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Abstract Assessing fertilized human embryos is crucial for in vitro fertilization, a task being revolutionized by artificial intelligence. Existing models used for embryo quality assessment and ploidy detection could be significantly improved by effectively utilizing time-lapse imaging to identify critical developmental time points for maximizing prediction accuracy. Addressing this, we develop and compare various embryo ploidy status prediction models across distinct embryo development stages. We present BELA, a state-of-the-art ploidy prediction model that surpasses previous image- and video-based models without necessitating input from embryologists. BELA uses multitask learning to predict quality scores that are thereafter used to predict ploidy status. By achieving an area under the receiver operating characteristic curve of 0.76 for discriminating between euploidy and aneuploidy embryos on the Weill Cornell dataset, BELA matches the performance of models trained on embryologists’ manual scores. While not a replacement for preimplantation genetic testing for aneuploidy, BELA exemplifies how such models can streamline the embryo evaluation process.

Abstract Synthetic long read sequencing techniques such as UST’s TELL-Seq and Loop Genomics’ LoopSeq combine 3 $$'$$ ′ barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of base-pairs. However, the lack of a 1:1 correspondence between a long fragment and a 3 $$'$$ ′ unique molecular identifier confounds the assignment of linkage between short reads. We introduce Ariadne, a novel assembly graph-based synthetic long read deconvolution algorithm, that can be used to extract single-species read-clouds from synthetic long read datasets to improve the taxonomic classification and de novo assembly of complex populations, such as metagenomes.

Abstract The annual Genome Informatics conference was held at the Wellcome Genome Campus on September 21–23, 2022. The conference covered a remarkable range of topics of which we highlight a few in this report.

Here, using clinical samples and autopsy tissues, the authors combine fast-colorimetric test (LAMP) for SARS-CoV-2 infection and large-scale shotgun metatranscriptomics for host, viral, and microbial profiling and provide a map of the viral genetic features of the New York City outbreak and associate specific host responses and gene expression perturbations with SARS-CoV-2 infection.

Summary: Background: Estimating tumor purity is especially important in the age of precision medicine. Purity estimates have been shown to be critical for correction of tumor sequencing results, and higher purity samples allow for more accurate interpretations from next-generation sequencing results. Molecular-based purity estimates using computational approaches require sequencing of tumors, which is both time-consuming and expensive. Methods: Here we propose an approach, weakly-supervised purity (wsPurity), which can accurately quantify tumor purity within a digitally captured hematoxylin and eosin (H&E) stained histological slide, using several types of cancer from The Cancer Genome Atlas (TCGA) as a proof-of-concept. Findings: Our model predicts cancer type with high accuracy on unseen cancer slides from TCGA and shows promising generalizability to unseen data from an external cohort (F1-score of 0.83 for prostate adenocarcinoma). In addition we compare performance of our model on tumor purity prediction with a comparable fully-supervised approach on our TCGA held-out cohort and show our model has improved performance, as well as generalizability to unseen frozen slides (0.1543 MAE on an independent test cohort). In addition to tumor purity prediction, our approach identified high resolution tumor regions within a slide, and can also be used to stratify tumors into high and low tumor purity, using different cancer-dependent thresholds. Interpretation: Overall, we demonstrate our deep learning model's different capabilities to analyze tumor H&E sections. We show our model is generalizable to unseen H&E stained slides from data from TCGA as well as data processed at Weill Cornell Medicine. Funding: Starr Cancer Consortium Grant (SCC I15-0027) to Iman Hajirasouliha.

Abstract Background Cancer progression reconstruction is an important development stemming from the phylogenetics field. In this context, the reconstruction of the phylogeny representing the evolutionary history presents some peculiar aspects that depend on the technology used to obtain the data to analyze: Single Cell DNA Sequencing data have great specificity, but are affected by moderate false negative and missing value rates. Moreover, there has been some recent evidence of back mutations in cancer: this phenomenon is currently widely ignored. Results We present a new tool, gpps, that reconstructs a tumor phylogeny from Single Cell Sequencing data, allowing each mutation to be lost at most a fixed number of times. The General Parsimony Phylogeny from Single cell (gpps) tool is open source and available at https://github.com/AlgoLab/gpps . Conclusions gpps provides new insights to the analysis of intra-tumor heterogeneity by proposing a new progression model to the field of cancer phylogeny reconstruction on Single Cell data.

