{MDL4BMF}: Minimum Description Length for Boolean Matrix Factorization

Matrix factorizations—where a given data matrix is approximated by a prod- uct of two or more factor matrices—are powerful data mining tools. Among other tasks, matrix factorizations are often used to separate global structure from noise. This, however, requires solving the ‘model order selection problem’ of determining where fine-grained structure stops, and noise starts, i.e., what is the proper size of the factor matrices. Boolean matrix factorization (BMF)—where data, factors, and matrix product are Boolean—has received increased attention from the data mining community in recent years. The technique has desirable properties, such as high interpretability and natural sparsity. However, so far no method for selecting the correct model order for BMF has been available. In this paper we propose to use the Minimum Description Length (MDL) principle for this task. Besides solving the problem, this well-founded approach has numerous benefits, e.g., it is automatic, does not require a likelihood function, is fast, and, as experiments show, is highly accurate. We formulate the description length function for BMF in general—making it applicable for any BMF algorithm. We discuss how to construct an appropriate encoding, starting from a simple and intuitive approach, we arrive at a highly efficient data-to-model based encoding for BMF. We extend an existing algorithm for BMF to use MDL to identify the best Boolean matrix factorization, analyze the complexity of the problem, and perform an extensive experimental evaluation to study its behavior

Identification of transcriptional and metabolic programs related to mammalian cell size

SummaryBackgroundRegulation of cell size requires coordination of growth and proliferation. Conditional loss of cyclin-dependent kinase 1 in mice permits hepatocyte growth without cell division, allowing us to study cell size in vivo using transcriptomics and metabolomics.ResultsLarger cells displayed increased expression of cytoskeletal genes but unexpectedly repressed expression of many genes involved in mitochondrial functions. This effect appears to be cell autonomous because cultured Drosophila cells induced to increase cell size displayed a similar gene-expression pattern. Larger hepatocytes also displayed a reduction in the expression of lipogenic transcription factors, especially sterol-regulatory element binding proteins. Inhibition of mitochondrial functions and lipid biosynthesis, which is dependent on mitochondrial metabolism, increased the cell size with reciprocal effects on cell proliferation in several cell lines.ConclusionsWe uncover that large cell-size increase is accompanied by downregulation of mitochondrial gene expression, similar to that observed in diabetic individuals. Mitochondrial metabolism and lipid synthesis are used to couple cell size and cell proliferation. This regulatory mechanism may provide a possible mechanism for sensing metazoan cell size

Magnetic Geometry and the Confinement of Electrically Conducting Plasmas

We develop an effective field theory approach to inspect the electromagnetic interactions in an electrically neutral plasma, with an equal number of negative and positive charge carriers. We argue that the static equilibrium configurations within the plasma are topologically stable solitons, that describe knotted and linked fluxtubes of helical magnetic fields.Comment: 9 pages 1 ps-figur

Valence-state mixing and separation in SmBaFe2O5+w

A mixed-valence state, formally denoted as Fe2.5+, is observed in the 300 K Mössbauer spectra of the most reduced samples of SmBaFe2O5+w. Upon cooling below the Verwey-type transition temperature (TV≈200K), the component assigned to Fe2.5+ separates into a high-spin Fe3+ state and an Fe2+ state with an unusually low internal field. The separation of the mixed-valence state at TV is also confirmed by magnetic susceptibility measurements and differential scanning calorimetry. A model is proposed which accounts for the variation of the amount of the mixed-valence state with the oxygen content parameter w.Peer reviewe

Valence-state mixing and separation in SmBaFe2O5+w

A mixed-valence state, formally denoted as Fe2.5+, is observed in the 300 K Mössbauer spectra of the most reduced samples of SmBaFe2O5+w. Upon cooling below the Verwey-type transition temperature (TV≈200K), the component assigned to Fe2.5+ separates into a high-spin Fe3+ state and an Fe2+ state with an unusually low internal field. The separation of the mixed-valence state at TV is also confirmed by magnetic susceptibility measurements and differential scanning calorimetry. A model is proposed which accounts for the variation of the amount of the mixed-valence state with the oxygen content parameter w.Peer reviewe

Kelan matkakorvausten kohdentuminen vammaispalvelulain ja sosiaalihuoltolain mukaisiin kuljetuksiin oikeutetuille : Rekisteritutkimus Oulusta vuodelta 2013

