Search results for: word memorization

Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

Abstract:

Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: Metagenomics, phenotype prediction, deep learning, embeddings, multiple instance learning.

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Authors: S. Jamshidi, E. Feizi Ashtiani, M. Ardestani

Abstract:

Waste Load Allocation (WLA) strategies usually intend to find economic policies for water resource management. Water quality trading (WQT) is an approach that uses discharge permit market to reduce total environmental protection costs. This primarily requires assigning discharge limits known as total maximum daily loads (TMDLs). These are determined by monitoring organizations with respect to the receiving water quality and remediation capabilities. The purpose of this study is to compare two approaches of TMDL assignment for WQT policy in small catchment area of Haraz River, in north of Iran. At first, TMDLs are assigned uniformly for the whole point sources to keep the concentrations of BOD and dissolved oxygen (DO) at the standard level at checkpoint (terminus point). This was simply simulated and controlled by Qual2kw software. In the second scenario, TMDLs are assigned using multi objective particle swarm optimization (MOPSO) method in which the environmental violation at river basin and total treatment costs are minimized simultaneously. In both scenarios, the equity index and the WLA based on trading discharge permits (TDP) are calculated. The comparative results showed that using economically optimized TMDLs (2nd scenario) has slightly more cost savings rather than uniform TMDL approach (1st scenario). The former annually costs about 1 M$ while the latter is 1.15 M$. WQT can decrease these annual costs to 0.9 and 1.1 M$, respectively. In other word, these approaches may save 35 and 45% economically in comparison with command and control policy. It means that using multi objective decision support systems (DSS) may find more economical WLA, however its outcome is not necessarily significant in comparison with uniform TMDLs. This may be due to the similar impact factors of dischargers in small catchments. Conversely, using uniform TMDLs for WQT brings more equity that makes stakeholders not feel that much envious of difference between TMDL and WQT allocation. In addition, for this case, determination of TMDLs uniformly would be much easier for monitoring. Consequently, uniform TMDL for TDP market is recommended as a sustainable approach. However, economical TMDLs can be used for larger watersheds.

Keywords: Waste load allocation (WLA), Water quality trading (WQT), Total maximum daily loads (TMDLs), Haraz River, Multi objective particle swarm optimization (MOPSO), Equity.

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Authors: M. Garcia-Alsina, J. Cobarsí

Abstract:

The role of controlled vocabularies in information retrieval is broadly recognized as a relevant feature. Besides, there is a standing demand that editors and databases should consider the effective introduction of controlled vocabularies in their procedures to index scientific literature. That is especially important because information retrieval is pointed out as a significant point to drive systematic literature review. Hence, a first question emerges: Are the controlled vocabularies at this moment considered? On the other hand, subject searching in the catalogs is complex mainly due to the dichotomy between keywords from authors versus keywords based on controlled vocabularies. Finally, there is some demand to unify the terminology related to health to make easier the medical history exploitation and research. Considering these features, this paper focuses on controlled vocabularies related to the health field and their role for storing, classifying, and retrieving relevant literature. The objective is knowing which role plays the controlled vocabularies related to the health field to index and retrieve research literature in data bases such as Web of Science (WoS) and Scopus. So, this exploratory research is grounded over two research questions: 1) Which are the terms considered in specific controlled vocabularies of the health field; and 2) How papers are indexed in relevant databases to be easily retrieved, considering keywords vs specific health’ controlled vocabularies? This research takes as fieldwork the controlled vocabularies related to health and the scientific interest for 1918 flu pandemic, also known equivocally as ‘Spanish flu’. This interest has been fostered by the emergence in the early 21st of epidemics of pneumonic diseases caused by virus. Searches about and with controlled vocabularies on WoS and Scopus databases are conducted. First results of this work in progress are surprising. There are different controlled vocabularies for the health field, into which the terms collected and preferred related to ‘1918 pandemic’ are identified. To summarize, ‘Spanish influenza epidemic’ or ‘Spanish flu’ are collected as not preferred terms. The preferred terms are: ‘influenza’ or ‘influenza pandemic, 1918-1919’. Although the controlled vocabularies are clear in their election, most of the literature about ‘1918 pandemic’ is retrievable either by ‘Spanish’ or by ‘1918’ disjunct, and the dominant word to retrieve literature is ‘Spanish’ rather than ‘1918’. This is surprising considering the existence of suitable controlled vocabularies related to health topics, and the modern guidelines of World Health Organization concerning naming of diseases that point out to other preferred terms. A first conclusion is the failure of using controlled vocabularies for a field such as health, and in consequence for WoS and Scopus. This research opens further research questions about which is the role that controlled vocabularies play in the instructions to authors that journals deliver to documents’ authors.

Keywords: Controlled vocabularies, indexing, 1918 influenza, information retrieval, keywords, 1918 pandemic, scientific databases.

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Authors: A. Appe, B. Poluparthi, L. Kasivajjula, U. Mv, S. Bagadi, P. Modi, A. Singh, H. Gunupudi, S. Troiano, J. Paul, J. Stovall, J. Yamamoto

Abstract:

The necessity of data-driven decisions in healthcare strategy formulation is rapidly increasing. A reliable framework which helps identify factors impacting a healthcare provider facility or a hospital (from here on termed as facility) market share is of key importance. This pilot study aims at developing a data-driven machine learning-regression framework which aids strategists in formulating key decisions to improve the facility’s market share which in turn impacts in improving the quality of healthcare services. The US (United States) healthcare business is chosen for the study, and the data spanning 60 key facilities in Washington State and about 3 years of historical data are considered. In the current analysis, market share is termed as the ratio of the facility’s encounters to the total encounters among the group of potential competitor facilities. The current study proposes a two-pronged approach of competitor identification and regression approach to evaluate and predict market share, respectively. Leveraged model agnostic technique, SHAP (SHapley Additive exPlanations), to quantify the relative importance of features impacting the market share. Typical techniques in literature to quantify the degree of competitiveness among facilities use an empirical method to calculate a competitive factor to interpret the severity of competition. The proposed method identifies a pool of competitors, develops Directed Acyclic Graphs (DAGs) and feature level word vectors, and evaluates the key connected components at the facility level. This technique is robust since it is data-driven, which minimizes the bias from empirical techniques. The DAGs factor in partial correlations at various segregations and key demographics of facilities along with a placeholder to factor in various business rules (for e.g., quantifying the patient exchanges, provider references, and sister facilities). Identified are the multiple groups of competitors among facilities. Leveraging the competitors' identified developed and fine-tuned Random Forest Regression model to predict the market share. To identify key drivers of market share at an overall level, permutation feature importance of the attributes was calculated. For relative quantification of features at a facility level, incorporated SHAP, a model agnostic explainer. This helped to identify and rank the attributes at each facility which impacts the market share. This approach proposes an amalgamation of the two popular and efficient modeling practices, viz., machine learning with graphs and tree-based regression techniques to reduce the bias. With these, we helped to drive strategic business decisions.

Keywords: Competition, DAGs, hospital, healthcare, machine learning, market share, random forest, SHAP.

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