Abstract Most existing methods for structural variant detection focus on discovery and genotyping of deletions, insertions, and mobile elements. Detection of balanced structural variants with no gain or loss of genomic segments, for example, inversions and translocations, is a particularly challenging task. Furthermore, there are very few algorithms to predict the insertion locus of large interspersed segmental duplications and characterize translocations. Here, we propose novel algorithms to characterize large interspersed segmental duplications, inversions, deletions, and translocations using linked-read sequencing data. We redesign our earlier algorithm, VALOR, and implement our new algorithms in a new software package, called VALOR2.

OBJECTIVES/GOALS: To develop a two-staged convolutional neural network to identify the ovary and antral follicles within ovarian ultrasound images and determine its reliability and feasibility compared to conventional techniques in 2D and 3D ultrasonography image analysis. METHODS/STUDY POPULATION: De-identified and archived ultrasonographic images of women across the reproductive spectrum (N=500) will be used in the study. These ultrasound images will be labeled by experienced raters to train a two-staged convolutional neural network (CU-Net). CU-Net will first separate the entire ovary from the background and subsequently identify all antral follicles within the ovary. Following training, the CU-Net will evaluate a second set of independent images (N=100) to determine performance accuracy. Three specialized raters will establish the reliability and feasibility of CU-Net compared to conventional 2D and 3D ovarian ultrasound image analysis methods. RESULTS/ANTICIPATED RESULTS: The labeled training dataset of ovarian ultrasound images is expected to successfully train the CU-Net and allow for accurate identification of the ovary and the total number of antral follicles in the second testing set of ultrasound images. When compared to conventional 2D and 3D ultrasound image analysis methods, CU-Net is expected to have similar accuracy when compared to the gold-standard method (2D-Offline with Grid) and outperform other approaches, such as 2D-Real Time and 3D volume software (VOCAL and Sono-AVC). However, CU-Net is anticipated to be the fastest and most reliable method across users, supporting its clinical feasibility. DISCUSSION/SIGNIFICANCE: This study will immediately translate to providing a standardized platform that can improve the accuracy, reliability, and time demand required for the evaluation of ovarian ultrasounds across users and clinical and research settings.

Abstract Background Intra-tumor heterogeneity is known to contribute to cancer complexity and drug resistance. Understanding the number of distinct subclones and the evolutionary relationships between them is scientifically and clinically very important and still a challenging problem. Results In this paper, we present BAMSE (BAyesian Model Selection for tumor Evolution), a new probabilistic method for inferring subclonal history and lineage tree reconstruction of heterogeneous tumor samples. BAMSE uses somatic mutation read counts as input and can leverage multiple tumor samples accurately and efficiently. In the first step, possible clusterings of mutations into subclones are scored and a user defined number are selected for further analysis. In the next step, for each of these candidates, a list of trees describing the evolutionary relationships between the subclones is generated. These trees are sorted by their posterior probability. The posterior probability is calculated using a Bayesian model that integrates prior belief about the number of subclones, the composition of the tumor and the process of subclonal evolution. BAMSE also takes the sequencing error into account. We benchmarked BAMSE against state of the art software using simulated datasets. Conclusions In this work we developed a flexible and fast software to reconstruct the history of a tumor’s subclonal evolution using somatic mutation read counts across multiple samples. BAMSE software is implemented in Python and is available open source under GNU GLPv3 at https://github.com/HoseinT/BAMSE.