Tutkimuksessa selvitettiin rekisteritietojen perusteella Kelan sairausvakuutuslain perusteella kiireettömistä matkoista (muut kuin ambulanssilla ja helikopterilla tehdyt matkat) maksamien matkakorvausten kohdentumista vammaispalvelulain ja sosiaalihuoltolain mukaisiin kuljetuksiin oikeutetuille Oulussa vuonna 2013. Lisäksi selvitettiin mm. Kelan kuntoutuksen ja vammaisetuuksien kohdentumista näille henkilöille. Tutkimusaineistona käytettiin meneillään olevaan laajaan, Oulua koskevaan tutkimushankkeeseen Kelan etuudet sosiaali- ja terveydenhuoltojärjestelmässä muodostettua rekisteriaineistoa vuodelta 2013. Vuoden 2013 aikana oikeus vammaispalvelulain mukaisiin kuljetuksiin oli Oulussa noin 3 300 henkilöllä ja sosiaalihuoltolain mukaisiin kuljetuksiin noin 900 henkilöllä. Kelan sairausvakuutuslain mukaisia matkakorvauksia oli saanut 10 700 oululaista, joista 16 %:lla oli oikeus vammaispalvelulain ja 4 %:lla sosiaalihuoltolain mukaisiin kuljetuksiin. Niin vammaispalvelulain ja sosiaalihuoltolain mukaiset kuljetukset kuin sairausvakuutuslain mukaan korvatut matkatkin kohdentuivat etenkin yli 65-vuotiaille. Rekisteriselvityksen mukaan noin puolet vammaispalvelulain ja sosiaalihuoltolain mukaisiin kuljetuksiin oikeutetuista oli saanut myös sairausvakuutuslain mukaisia matkakorvauksia kiireettömistä matkoista. Nämä henkilöt tekivät yli puolet (52 %) kaikista sairausvakuutuksen korvaamista kiireettömistä matkoista ja näistä matkoista aiheutui lähes puolet (46 %) matkakorvauksista. Osuus oli erityisen suuri vammaismatkoihin oikeutetuilla, ja heistä etenkin 16–64-vuotiailla. He olivat vain 11 % kaikista ikäryhmään kuuluvista matkakorvauksia saaneista, mutta tekivät 56 % korvatuista matkoista ja aiheuttivat 51 % matkakorvauksista. Esitetyt tulokset koskevat Oulua eivätkä ne ole suoraan yleistettävissä koko maahan. Oulussa väestö on melko nuorta, ja lisäksi yliopistosairaalakaupungissa sairaanhoitoon ja kuntoutukseen liittyvät matkat ovat suhteellisen lyhyitä ja sairausvakuutuksen matkakorvausten käyttö on vähäistä, mikä ylikorostaa vammaispalvelu- ja sosiaalihuoltolain mukaisiin kuljetuksiin oikeutettujen osuuksia sairausvakuutuslain mukaisista matkakorvauksista koko maahan verrattuna. Tarve yhteiskunnan eri sektorien järjestämien tai korvaamien henkilökuljetusten välisen yhteistyön lisäämiselle on ollut esillä jo vuosia. Uudistustarve on mainittu myös nykyisen hallituksen ohjelmassa. Myös tuleva sosiaali- ja terveydenhuollon ns. sote-uudistus tulee muuttamaan toimintatapoja, kun vastuu sosiaali- ja terveyspalvelujen järjestämisestä on siirtymässä kunnilta maakunnille. Tällöin nyt eri tahojen rahoittamia henkilökuljetuksia voi olla yhden tahon vastuulla, mikä edistänee yhteistyön syntymistä

Pareto optimality in multilayer network growth

We model the formation of multi-layer transportation networks as a multi-objective optimization process, where service providers compete for passengers, and the creation of routes is determined by a multi-objective cost function encoding a trade-off between efficiency and competition. The resulting model reproduces well real-world systems as diverse as airplane, train and bus networks, thus suggesting that such systems are indeed compatible with the proposed local optimization mechanisms. In the specific case of airline transportation systems, we show that the networks of routes operated by each company are placed very close to the theoretical Pareto front in the efficiency-competition plane, and that most of the largest carriers of a continent belong to the corresponding Pareto front. Our results shed light on the fundamental role played by multi-objective optimization principles in shaping the structure of large-scale multilayer transportation systems, and provide novel insights to service providers on the strategies for the smart selection of novel routes

Disorders of sex development : timing of diagnosis and management in a single large tertiary center

Background: We describe the phenotypic spectrum and timing of diagnosis and management in a large series of patients with disorders of sexual development (DSD) treated in a single pediatric tertiary center. Methods: DSD patients who had visited our tertiary center during the survey period (between 2004 and 2014) were identified based on an ICD-10 inquiry, and their phenotypic and molecular genetic findings were recorded from patient charts. Results: Among the 550 DSD patients, 53.3% had 46,XY DSD; 37.1% had sex chromosome DSD and 9.6% had 46,XX DSD. The most common diagnoses were Turner syndrome (19.8%, diagnosed at the mean age of 4.7 +/- 5.5 years), Klinefelter syndrome (14.5%, 6.8 +/- 6.2 years) and bilateral cryptorchidism (23.1%). Very few patients with 46,XY DSD (7%) or 46,XX DSD (21%) had molecular genetic diagnosis. The yearly rate of DSD diagnoses remained stable over the survey period. After the release of the Nordic consensus on the management of undescended testes, the age at surgery for bilateral cryptorchidism declined significantly (P <0.001). Conclusions: Our results show that (i) Turner syndrome and Klinefelter syndrome, the most frequent single DSD diagnoses, are still diagnosed relatively late; (ii) a temporal shift was observed in the management of bilateral cryptorchidism, which may favorably influence patients' adulthood semen quality and (iii) next-generation sequencing methods are not fully employed in the diagnostics of DSD patients.Peer reviewe

A factor model to analyze heterogeneity in gene expression

<p>Abstract</p> <p>Background</p> <p>Microarray technology allows the simultaneous analysis of thousands of genes within a single experiment. Significance analyses of transcriptomic data ignore the gene dependence structure. This leads to correlation among test statistics which affects a strong control of the false discovery proportion. A recent method called FAMT allows capturing the gene dependence into factors in order to improve high-dimensional multiple testing procedures. In the subsequent analyses aiming at a functional characterization of the differentially expressed genes, our study shows how these factors can be used both to identify the components of expression heterogeneity and to give more insight into the underlying biological processes.</p> <p>Results</p> <p>The use of factors to characterize simple patterns of heterogeneity is first demonstrated on illustrative gene expression data sets. An expression data set primarily generated to map QTL for fatness in chickens is then analyzed. Contrarily to the analysis based on the raw data, a relevant functional information about a QTL region is revealed by factor-adjustment of the gene expressions. Additionally, the interpretation of the independent factors regarding known information about both experimental design and genes shows that some factors may have different and complex origins.</p> <p>Conclusions</p> <p>As biological information and technological biases are identified in what was before simply considered as statistical noise, analyzing heterogeneity in gene expression yields a new point of view on transcriptomic data.</p