| 1. |
- Wöhri, Annemarie, 1976, et al.
(author)
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A Lipidic-Sponge Phase Screen for Membrane Protein Crystallization
- 2008
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In: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 16:7, s. 1003-1009
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Journal article (peer-reviewed)abstract
- A major current deficit in structural biology is the lack of high-resolution structures of eukaryotic membrane proteins, many of which are key drug targets for the treatment of disease. Numerous eukaryotic membrane proteins require specific lipids for their stability and activity, and efforts to crystallize and solve the structures of membrane proteins that do not address the issue of lipids frequently end in failure rather than success. To help address this problem, we have developed a sparse matrix crystallization screen consisting of 48 lipidic-sponge phase conditions. Sponge phases form liquid lipid bilayer environments which are suitable for conventional hanging- and sitting-drop crystallization experiments. Using the sponge phase screen, we obtained crystals of several different membrane proteins from bacterial and eukaryotic sources. We also demonstrate how the screen may be manipulated by incorporating specific lipids such as cholesterol; this modification led to crystals being recovered from a bacterial photosynthetic core complex.
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| 2. |
- Adesam, Yvonne, 1975, et al.
(author)
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Defining the Eukalyptus forest – the Koala treebank of Swedish
- 2015
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In: Proceedings of the 20th Nordic Conference of Computational Linguistics, NODALIDA 2015, May 11-13, 2015, Vilnius, Lithuania. Edited by Beáta Megyesi. - 1650-3686 .- 1650-3740. - 9789175190983 ; , s. 1-9
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Conference paper (peer-reviewed)abstract
- This paper details the design of the lexical and syntactic layers of a new annotated corpus of Swedish contemporary texts. In order to make the corpus adaptable into a variety of representations, the annotation is of a hybrid type with head-marked constituents and function-labeled edges, and with a rich annotation of non-local dependencies. The source material has been taken from public sources, to allow the resulting corpus to be made freely available.
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| 3. |
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| 4. |
- Adesam, Yvonne, 1975, et al.
(author)
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Multiwords, Word Senses and Multiword Senses in the Eukalyptus Treebank of Written Swedish
- 2015
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In: Proceedings of the Fourteenth International Workshop on Treebanks and Linguistic Theories (TLT14), 11–12 December 2015 Warsaw, Poland. - 9788363159184 ; , s. 3-12
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Conference paper (peer-reviewed)abstract
- Multiwords reside at the intersection of the lexicon and syntax and in an annotation project, they will affect both levels. In the Eukalyptus treebank of written Swedish, we treat multiwords formally as syntactic objects, which are assigned a lexical type and sense. With the help of a simple dichotomy, analyzed vs unanalyzed multiwords, and the expressiveness of the syntactic annotation formalism employed, we are able to flexibly handle most multiword types and usages.
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| 5. |
- Adesam, Yvonne, 1975, et al.
(author)
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The Eukalyptus Treebank of Written Swedish
- 2018
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In: Seventh Swedish Language Technology Conference (SLTC), Stockholm, 7–9 November 2018.
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Conference paper (other academic/artistic)
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| 6. |
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| 7. |
- Brändén, Gisela, 1975, et al.
(author)
-
Coherent diffractive imaging of microtubules using an X-ray laser.
- 2019
-
In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
-
Journal article (peer-reviewed)abstract
- X-ray free electron lasers (XFELs) create new possibilities for structural studies of biological objects that extend beyond what is possible with synchrotron radiation. Serial femtosecond crystallography has allowed high-resolution structures to be determined from micro-meter sized crystals, whereas single particle coherent X-ray imaging requires development to extend the resolution beyond a few tens of nanometers. Here we describe an intermediate approach: the XFEL imaging of biological assemblies with helical symmetry. We collected X-ray scattering images from samples of microtubules injected across an XFEL beam using a liquid microjet, sorted these images into class averages, merged these data into a diffraction pattern extending to 2nm resolution, and reconstructed these data into a projection image of the microtubule. Details such as the 4nm tubulin monomer became visible in this reconstruction. These results illustrate the potential of single-molecule X-ray imaging of biological assembles with helical symmetry at room temperature.
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| 8. |
- Dods, Robert, 1989, et al.
(author)
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Ultrafast structural changes within a photosynthetic reaction centre.
- 2021
-
In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 589:7841, s. 310-314
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Journal article (peer-reviewed)abstract
- Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.
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| 9. |
- Forsberg, Markus, 1974, et al.