Abstract The 19th Annual Advances in Genome Biology and Technology (AGBT) meeting came back to Marco Island, Florida, and was held in the renovated venue from 27 February to 2 March 2019. The meeting showed a variety of new technology, both in wet lab and in bioinformatics. This year’s themes included single-cell technology and applications, spatially resolved gene expression measurements, new sequencing platforms, genome assembly and variation, and long and linked reads.

Pathological evaluation of tumor tissue is pivotal for diagnosis in cancer patients and automated image analysis approaches have great potential to increase precision of diagnosis and help reduce human error. In this study, we utilize several computational methods based on convolutional neural networks (CNN) and build a stand-alone pipeline to effectively classify different histopathology images across different types of cancer. In particular, we demonstrate the utility of our pipeline to discriminate between two subtypes of lung cancer, four biomarkers of bladder cancer, and five biomarkers of breast cancer. In addition, we apply our pipeline to discriminate among four immunohistochemistry (IHC) staining scores of bladder and breast cancers. Our classification pipeline includes a basic CNN architecture, Google's Inceptions with three training strategies, and an ensemble of two state-of-the-art algorithms, Inception and ResNet. Training strategies include training the last layer of Google's Inceptions, training the network from scratch, and fine-tunning the parameters for our data using two pre-trained version of Google's Inception architectures, Inception-V1 and Inception-V3. We demonstrate the power of deep learning approaches for identifying cancer subtypes, and the robustness of Google's Inceptions even in presence of extensive tumor heterogeneity. On average, our pipeline achieved accuracies of 100%, 92%, 95%, and 69% for discrimination of various cancer tissues, subtypes, biomarkers, and scores, respectively. Our pipeline and related documentation is freely available at https://github.com/ih-_lab/CNN_Smoothie.

Architectural heritage is continuously exposed to natural disasters, such as strong earthquakes and this highlights the importance of reducing their vulnerability. While it is not possible to simultaneously strengthen all architectural heritage structures due to the limited skilled labour and budget restrictions, different buildings may need different treatments due to differences in exposure to seismic hazard, relative importance and vulnerability. Therefore, there is a need for a decision making strategy to find optimized solutions to achieve the highest possible stability and benefits. The primary objective of this research is to develop a practical step-by-step decision making process for the planning and prioritization of interventions in architectural heritage structures based on the level of seismic hazard, vulnerability and condition assessment, available preservation and strengthening techniques, compatibility with conservation ethics, available budget and expected benefits in various time schedules. The proposed methodology, is shown by diagram and mathematical formulae, and is demonstrated through a case study example.

Modified Augmented Lagrangian Genetic Algorithm (ALGA) and Quadratic Penalty Function Genetic Algo­rithm (QPGA) optimization methods are proposed to obtain truss structures with minimum structural weight using both continuous and discrete design variables. To achieve robust solutions, Compressed Sparse Row (CSR) with reordering of Cholesky factorization and Moore Penrose Pseudoinverse are used in case of non-singular and singular stiffness matrix, respectively. The efficiency of the proposed nonlinear optimization methods is demonstrated on several practical exam­ples. The results obtained from the Pratt truss bridge show that the optimum design solution using discrete parameters is 21% lighter than the traditional design with uniform cross sections. Similarly, the results obtained from the 57-bar planar tower truss indicate that the proposed design method using continuous and discrete design parameters can be up to 29% and 9% lighter than traditional design solutions, respectively. Through sensitivity analysis, it is shown that the proposed methodology is robust and leads to significant improvements in convergence rates, which should prove useful in large-scale applications. First published online: 12 Feb 2016

BACKGROUND: Non-coding RNAs (ncRNAs) have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that can identify micro RNAs. METHODOLOGY/PRINCIPAL FINDINGS: We present a very general ab initio ncRNA gene finder that exploits differential distributions of sequence motifs between ncRNAs and background genome sequences. CONCLUSIONS/SIGNIFICANCE: Our method, once trained on a set of ncRNAs from a given species, can be applied to a genome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentially belong to novel (and perhaps unknown) ncRNA families. AVAILABILITY: (http://compbio.cs.sfu.ca/taverna/smyrna).