Flowering in cassava is crucial for generation of botanical seed for breeding. However, most farmer preferred genotypes are poor at flowering, exhibit great disparity in time and amount of flowering or never flower. To elucidate the genetic basis of such a flowering behaviour, 293 diverse cassava accessions were evaluated for flowering traits under two locations and seasons in Uganda. Genotyping by the Diversity Array Technology Pty Ltd. (DArTseq) platform identified 24,040 single-nucleotide polymorphisms (SNPs) distributed on the 18 cassava chromosomes. Population structure analysis using principal components (PC) and kinships showed clustering, the first five PCs accounted for 49.2% of the observed genetic variation. Linkage disequilibrium (LD) estimation was averagely 0.32 at a distance of ~2850kb (kilo base pairs). Polymorphism information content (PIC) and minor allele frequency (MAF) were 0.25 and 0.23, respectively. Genome-wide association study (GWAS) analysis uncovered 53 significant marker-trait associations (MTA) with flowering traits involving 27 loci. Two loci, SNPs S5_29309724 and S15_11747301 were associated with all the flowering traits. Using five of the 27 SNPs with Phenotype_Variance_Explained (PVE) ≥ 5%, 37 candidate genes were identified in the peak SNP sites located within 50kb upstream or downstream, most were associated with branching traits. Eight of the genes, orthologous to Arabidopsis and other plant species, had known functional annotations related to flowering, e.g. eukaryotic translation initiation factor and myb family transcription factor. This study identified genomic regions associated with flowering in cassava, the identified SNPs could be useful in marker-assisted selection to overcome hybridization challenges like unsynchronized flowering, and candidate gene validation.

Development of supervised AI algorithms requires a large amount of labeled images. Image labelling is both time-consuming and expensive. Therefore, we explored the value of e-learning derived annotations for AI algorithm development in medical imaging. Methods We have developed an e-learning platform that involves image-based single click labelling as part of the educational learning process. Ten radiology residents, as part of their residency training, trained the recognition of pneumothorax on 1161 chest X-rays in posterior-anterior projection. Using this data, multiple AI algorithms for detecting pneumothorax were developed. Classification and localization performance of the models was tested on an independent internal testing dataset and on the public NIH ChestX-ray14 dataset. Results The AI models F1 scores on the internal and the NIH dataset were 0.87 and 0.44, respectively. Sensitivity was 0.85 and 0.80 for classification and specificity 0.96 and 0.48 for classification. F1 scores were 0.72 and 0.66, sensitivity 0.72 and 0.72. False positive rate was 0.36 and 0.32 for localisation. Conclusion Our results demonstrated that e-learning derived annotations are a valuable data source for algorithm development. Further work is needed to include additional parameters such as user performance, consensus of diagnosis, and quality control in the development pipeline.

Annotating training data is a time consuming and labor intensive process in deep learning, especially for images with many objects present. In this paper, we propose a method to allow deep networks to be trained on data with reduced numbers of annotations (per image) in heatmap regression tasks (e.g. object detection and counting), by applying an asymmetric loss function. In a real scenario, this reduction of annotations can be imposed by the researchers (e.g. ask the annotators to label only 50% of what they see in each image), or can potentially counteract unintentionally missing labels from the annotators. To demonstrate the effectiveness of our method, we conduct experiments in two domains, crowd counting and wheat spikelet detection, using different deep network architecture. We drop various percentages of instance annotations per image in training. Results show that an asymmetric loss function is effective across different models and datasets, even in very extreme cases with limited annotations provided (e.g. 90% of the original annotations reduced). Whilst tuning of the key parameters are required, we find that setting conservative parameter values can help more realistic situations, where only small amounts of data have been missed by annotators.

Traditional gene set enrichment analysis falters when applied to large genomic domains, where neighboring genes often share functions. This spatial dependency creates misleading enrichments, mistaking mere physical proximity for genuine biological connections. Here we present Spatial Adjusted Gene Ontology (SAGO), a novel cyclic permutation-based approach, to tackle this challenge. SAGO separates enrichments due to spatial proximity from genuine biological links by incorporating the genes' spatial arrangement into the analysis. We applied SAGO to various datasets in which the identified genomic intervals are large, including replication timing domains, H3K9me3 and H3K27me3 large domains, HiC compartments and lamina associated domains (LADs). Intriguingly, applying SAGO to prostate cancer samples with large copy number alteration (CNAs) domains eliminated most of the enriched GO terms, thus helping to accurately identify biologically relevant gene sets linked to oncogenic processes, free from spatial bias.

The detection and recognition of tables in image-based documents is a challenging and essential task for automated data extraction and anal- ysis. This paper introduces a methodology that utilizes Convolutional Neural Networks (CNNs) to address this problem. By harnessing the ro- bust visual recognition abilities of CNNs, the proposed method effectively detects and extracts tables from image-based documents. Additionally, an Encoder-Dual Decoder (EDD) architecture is employed to extract the textual content from table cells, enabling the transformation of visual data into structured, machine-readable formats. This structured data is then further processed using a Vector Space Model (VSM)-based language modeling technique for query-based table retrieval. The methodology’s accuracy is assessed by analyzing the spatial relationships between the extracted cells and comparing them against a pre-defined table structure. The results provide an evidence to the effectiveness of the proposed ap- proach, with an impressive 85% accuracy rate and a corresponding error rate of 15%. This accurate extraction and recognition of tables from image-based documents can significantly enhance applications in data analysis, information retrieval, and knowledge extraction.