(author)
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From construction candidates to constructicon entries: An experiment using semi-automatic methods for identifying constructions in corpora
- 2014
-
In: Constructions and Frames. - : John Benjamins Publishing Company. - 1876-1933 .- 1876-1941. ; 6:1, 2014, s. 114-135
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Journal article (peer-reviewed)abstract
- We present an experiment where natural language processing tools are used to automatically identify potential constructions in a corpus. e experiment was conducted as part of the ongoing efforts to develop a Swedish constructicon. Using an automatic method to suggest constructions has advantages not only for efficiency but also methodologically: it forces the analyst to look more objec-tively at the constructions actually occurring in corpora, as opposed to focusing on “interesting” constructions only. As a heuristic for identifying potential con-structions, the method has proved successful, yielding about 200 (out of 1,200) highly relevant construction candidates.
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| 10. |
- Hagström, Lovisa, 1995, et al.
(author)
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The Effect of Scaling, Retrieval Augmentation and Form on the Factual Consistency of Language Models
- 2023
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In: Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing, pages 5457–5476, Singapore. - : Association for Computational Linguistics.
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Conference paper (peer-reviewed)abstract
- Large Language Models (LLMs) make natural interfaces to factual knowledge, but their usefulness is limited by their tendency to deliver inconsistent answers to semantically equivalent questions. For example, a model might supply the answer “Edinburgh” to “Anne Redpath passed away in X.” and “London” to “Anne Redpath’s life ended in X.” In this work, we identify potential causes of inconsistency and evaluate the effectiveness of two mitigation strategies: up-scaling and augmenting the LM with a passage retrieval database. Our results on the LLaMA and Atlas models show that both strategies reduce inconsistency but that retrieval augmentation is considerably more efficient. We further consider and disentangle the consistency contributions of different components of Atlas. For all LMs evaluated we find that syntactical form and task artifacts impact consistency. Taken together, our results provide a better understanding of the factors affecting the factual consistency of language models.
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| 11. |
- Johansson, Linda C, 1983, et al.
(author)
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Lipidic phase membrane protein serial femtosecond crystallography.
- 2012
-
In: Nature methods. - : Springer Science and Business Media LLC. - 1548-7105 .- 1548-7091. ; 9:3, s. 263-265
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Journal article (peer-reviewed)abstract
- X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.
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| 12. |
- Johansson, Linda C, 1983, et al.
(author)
-
Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography.
- 2013
-
In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4
-
Journal article (peer-reviewed)abstract
- Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8Å resolution and determine its serial femtosecond crystallography structure to 3.5Å resolution. Although every microcrystal is exposed to a dose of 33MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.
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| 13. |
- Johansson, Richard, 1975, et al.
(author)
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A Multi-domain Corpus of Swedish Word Sense Annotation
- 2016
-
In: 10th edition of the Language Resources and Evaluation Conference, 23-28 May 2016, Portorož (Slovenia). - : European Language Resources Association. - 9782951740891
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Conference paper (peer-reviewed)abstract
- We describe the word sense annotation layer in Eukalyptus, a freely available five-domain corpus of contemporary Swedish with several annotation layers. The annotation uses the SALDO lexicon to define the sense inventory, and allows word sense annotation of compound segments and multiword units. We give an overview of the new annotation tool developed for this project, and finally present an analysis of the inter-annotator agreement between two annotators.
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| 14. |
- Johansson, Richard, 1975, et al.
(author)
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Training a Swedish Constituency Parser on Six Incompatible Treebanks
- 2020
-
In: Proceedings of the 12th International Conference on Language Resources and Evaluation (LREC 2020). - : European Language Resources Association (ELRA).
-
Conference paper (peer-reviewed)abstract
- We investigate a transition-based parser that usesEukalyptus, a function-tagged constituent treebank for Swedish which includesdiscontinuous constituents. In addition, we show that the accuracy of this parser can be improved by using a multitask learning architecture that makes it possible to train the parser on additional treebanks that use other annotation models.
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| 15. |
- Kågebäck, Mikael, 1981, et al.
(author)
-
Neural context embeddings for automatic discovery of word senses
- 2015
-
In: Proceedings of the 1st Workshop on Vector Space Modeling for Natural Language Processing. Denver, United States. - 9781941643464 ; , s. 25-32
-
Conference paper (peer-reviewed)abstract
- Word sense induction (WSI) is the problem of automatically building an inventory of senses for a set of target words using only a text corpus. We introduce a new method for embedding word instances and their context, for use in WSI. The method, Instance-context embedding (ICE), leverages neural word embeddings, and the correlation statistics they capture, to compute high quality embeddings of word contexts. In WSI, these context embeddings are clustered to find the word senses present in the text. ICE is based on a novel method for combining word embeddings using continuous Skip-gram, based on both se- mantic and a temporal aspects of context words. ICE is evaluated both in a new system, and in an extension to a previous system for WSI. In both cases, we surpass previous state-of-the-art, on the WSI task of SemEval-2013, which highlights the generality of ICE. Our proposed system achieves a 33% relative improvement.
