Optimal coding and the origins of Zipfian laws

The problem of compression in standard information theory consists of assigning codes as short as possible to numbers. Here we consider the problem of optimal coding -- under an arbitrary coding scheme -- and show that it predicts Zipf's law of abbreviation, namely a tendency in natural languages for more frequent words to be shorter. We apply this result to investigate optimal coding also under so-called non-singular coding, a scheme where unique segmentation is not warranted but codes stand for a distinct number. Optimal non-singular coding predicts that the length of a word should grow approximately as the logarithm of its frequency rank, which is again consistent with Zipf's law of abbreviation. Optimal non-singular coding in combination with the maximum entropy principle also predicts Zipf's rank-frequency distribution. Furthermore, our findings on optimal non-singular coding challenge common beliefs about random typing. It turns out that random typing is in fact an optimal coding process, in stark contrast with the common assumption that it is detached from cost cutting considerations. Finally, we discuss the implications of optimal coding for the construction of a compact theory of Zipfian laws and other linguistic laws.Comment: in press in the Journal of Quantitative Linguistics; definition of concordant pair corrected, proofs polished, references update

Implicit reference to citations: a study of astronomy

The research in this paper presents results in the automatic classification of pronouns within articles into those which refer to cited research and those which do not. It also discusses the automatic linking of pronouns which do refer to citations to their corresponding citations. The current study focused on the pronoun they as used in papers in Astronomy journals. The paper describes a classifier trained on maximum entropy principles using features defined by the distance to preceding citations and the category of verbs associated to the pronoun under consideration

NetiNeti : Discovery of Scientific Names from Text Using Machine Learning Methods Figure 1

Figure 1 demonstrates a series of training experiments with the Naïve Bayes classifier using different neighborhoods for contextual features, different sizes of positive and negative training examples and evaluated the resulting classifiers with our annotated gold standard corpus. The data sets are the results of running NetiNeti on subset of 136 PubMedCentral tagged open access articles and with no stop list.A scientific name for an organism can be associated with almost all biological data. Name identification is an important step in many text mining tasks aiming to extract useful information from biological, biomedical and biodiversity text sources. A scientific name acts as an important metadata element to link biological information.We present NetiNeti, a machine learning based approach for identification and discovery of scientific names. The system implementing the approach can be accessed at http://namefinding.ubio.org we present the comparison results of various machine learning algorithms on our annotated corpus. Naïve Bayes and Maximum Entropy with Generalized Iterative Scaling (GIS) parameter estimation are the top two performing algorithms

A new species, Lasioglossum (Eickwortia) hienae, from Mexico (Apoidea: Halictidae)

A new species from Colima, Mexico, Lasioglossum (Eickwortia) hienae Gibbs & Dumesh, new species, is described and illustrated.  Lasioglossum hienae is distinguished from related species based on a combination of morphological, geographical, and molecular evidence.  A species distribution model is used to predict the potential distribution of the known species of L. (Eickwortia).  An identification key is provided

Boosting Drug Named Entity Recognition using an Aggregate Classifier

AbstractObjectiveDrug named entity recognition (NER) is a critical step for complex biomedical NLP tasks such as the extraction of pharmacogenomic, pharmacodynamic and pharmacokinetic parameters. Large quantities of high quality training data are almost always a prerequisite for employing supervised machine-learning techniques to achieve high classification performance. However, the human labour needed to produce and maintain such resources is a significant limitation. In this study, we improve the performance of drug NER without relying exclusively on manual annotations.MethodsWe perform drug NER using either a small gold-standard corpus (120 abstracts) or no corpus at all. In our approach, we develop a voting system to combine a number of heterogeneous models, based on dictionary knowledge, gold-standard corpora and silver annotations, to enhance performance. To improve recall, we employed genetic programming to evolve 11 regular-expression patterns that capture common drug suffixes and used them as an extra means for recognition.MaterialsOur approach uses a dictionary of drug names, i.e. DrugBank, a small manually annotated corpus, i.e. the pharmacokinetic corpus, and a part of the UKPMC database, as raw biomedical text. Gold-standard and silver annotated data are used to train maximum entropy and multinomial logistic regression classifiers.ResultsAggregating drug NER methods, based on gold-standard annotations, dictionary knowledge and patterns, improved the performance on models trained on gold-standard annotations, only, achieving a maximum F-score of 95%. In addition, combining models trained on silver annotations, dictionary knowledge and patterns are shown to achieve comparable performance to models trained exclusively on gold-standard data. The main reason appears to be the morphological similarities shared among drug names.ConclusionWe conclude that gold-standard data are not a hard requirement for drug NER. Combining heterogeneous models build on dictionary knowledge can achieve similar or comparable classification performance with that of the best performing model trained on gold-standard annotations

Named Entity Recognition for the Estonian Language

Käesoleva töö raames uuriti eestikeelsetes tekstides nimega üksuste tuvastamise probleemi (NÜT) kasutades masinõppemeetodeid. NÜT süsteemi väljatöötamisel käsitleti kahte põhiaspekti: nimede tuvastamise algoritmi valikut ja nimede esitusviisi. Selleks võrreldi maksimaalse entroopia (MaxEnt) ja lineaarse ahela tinglike juhuslike väljade (CRF) masinõppemeetodeid. Uuriti, kuidas mõjutavad masinõppe tulemusi kolme liiki tunnused: 1) lokaalsed tunnused (sõnast saadud informatsioon), 2) globaalsed tunnused (sõna kõikide esinemiskontekstide tunnused) ja 3) väline teadmus (veebist saadud nimede nimekirjad). Masinõppe algoritmide treenimiseks ja võrdlemiseks annoteeriti käsitsi ajakirjanduse artiklitest koosnev tekstikorpus, milles märgendati asukohtade, inimeste, organisatsioonide ja ehitise-laadsete objektide nimed. Eksperimentide tulemusena ilmnes, et CRF ületab oluliselt MaxEnt meetodit kõikide vaadeldud nimeliikide tuvastamisel. Parim tulemus, 0.86 F1 skoor, saavutati annoteeritud korpusel CRF meetodiga, kasutades kombinatsiooni kõigist kolmest nime esitusvariandist. Vaadeldi ka süsteemi kohanemisvõimet teiste tekstižanridega spordi domeeni näitel ja uuriti võimalusi süsteemi kasutamiseks teistes keeltes nimede tuvastamisel.In this thesis we study the applicability of recent statistical methods to extraction of named entities from Estonian texts. In particular, we explore two fundamental design challenges: choice of inference algorithm and text representation. We compare two state-of-the-art supervised learning methods, Linear Chain Conditional Random Fields (CRF) and Maximum Entropy Model (MaxEnt). In representing named entities, we consider three sources of information: 1) local features, which are based on the word itself, 2) global features extracted from other occurrences of the same word in the whole document and 3) external knowledge represented by lists of entities extracted from the Web. To train and evaluate our NER systems, we assembled a text corpus of Estonian newspaper articles in which we manually annotated names of locations, persons, organisations and facilities. In the process of comparing several solutions we achieved F1 score of 0.86 by the CRF system using combination of local and global features and external knowledge