Long non-coding RNAs (lncRNAs) are widely recognized as important regulators of gene expression. Their molecular functions range from miRNA sponging to chromatin-associated mechanisms, leading to effects in disease progression and establishing them as diagnostic and therapeutic targets. Still, only a few representatives of this diverse class of RNAs are well studied, while the vast majority is poorly described beyond the existence of their transcripts. In this review we survey common in silico approaches for lncRNA annotation. We focus on the well-established sets of features used for classification and discuss their specific advantages and weaknesses. While the available tools perform very well for the task of distinguishing coding sequence from other RNAs, we find that current methods are not well suited to distinguish lncRNAs or parts thereof from other non-protein-coding input sequences. We conclude that the distinction of lncRNAs from intronic sequences and untranslated regions of coding mRNAs remains a pressing research gap.

Yes / Novel machine-learning and feature-selection algorithms have been developed to study: (i) the flare prediction capability of magnetic feature (MF) properties generated by the recently developed Solar Monitor Active Region Tracker (SMART); (ii) SMART's MF properties that are most significantly related to flare occurrence. Spatio-temporal association algorithms are developed to associate MFs with flares from April 1996 to December 2010 in order to differentiate flaring and non-flaring MFs and enable the application of machine learning and feature selection algorithms. A machine-learning algorithm is applied to the associated datasets to determine the flare prediction capability of all 21 SMART MF properties. The prediction performance is assessed using standard forecast verification measures and compared with the prediction measures of one of the industry's standard technologies for flare prediction that is also based on machine learning - Automated Solar Activity Prediction (ASAP). The comparison shows that the combination of SMART MFs with machine learning has the potential to achieve more accurate flare prediction than ASAP. Feature selection algorithms are then applied to determine the MF properties that are most related to flare occurrence. It is found that a reduced set of 6 MF properties can achieve a similar degree of prediction accuracy as the full set of 21 SMART MF properties.

Magister Scientiae - MSc (Computer Science) / A machine translation system that can convert South African Sign Language (SASL) video to audio or text and vice versa would be bene cial to people who use SASL to communicate. Five fundamental parameters are associated with sign language gestures, these are: hand location; hand orientation; hand shape; hand movement and facial expressions. The aim of this research is to recognise facial expressions and to compare both feature descriptors and machine learning techniques. This research used the Design Science Research (DSR) methodology. A DSR artefact was built which consisted of two phases. The rst phase compared local binary patterns (LBP), compound local binary patterns (CLBP) and histogram of oriented gradients (HOG) using support vector machines (SVM). The second phase compared the SVM to arti cial neural networks (ANN) and random forests (RF) using the most promising feature descriptor|HOG|from the rst phase. The performance was evaluated in terms of accuracy, robustness to classes, robustness to subjects and ability to generalise on both the Binghamton University 3D facial expression (BU-3DFE) and Cohn Kanade (CK) datasets. The evaluation rst phase showed HOG to be the best feature descriptor followed by CLBP and LBP. The second showed ANN to be the best choice of machine learning technique closely followed by the SVM and RF.