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| 16. |
- Redecke, Lars, et al.
(author)
-
Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser.
- 2013
-
In: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 339:6116, s. 227-30
-
Journal article (peer-reviewed)abstract
- The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.
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| 17. |
- Saynova, Denitsa, et al.
(author)
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Class Explanations: the Role of Domain-Specific Content and Stop Words
- 2023
-
In: Proceedings of the 24th Nordic Conference on Computational Linguistics (NoDaLiDa), pages 103–112, Tórshavn, Faroe Islands. - : University of Tartu Library.
-
Conference paper (peer-reviewed)abstract
- We address two understudied areas related to explainability for neural text models. First, class explanations. What features are descriptive across a class, rather than explaining single input instances? Second, the type of features that are used for providing explanations. Does the explanation involve the statistical pattern of word usage or the presence of domain-specific content words? Here, we present a method to extract both class explanations and strategies to differentiate between two types of explanations – domain-specific signals or statistical variations in frequencies of common words. We demonstrate our method using a case study in which we analyse transcripts of political debates in the Swedish Riksdag.
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| 18. |
- Tahmasebi, Nina, 1982, et al.
(author)
-
Visions and open challenges for a knowledge-based culturomics
- 2015
-
In: International Journal on Digital Libraries. - : Springer Science and Business Media LLC. - 1432-5012 .- 1432-1300. ; 15:2-4, s. 169-187
-
Journal article (peer-reviewed)abstract
- The concept of culturomics was born out of the availability of massive amounts of textual data and the interest to make sense of cultural and language phenomena over time. Thus far however, culturomics has only made use of, and shown the great potential of, statistical methods. In this paper, we present a vision for a knowledge-based culturomics that complements traditional culturomics. We discuss the possibilities and challenges of combining knowledge-based methods with statistical methods and address major challenges that arise due to the nature of the data; diversity of sources, changes in language over time as well as temporal dynamics of information in general. We address all layers needed for knowledge-based culturomics, from natural language processing and relations to summaries and opinions.
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| 19. |
- Volodina, Elena, 1973, et al.
(author)
-
Semi-automatic selection of best corpus examples for Swedish: Initial algorithm evaluation.
- 2012
-
In: Proceedings of the SLTC 2012 workshop on NLP for CALL, Lund, 25th October, 2012.. - 1650-3740. ; :080, s. 59-70
-
Conference paper (peer-reviewed)abstract
- The study presented here describes the results of the initial evaluation of two sorting approaches to automatic ranking of corpus examples for Swedish. Representatives from two potential target user groups have been asked to rate top three hits per approach for sixty search items from the point of view of the needs of their professional target groups, namely second/foreign language (L2) teachers and lexicographers. This evaluation has shown, on the one hand, which of the two approaches to example rating (called in the text below algorithms #1 and #2) performs better in terms of finding better examples for each target user group; and on the other hand, which features evaluators associate with good examples. It has also facilitated statistic analysis of the “good” versus “bad” examples with reference to the measurable features, such as sentence length, word length, lexical frequency profiles, PoS constitution, dependency structure, etc. with a potential to find out new reliable classifiers.
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| 20. |
- Adouane, Wafia, 1985, et al.
(author)
-
Arabicized and Romanized Berber Automatic Identification
- 2016
-
In: Proceedings of TICAM 2016. - Morocco : IRCAM.
-
Conference paper (peer-reviewed)abstract
- We present an automatic language identification tool for both Arabicized Berber (Berber written in the Arabic script) and Romanized Berber (Berber written in the Latin script). The focus is on short texts (social media content). We use supervised machine learning method with character and word-based n-gram models as features. We also describe the corpora used in this paper. For both Arabicized and Romanized Berber, character-based 5-grams score the best giving an F-score of 99.50%.
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| 21. |
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| 22. |
- Adouane, Wafia, 1985, et al.
(author)
-
Automatic Detection of Arabicized Berber and Arabic Varieties
- 2016
-
In: Proceedings of the Third Workshop on NLP for Similar Languages, Varieties and Dialects; 63–72; December 12; Osaka, Japan.
-
Conference paper (peer-reviewed)abstract
- Automatic Language Identification (ALI) is the detection of the natural language of an input text by a machine. It is the first necessary step to do any language-dependent natural language processing task. Various methods have been successfully applied to a wide range of languages, and the state-of-the-art automatic language identifiers are mainly based on character n-gram models trained on huge corpora. However, there are many languages which are not yet automatically processed, for instance minority and informal languages. Many of these languages are only spoken and do not exist in a written format. Social media platforms and new technologies have facilitated the emergence of written format for these spoken languages based on pronunciation. The latter are not well represented on the Web, commonly referred to as under-resourced languages, and the current available ALI tools fail to properly recognize them. In this paper, we revisit the problem of ALI with the focus on Arabicized Berber and dialectal Arabic short texts. We introduce new resources and evaluate the existing methods. The results show that machine learning models combined with lexicons are well suited for detecting Arabicized Berber and different Arabic varieties and distinguishing between them, giving a macro-average F-score of 92.94%.
