a traveling salesman problem solved by bio-lab experiments. Our experimental results show that the evolutionary sequence design by NACST/Seq outperforms in its reliability the existing sequence design techniques such as conventional EAs, simulated annealing, and specialized heuristic methods.Index Terms-DNA computing, DNA sequence design, multiobjective evolutionary algorithm (MOEA), nucleic acid computing simulation toolkit/sequence generator (NACST/Seq).

We proposed an optimal deep learning architecture and its parameters for stress recognition, and the theoretical consideration on how to design the deep learning structure based on the periodic patterns of the raw ECG data. Experimental results in this study have proved that the proposed deep learning model, the Deep ECGNet, is an optimal structure to recognize the stress conditions using ultra short-term ECG data.

We introduce a DNA encoding method to represent numerical values and a biased molecular algorithm based on the thermodynamic properties of DNA. DNA strands are designed to encode real values by variation of their melting temperatures. The thermodynamic properties of DNA are used for effective local search of optimal solutions using biochemical techniques, such as denaturation temperature gradient polymerase chain reaction and temperature gradient gel electrophoresis. The proposed method was successfully applied to the traveling salesman problem, an instance of optimization problems on weighted graphs. This work extends the capability of DNA computing to solving numerical optimization problems, which is contrasted with other DNA computing methods focusing on logical problem solving.

We present a novel active mixing method in a microfluidic chip, where the controlled stirring of magnetic particles is used to achieve an effective mixing of fluids. To perform mixing, the ferromagnetic particles were embedded and manipulated under the influence of a rotating magnetic field. By aligning the magnetic beads along the magnetic field lines, rod-like structures are formed, functioning as small stir bars. Under higher flow conditions the particles did not form the typical rod structure but rather formed aggregates, which were even more beneficial for mixing. Our system reached a 96% mixing efficiency in a relatively short distance (800 microm) at a flow rate of 1.2-4.8 mm/s. These results demonstrate that our mixing method is useful for microfluidic devices with low aspect ratios and molecules with large molecular weights.

We propose a new representation named S-trees for both the structural and dynamical modeling of a biochemical network within a unified scheme. We further present S-tree based genetic programming to identify the structure of a biochemical network and to estimate the corresponding parameter values at the same time. While other evolutionary algorithms require additional techniques for sparse structure identification, our approach can automatically assemble the sparse primitives of a biochemical network in an efficient way. We evaluate our algorithm on the dynamic profiles of an artificial genetic network. In 20 trials for four settings, we obtain the true structure and their relative squared errors are <5% regardless of releasing constraints about structural sparseness. In addition, we confirm that the proposed algorithm is robust within +/-10% noise ratio. Furthermore, the proposed approach ensures a reasonable estimate of a real yeast fermentation pathway. The comparatively less important connections with non-zero parameters can be detected even though their orders are below 10(-2). To demonstrate the usefulness of the proposed algorithm for real experimental biological data, we provide an additional example on the transcriptional network of SOS response to DNA damage in Escherichia coli. We confirm that the proposed algorithm can successfully identify the true structure except only one relation.