Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph

Background Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount of gaps. To fill these gaps, a feasible way is to search genome assembly graph for the best-matching contig paths that connect boundary contigs of gaps. The combination of searching and evaluation procedures might be “searching followed by evaluation”, which is infeasible for long gaps, or “searching by evaluation”, which heavily relies on heuristics and thus usually yields unreliable contig paths. Results We here report an accurate and efficient approach to filling gaps of genome scaffolds with aids of optical maps. Using simulated data from 12 species and real data from 3 species, we demonstrate the successful application of our approach in gap filling with improved accuracy and completeness of genome scaffolds. Conclusion Our approach applies a sequential Bayesian updating technique to measure the similarity between optical maps and candidate contig paths. Using this similarity to guide path searching, our approach achieves higher accuracy than the existing “searching by evaluation” strategy that relies on heuristics. Furthermore, unlike the “searching followed by evaluation” strategy enumerating all possible paths, our approach prunes the unlikely sub-paths and extends the highly-probable ones only, thus significantly increasing searching efficiency.

Reliable Memory Model for Visual Tracking

Effectively learning the appearance change of a target is the key point of an online tracker. When occlusion and misalignment occur, the tracking results usually contain a great amount of background information, which heavily affects the ability of a tracker to distinguish between targets and backgrounds, eventually leading to tracking failure. To solve this problem, we propose a simple and robust reliable memory model. In particular, an adaptive evaluation strategy (AES) is proposed to assess the reliability of tracking results. AES combines the confidence of the tracker predictions and the similarity distance, which is between the current predicted result and the existing tracking results. Based on the reliable results of AES selection, we designed an active–frozen memory model to store reliable results. Training samples stored in active memory are used to update the tracker, while frozen memory temporarily stores inactive samples. The active–frozen memory model maintains the diversity of samples while satisfying the limitation of storage. We performed comprehensive experiments on five benchmarks: OTB-2013, OTB-2015, UAV123, Temple-color-128, and VOT2016. The experimental results show that our tracker achieves state-of-the-art performance.

A bioinspired neural architecture search based convolutional neural network for breast cancer detection using histopathology images

The design of neural architecture to address the challenge of detecting abnormalities in histopathology images can leverage the gains made in the field of neural architecture search (NAS). The NAS model consists of a search space, search strategy and evaluation strategy. The approach supports the automation of deep learning (DL) based networks such as convolutional neural networks (CNN). Automating the process of CNN architecture engineering using this approach allows for finding the best performing network for learning classification problems in specific domains and datasets. However, the engineering process of NAS is often limited by the potential solutions in search space and the search strategy. This problem often narrows the possibility of obtaining best performing networks for challenging tasks such as the classification of breast cancer in digital histopathological samples. This study proposes a NAS model with a novel search space initialization algorithm and a new search strategy. We designed a block-based stochastic categorical-to-binary (BSCB) algorithm for generating potential CNN solutions into the search space. Also, we applied and investigated the performance of a new bioinspired optimization algorithm, namely the Ebola optimization search algorithm (EOSA), for the search strategy. The evaluation strategy was achieved through computation of loss function, architectural latency and accuracy. The results obtained using images from the BACH and BreakHis databases showed that our approach obtained best performing architectures with the top-5 of the architectures yielding a significant detection rate. The top-1 CNN architecture demonstrated a state-of-the-art performance of base on classification accuracy. The NAS strategy applied in this study and the resulting candidate architecture provides researchers with the most appropriate or suitable network configuration for using digital histopathology.

New interinstitutional, multimodal presurgical evaluation protocol associated with improved seizure freedom for poorly defined cases of focal epilepsy in children

OBJECTIVE In an attempt to improve postsurgical seizure outcomes for poorly defined cases (PDCs) of pediatric focal epilepsy (i.e., those that are not visible or well defined on 3T MRI), the authors modified their presurgical evaluation strategy. Instead of relying on concordance between video-electroencephalography and 3T MRI and using functional imaging and intracranial recording in select cases, the authors systematically used a multimodal, 3-tiered investigation protocol that also involved new collaborations between their hospital, the Montreal Children’s Hospital, and the Montreal Neurological Institute. In this study, the authors examined how their new strategy has impacted postsurgical outcomes. They hypothesized that it would improve postsurgical seizure outcomes, with the added benefit of identifying a subset of tests contributing the most. METHODS Chart review was performed for children with PDCs who underwent resection following the new strategy (i.e., new protocol [NP]), and for the same number who underwent treatment previously (i.e., preprotocol [PP]); ≥ 1-year follow-up was required for inclusion. Well-defined, multifocal, and diffuse hemispheric cases were excluded. Preoperative demographics and clinical characteristics, resection volumes, and pathology, as well as seizure outcomes (Engel class Ia vs > Ia) at 1 year postsurgery and last follow-up were reviewed. RESULTS Twenty-two consecutive NP patients were compared with 22 PP patients. There was no difference between the two groups for resection volumes, pathology, or preoperative characteristics, except that the NP group underwent more presurgical evaluation tests (p < 0.001). At 1 year postsurgery, 20 of 22 NP patients and 10 of 22 PP patients were seizure free (OR 11.81, 95% CI 2.00–69.68; p = 0.006). Magnetoencephalography and PET/MRI were associated with improved postsurgical seizure outcomes, but both were highly correlated with the protocol group (i.e., independent test effects could not be demonstrated). CONCLUSIONS A new presurgical evaluation strategy for children with PDCs of focal epilepsy led to improved postsurgical seizure freedom. No individual presurgical evaluation test was independently associated with improved outcome, suggesting that it may be the combined systematic protocol and new interinstitutional collaborations that makes the difference rather than any individual test.