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| 23. |
- Adouane, Wafia, 1985, et al.
(author)
-
Gulf Arabic Resource Building for Sentiment Analysis
- 2016
-
In: Proceedings of the Language Resources and Evaluation Conference (LREC), 23-28 May 2016, Portorož, Slovenia. - : European Language Resources Association. - 9782951740891
-
Conference paper (peer-reviewed)abstract
- This paper deals with building linguistic resources for Gulf Arabic, one of the Arabic variations, for sentiment analysis task using machine learning. To our knowledge, no previous works were done for Gulf Arabic sentiment analysis despite the fact that it is present in different online platforms. Hence, the first challenge is the absence of annotated data and sentiment lexicons. To fill this gap, we created these two main linguistic resources. Then we conducted different experiments: use Naive Bayes classifier without any lexicon; add a sentiment lexicon designed basically for MSA; use only the compiled Gulf Arabic sentiment lexicon and finally use both MSA and Gulf Arabic sentiment lexicons. The Gulf Arabic lexicon gives a good improvement of the classifier accuracy (90.54 %) over a baseline that does not use the lexicon (82.81%), while the MSA lexicon causes the accuracy to drop to (76.83%). Moreover, mixing MSA and Gulf Arabic lexicons causes the accuracy to drop to (84.94%) compared to using only Gulf Arabic lexicon. This indicates that it is useless to use MSA resources to deal with Gulf Arabic due to the considerable differences and conflicting structures between these two languages.
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| 24. |
- Adouane, Wafia, 1985, et al.
(author)
-
Romanized Arabic and Berber Detection Using PPM and Dictionary Methods
- 2017
-
In: 13th ACS/IEEE International Conference on Computer Systems and Applications AICCSA 2016. - Morocco. - 2161-5322. - 9781509043200
-
Conference paper (peer-reviewed)abstract
- Arabic is one of the Semitic languages written in Arabic script in its standard form. However, the recent rise of social media and new technologies has contributed considerably to the emergence of a new form of Arabic, namely Arabic written in Latin scripts, often called Romanized Arabic or Arabizi. While Romanized Arabic is an informal language, Berber or Tamazight uses Latin script in its standard form with some orthography differences depending on the country it is used in. Both these languages are under-resourced and unknown to the state-of-the-art language identifiers. In this paper, we present a language automatic identifier for both Romanized Arabic and Romanized Berber. We also describe the built linguistic resources (large dataset and lexicons) including a wide range of Arabic dialects (Algerian, Egyptian, Gulf, Iraqi, Levantine, Moroccan and Tunisian dialects) as well as the most popular Berber varieties (Kabyle, Tashelhit, Tarifit, Tachawit and Tamzabit). We use the Prediction by Partial Matching (PPM) and dictionary-based methods. The methods reach a macro-average F-Measure of 98.74% and 97.60% respectively.
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| 25. |
- Adouane, Wafia, 1985, et al.
(author)
-
Romanized Arabic and Berber Detection Using Prediction by Partial Matching and Dictionary Methods
- 2016
-
In: 2016 IEEE/ACS 13TH INTERNATIONAL CONFERENCE OF COMPUTER SYSTEMS AND APPLICATIONS (AICCSA). - 9781509043200
-
Conference paper (peer-reviewed)abstract
- Arabic is one of the Semitic languages written in Arabic script in its standard form. However, the recent rise of social media and new technologies has contributed considerably to the emergence of a new form of Arabic, namely Arabic written in Latin scripts, often called Romanized Arabic or Arabizi. While Romanized Arabic is an informal language, Berber or Tamazight uses Latin script in its standard form with some orthography differences depending on the country it is used in. Both these languages are under-resourced and unknown to the state-of-theart language identifiers. In this paper, we present a language automatic identifier for both Romanized Arabic and Romanized Berber. We also describe the built linguistic resources (large dataset and lexicons) including a wide range of Arabic dialects (Algerian, Egyptian, Gulf, Iraqi, Levantine, Moroccan and Tunisian dialects) as well as the most popular Berber varieties (Kabyle, Tashelhit, Tarifit, Tachawit and Tamzabit). We use the Prediction by Partial Matching (PPM) and dictionary-based methods. The methods reach a macro-average F-Measure of 98.74% and 97.60% respectively.
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