Abstract Image description plays an important role in representing inherent properties of entities and scenes in static images. Within the last few decades, it has become a fundamental issue of many practical vision tasks, such as texture classification, face recognition, material categorization, and medical image processing. The study of static image analysis can also be extended to video analysis, such as dynamic texture recognition, classification and synthesis. This thesis contributes to the research and development of image and video analysis from two aspects. In the first part of this work, two image description methods are presented to provide discriminative representations for image classification. They are designed in unsupervised (i.e., class labels of texture images are not available) and supervised (i.e., class labels of texture images are available) manner, respectively. First, a supervised model is developed to learn discriminative local patterns, which formulates the image description as an integrated three-layered model to estimate an optimal pattern subset of interest by simultaneously considering the robustness, discriminative power and representation capability of features. Second, in the case that class labels of training images are unavailable, a linear configuration model is presented to describe microscopic image structures in an unsupervised manner, which is subsequently combined together with a local descriptor: local binary pattern (LBP). This description is theoretically verified to be rotation invariant and is able to provide a discriminative complement to the conventional LBPs. In the second part of the thesis, based on static image description and deformable image registration, video analysis is studied for the applications of dynamic texture description, synthesis and recognition. First, a dynamic texture synthesis model is proposed to create a continuous and infinitely varying stream of images given a finite input video, which stitches video clips in the time domain by selecting proper matching frames and organizing them into a logical order. Second, a method for the application of facial expression recognition, which formulates the dynamic facial expression recognition problem as the construction of longitudinal atlases and groupwise image registration problem, is proposed. / Tiivistelmä Kuvan deskriptiolla on tärkeä rooli staattisissa kuvissa esiintyvien luontaisten kokonaisuuksien ja näkymien kuvaamisessa. Viime vuosikymmeninä se on tullut perustavaa laatua olevaksi ongelmaksi monissa käytännön konenäön tehtävissä, kuten tekstuurien luokittelu, kasvojen tunnistaminen, materiaalien luokittelu ja lääketieteellisten kuvien analysointi. Staattisen kuva-analyysin tutkimusala voidaan myös laajentaa videoanalyysiin, kuten dynaamisten tekstuurien tunnistukseen, luokitteluun ja synteesiin. Tämä väitöskirjatutkimus myötävaikuttaa kuva- ja videoanalyysin tutkimukseen ja kehittymiseen kahdesta näkökulmasta. Työn ensimmäisessä osassa esitetään kaksi kuvan deskriptiomenetelmää erottelukykyisten esitystapojen luomiseksi kuvien luokitteluun. Ne suunnitellaan ohjaamattomiksi (eli tekstuurikuvien luokkien leimoja ei ole käytettävissä) tai ohjatuiksi (eli luokkien leimat ovat saatavilla). Aluksi kehitetään ohjattu malli oppimaan erottelukykyisiä paikallisia kuvioita, mikä formuloi kuvan deskriptiomenetelmän integroituna kolmikerroksisena mallina - tavoitteena estimoida optimaalinen kiinnostavien kuvioiden alijoukko ottamalla samanaikaisesti huomioon piirteiden robustisuus, erottelukyky ja esityskapasiteetti. Seuraavaksi, sellaisia tapauksia varten, joissa luokkaleimoja ei ole saatavilla, esitetään työssä lineaarinen konfiguraatiomalli kuvaamaan kuvan mikroskooppisia rakenteita ohjaamattomalla tavalla. Tätä käytetään sitten yhdessä paikallisen kuvaajan, eli local binary pattern (LBP) –operaattorin kanssa. Teoreettisella tarkastelulla osoitetaan kehitetyn kuvaajan olevan rotaatioinvariantti ja kykenevän tuottamaan erottelukykyistä, täydentävää informaatiota perinteiselle LBP-menetelmälle. Työn toisessa osassa tutkitaan videoanalyysiä, perustuen staattisen kuvan deskriptioon ja deformoituvaan kuvien rekisteröintiin – sovellusaloina dynaamisten tekstuurien kuvaaminen, synteesi ja tunnistaminen. Aluksi ehdotetaan sellainen malli dynaamisten tekstuurien synteesiin, joka luo jatkuvan ja äärettömän kuvien virran annetusta äärellisen mittaisesta videosta. Menetelmä liittää yhteen videon pätkiä aika-avaruudessa valitsemalla keskenään yhteensopivia kuvakehyksiä videosta ja järjestämällä ne loogiseen järjestykseen. Seuraavaksi työssä esitetään sellainen uusi menetelmä kasvojen ilmeiden tunnistukseen, joka formuloi dynaamisen kasvojen ilmeiden tunnistusongelman pitkittäissuuntaisten kartastojen rakentamisen ja ryhmäkohtaisen kuvien rekisteröinnin ongelmana.