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Efficient construction of approximate ad-hoc ML models through materialization and reuse

Sona Hasani, Saravanan Thirumuruganathan, Abolfazl Asudeh, Nick Koudas, Gautam Das
2018 Proceedings of the VLDB Endowment  
In this paper, we investigate the feasibility of efficiently constructing approximate ML models for new queries from previously constructed ML models by leveraging the concepts of model materialization  ...  and reuse.  ...  -materialization and reuse.  ... 
doi:10.14778/3236187.3236199 fatcat:og4kklcwurf5zptriid4aehvfu

ApproxML

Sona Hasani, Faezeh Ghaderi, Shohedul Hasan, Saravanan Thirumuruganathan, Abolfazl Asudeh, Nick Koudas, Gautam Das
2019 Proceedings of the VLDB Endowment  
In this paper, we propose to demonstrate ApproxML, a system that efficiently constructs approximate ML models for new queries from previously constructed ML models using the concepts of model materialization  ...  and reuse.  ...  SUMMARY We demonstrate ApproxML, a system that efficiently constructs approximate ML models for new queries from previously constructed ML models by leveraging the concepts of model materialization and  ... 
doi:10.14778/3352063.3352096 fatcat:air2xsgtzvgrndqmdk7ihn5ise

Toward Community Standards and Software for Whole-Cell Modeling

Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K Aranganathan (+45 others)
2016 IEEE Transactions on Biomedical Engineering  
Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.  ...  The original model used these ad hoc algorithms and rate laws to achieve sufficient performance.  ...  They would help researchers reuse, reproduce, and compare models, as well as share models through repositories such as BioModels [18] .  ... 
doi:10.1109/tbme.2016.2560762 pmid:27305665 pmcid:PMC5451320 fatcat:t2aodo6sbzfkvjg7qthez5bhwm

Materialization and Reuse Optimizations for Production Data Science Pipelines

Behrouz Derakhshan, Alireza Rezaei Mahdiraji, Zoi Kaoudi, Tilmann Rabl, Volker Markl
2022 Proceedings of the 2022 International Conference on Management of Data  
A typical approach to ensure that ML models are up-to-date is to retrain the ML pipelines following a schedule, e.g., every day on the last seven days of data.  ...  Our goal is to eliminate redundant data processing in such scenarios using materialization and reuse optimizations. Our solution comprises of two main parts.  ...  This work was funded by the German Ministry for Education and Research as BIFOLD -Berlin Institute for the Foundations of Learning and Data (01IS18025A and 01IS18037A) and the German Federal Ministry for  ... 
doi:10.1145/3514221.3526186 fatcat:wujxdky7ubempo3mnl5wbgzprq

Evaluation of geotextile filtration applying coagulant and flocculant amendments for aquaculture biosolids dewatering and phosphorus removal

Mark J. Sharrer, Kata Rishel, Steven Summerfelt
2009 Aquacultural Engineering  
We would like to thank Brain Mason, Daniel Coffinberger, and Fred Ford for their assistance constructing the geotextile bag filter system.  ...  Acknowledgments This work was supported by the United States Department of Agriculture, Agricultural Research Service under grant Agreement No. 59-1930-1-130.  ...  Geotextile material Geotextile fabric is a woven, porous polyethylene material used for construction site erosion control (Rickson, 2006) , improving drainage and enhancing reinforcement of marginally  ... 
doi:10.1016/j.aquaeng.2008.10.001 fatcat:iqvaunk3qbg2ngqysavnsuhvym

Evaluation of low-cost materials for sorption of hydrophobic organic pollutants in stormwater

Karin Björklund, Loretta Li
2015 Journal of Environmental Management  
This could lead to early saturation of the materials and should be investigated in future studies through repeated adsorption of HOCs, for example in column studies. 2 HIGHLIGHTS  Adsorbing media can  ...  Agreement between empirical data and the Langmuir isotherm model, as well as the pseudo-second order kinetic model, suggest chemisorption of HOCs onto a monolayer on wood-based media.  ...  Leaching from Raw Materials To 50 mL Milli-Q water, 1.0 g of each material was added and mixed for 24 h, passed through a 0.45 µm filter and analyzed for leached DOC using a Lachat Instrument IL 500 TOC  ... 
doi:10.1016/j.jenvman.2015.05.005 pmid:26063514 fatcat:p4acienojjhazbiosy6joonqhe

