| 1. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
|
|
| 2. |
- Dakota, Daniel, et al.
(författare)
-
Bidirectional Domain Adaptation Using Weighted Multi-Task Learning
- 2021
-
Ingår i: IWPT 2021. - Stroudsburg, PA, USA : Association for Computational Linguistics. - 9781954085800 ; , s. 93-105
-
Konferensbidrag (refereegranskat)abstract
- Domain adaption in syntactic parsing is still a significant challenge. We address the issue of data imbalance between the in-domain and out-of-domain treebank typically used for the problem. We define domain adaptation as a Multi-task learning (MTL) problem, which allows us to train two parsers, one for each domain. Our results show that the MTL approach is beneficial for the smaller treebank. For the larger treebank, we need to use loss weighting in order to avoid a decrease in performance below the single task. In order to determine to what degree the data imbalance between two domains and the domain differences affect results, we also carry out an experiment with two imbalanced in-domain treebanks and show that loss weighting also improves performance in an in-domain setting. Given loss weighting in MTL, we can improve results for both parsers.
|
|
| 3. |
- Tsarfaty, Reut, et al.
(författare)
-
Parsing Morphologically Rich Languages : Introduction to the Special Issue
- 2013
-
Ingår i: Computational linguistics - Association for Computational Linguistics (Print). - 0891-2017 .- 1530-9312. ; 39:1, s. 15-22
-
Tidskriftsartikel (refereegranskat)abstract
- Parsing is a key task in natural language processing. It involves predicting, for each natural language sentence, an abstract representation of the grammatical entities in the sentence and the relations between these entities. This representation provides an interface to compositional semantics and to the notions of "who did what to whom." The last two decades have seen great advances in parsing English, leading to major leaps also in the performance of applications that use parsers as part of their backbone, such as systems for information extraction, sentiment analysis, text summarization, and machine translation. Attempts to replicate the success of parsing English for other languages have often yielded unsatisfactory results. In particular, parsing languages with complex word structure and flexible word order has been shown to require non-trivial adaptation. This special issue reports on methods that successfully address the challenges involved in parsing a range of morphologically rich languages (MRLs). This introduction characterizes MRLs, describes the challenges in parsing MRLs, and outlines the contributions of the articles in the special issue. These contributions present up-to-date research efforts that address parsing in varied, cross-lingual settings. They show that parsing MRLs addresses challenges that transcend particular representational and algorithmic choices.
|
|