Programmable and Contractile Materials Through Cell Encapsulation in Fibrous Hydrogel Assemblies [article]

Matthew D Davidson, Margaret E Prendergast, Ehsan Ban, Karen L Xu, Gabriel Mickel, Patricia Mensah, Abhishek Dhand, Paul A Janmey, Vivek B Shenoy, Jason A Burdick
2021 bioRxiv   pre-print
Synthetic materials that facilitate self-assembly similar to natural ECM are needed for cell culture, tissue engineering, and in vitro models of development and disease.  ...  Due to properties such as shear-thinning and self-healing, assemblies can be processed into microtissues with aligned ECM deposition or through extrusion bioprinting and photopatterning to fabricate constructs  ...  Leo Wang, and Victoria Muir for help and advice with MSC isolation and culture, polymer synthesis, material fabrication, and NMR spectroscopy, respectively.  ... 
doi:10.1101/2021.04.19.440470 fatcat:cvab2o6qcfdn5bv7c2sacwcsve

Stem cell-laden hydrogel bioink for generation of high resolution and fidelity engineered tissues with complex geometries [article]

Oju Jeon, Yu Bin Lee, Sang Jin Lee, Nazilya Guliyeva, Joanna Lee, Eben Alsberg
2021 bioRxiv   pre-print
Cell encapsulated hydrogels composed of materials such as gelatin, collagen, hyaluronic acid, alginate and polyethylene glycol have been widely used as bioinks for 3D bioprinting.  ...  Additional photocrosslinking enables long-term culture of 3D bioprinted constructs for formation of functional tissue by differentiation of encapsulated human mesenchymal stem cells.  ...  Acknowledgements The authors gratefully acknowledge funding from the National Institutes of Health's National Data availability The datasets generated and/or analyzed during the current study are available  ... 
doi:10.1101/2021.04.15.439978 fatcat:ljdwmp3virbwrpfwrpfuvffwpi

Helix: Holistic Optimization for Accelerating Iterative Machine Learning [article]

Doris Xin, Stephen Macke, Litian Ma, Jialin Liu, Shuchen Song, Aditya Parameswaran
2018 arXiv   pre-print
Unfortunately, existing machine learning systems focus narrowly on model training---a small fraction of the overall development time---and neglect to address iterative development.  ...  Helix captures a wide variety of application needs within its Scala DSL, with succinct syntax defining unified processes for data preprocessing, model specification, and learning.  ...  steps, thereby alleviating engineers from the labor of ad-hoc solutions.  ... 
arXiv:1812.05762v1 fatcat:v4jrdttdq5aj3jngnvs3n27t4u

Silk fabric as a protective barrier for personal protective equipment and as a functional material for face coverings during the COVID-19 pandemic [article]

Adam F. Parlin, Samuel M. Stratton, Theresa M. Culley, Patrick Anthony Guerra
2020 medRxiv   pre-print
Therefore, silk can serve as an effective material for protecting respirators under clinical conditions and as a material for face coverings.  ...  Tests were done when fabrics were fashioned as an overlaying barrier and also when constructed as do-it-yourself face coverings.  ...  We modified an aerosol can with a standard valve, and added 150 ml of black-dyed water (10ml black dye, 140ml water; McCormick, MD, USA).  ... 
doi:10.1101/2020.06.25.20136424 fatcat:idqu4x4lkfe5noyf3qsvarjosq

A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus [article]

Daniel Conde, Paolo M Triozzi, Kelly M Balmant, Andria L Doty, Mariza Miranda, Anthony Boullosa, Henry W Schmidt, Wendell J Pereira, Christopher Dervinis, Matias Kirst
2021 bioRxiv   pre-print
Single-cell transcriptome analysis has been extensively applied in humans and animal models to uncover gene expression heterogeneity between the different cell types of a tissue or an organ.  ...  We developed the protocol using two different plant materials with varying cellular complexity levels and cell-wall structure, Populus shoot apices, and more lignified stems.  ...  Samples were then filtered through one layer 171 of pre-wetted (using NIB) miracloth (CALBIOCHEM) laid on top of a 50 ml conical tube placed 172 on ice and tilted on its side.  ... 
doi:10.1101/2021.02.11.430521 fatcat:umtpr4nu4vgb3muq4iuhhcvz74

Accelerating Human-in-the-loop Machine Learning

Doris Xin, Litian Ma, Jialin Liu, Stephen Macke, Shuchen Song, Aditya Parameswaran
2018 Proceedings of the Second Workshop on Data Management for End-To-End Machine Learning - DEEM'18  
Unfortunately, existing machine learning systems focus narrowly on model training-a small fraction of the overall development time-and neglect to address iterative development.  ...  Helix captures a wide variety of application needs within its Scala DSL, with succinct syntax defining unified processes for data preprocessing, model specification, and learning.  ...  steps, thereby alleviating engineers from the labor of ad-hoc solutions.  ... 
doi:10.1145/3209889.3209897 dblp:conf/sigmod/XinMLMSP18 fatcat:3arqg55lyvfmdngqy4cupmyimm

In vivo high-throughput screening of novel adeno-associated viral capsids targeting adult neural stem cells in the subventricular zone [article]

Sascha Dehler, Lukas PM Kremer, Santiago Cerrizuela, Thomas Stiehl, Jonas Weinmann, Heike Abendroth, Susanne Kleber, Alexander Laure, Jihad El Andari, Simon Anders, Anna Marciniak-Czochra, Dirk Grimm (+1 others)
2021 bioRxiv   pre-print
Further optimization of AAV1_P5 by judicious selection of promoter and dose of injected viral genomes enabled labeling of 30-60% of the NSC compartment, which was validated by FACS analyses and single  ...  Recombinant adeno-associated viruses (AAVs) are ideal gene therapy vectors due to an excellent safety profile and high transduction efficiency.  ...  , the model indicates that approximately 57% 277 of NSCs are labeled in the high-label group and 26% of NSCs in the other group (see Supplemental 278 Material).  ... 
doi:10.1101/2021.03.05.434064 fatcat:p4oooml2dfa5tof47dsw4is5w4

Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease relevant pathologies [article]

Nadeem Murtaza, Annie A Cheng, Chad O Brown, Durga Praveen Meka, Shuai Hong, Jarryll A Uy, Joelle El-Hajjar, Neta Pipko, Brianna K Unda, Birgit Schwanke, Sansi Xing, Bhooma Thiruvahindrapuram (+11 others)
2022 bioRxiv   pre-print
Investigation of the mitochondrial and metabolic network using gene knockouts revealed a functional hub in neurons for multiple risk genes not previously associated with this pathway.  ...  Together, our data reveal that using PPI networks to map ASD risk genes can identify previously unknown individual and convergent neuronal signaling networks, provide a method to assess the impact of patient  ...  ASD proband variant information and clinical scores are available through the MSSNG database (research.mss.ng) 12 and the associated Metabase (data-explorer.mss.ng), respectively.  ... 
doi:10.1101/2022.01.17.476220 fatcat:7wwdrulrnnfxtjfr233n4r4z2i

Programmable in vivo CRISPR activation elucidates the oncogenic and immunosuppressive role of MYC in lung adenocarcinoma [article]

Fredrik I Thege, Dhwani N Rupani, Bhargavi B Bharati, Sara L Manning, Anirban Maitra, Andrew D Rhim, Sonja M Woermann
2021 bioRxiv   pre-print
Unlike conventional GEMMs, our model system allows for flexible, sustained and timed activation of one or more target genes using single or pooled lentiviral guides.  ...  through competitive screening.  ...  Acknowledgements: We thank members of the Rhim and Maitra laboratories for critical reading of the manuscript. F.I.T. is supported by the  ... 
doi:10.1101/2021.12.09.471859 fatcat:m4wlb64fijhp7pif4zrbqramhe
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