Committee-Based Sample Selection for Probabilistic Classifiers

In many real-world learning tasks, it is expensive to acquire a sufficient number of labeled examples for training. This paper investigates methods for reducing annotation cost by `sample selection'. In this approach, during training the learning program examines many unlabeled examples and selects for labeling only those that are most informative at each stage. This avoids redundantly labeling examples that contribute little new information. Our work follows on previous research on Query By Committee, extending the committee-based paradigm to the context of probabilistic classification. We describe a family of empirical methods for committee-based sample selection in probabilistic classification models, which evaluate the informativeness of an example by measuring the degree of disagreement between several model variants. These variants (the committee) are drawn randomly from a probability distribution conditioned by the training set labeled so far. The method was applied to the real-world natural language processing task of stochastic part-of-speech tagging. We find that all variants of the method achieve a significant reduction in annotation cost, although their computational efficiency differs. In particular, the simplest variant, a two member committee with no parameters to tune, gives excellent results. We also show that sample selection yields a significant reduction in the size of the model used by the tagger

Tractability of Theory Patching

In this paper we consider the problem of `theory patching', in which we are given a domain theory, some of whose components are indicated to be possibly flawed, and a set of labeled training examples for the domain concept. The theory patching problem is to revise only the indicated components of the theory, such that the resulting theory correctly classifies all the training examples. Theory patching is thus a type of theory revision in which revisions are made to individual components of the theory. Our concern in this paper is to determine for which classes of logical domain theories the theory patching problem is tractable. We consider both propositional and first-order domain theories, and show that the theory patching problem is equivalent to that of determining what information contained in a theory is `stable' regardless of what revisions might be performed to the theory. We show that determining stability is tractable if the input theory satisfies two conditions: that revisions to each theory component have monotonic effects on the classification of examples, and that theory components act independently in the classification of examples in the theory. We also show how the concepts introduced can be used to determine the soundness and completeness of particular theory patching algorithms.Comment: See http://www.jair.org/ for any accompanying file

The excited hadron spectrum in lattice QCD using a new method of estimating quark propagation

Progress in determining the spectrum of excited baryons and mesons in lattice QCD is described. Large sets of carefully-designed hadron operators have been studied and their effectiveness in facilitating the extraction of excited-state energies is demonstrated. A new method of stochastically estimating the low-lying effects of quark propagation is proposed which will allow reliable determinations of temporal correlations of single-hadron and multi-hadron operators.Comment: 5 pages, 4 figures, talk given at Hadron 2009, Tallahassee, Florida, December 1, 200

Nucleon, Δ\Delta and Ω\Omega excited states in Nf=2+1N_f=2+1 lattice QCD

The energies of the excited states of the Nucleon, $\Delta$ and $\Omega$ are computed in lattice QCD, using two light quarks and one strange quark on anisotropic lattices. The calculation is performed at three values of the light quark mass, corresponding to pion masses $m_{\pi}$ = 392(4), 438(3) and 521(3) MeV. We employ the variational method with a large basis of interpolating operators enabling six energies in each irreducible representation of the lattice to be distinguished clearly. We compare our calculation with the low-lying experimental spectrum, with which we find reasonable agreement in the pattern of states. The need to include operators that couple to the expected multi-hadron states in the spectrum is clearly identified.Comment: Revised for publication. References added, Table VI expanded to add strange baryon multiparticle thresholds and multiparticle thresholds added to Figs. 4, 5 and 6. 15 pages, 6 figure

A systematic review of the effects of exercise interventions on body composition in HIV+ adults

Over the years, physical activity and exercise have been used to positively impact the health and quality of life of persons infected with HIV and, more recently, has been associated with a spectrum of body composition changes. The aim of this review was to examine the effects of various exercise interventions on body composition in HIV positive adults, using a search strategy of randomized, controlled trials (RCTs). A systematic review was performed by five independent reviewers using a predetermined protocol adapted from previous research for assessing the articles for inclusion, the extracted data, and methodological quality. Eight RCTs involving 430 (26% female) HIV positive adults performing exercise a minimum of thrice weekly for at least six weeks were finally selected: Four were progressive resistance training (PRT) studies, three were aerobic training (AT) studies, and one involved yoga. In the PRT studies, there were significant increases in three anthropometric measures, namely, body mass, sum of skinfolds and sum of limb girths. In the AT studies, significant decreases were found in seven anthropometric measures, namely, body mass index, waist-hip ratio, body mass, triceps skinfold, waist circumference and sum of skinfolds. With yoga, the changes were nonsignificant. Exercise contributes to improved body composition and, when applied safely, appears to be beneficial for adults living with HIV/AIDS. However, these findings should be interpreted cautiously due to the relatively few RCTs published to date. Future studies would benefit from increased attention to sample size, female participants, participant follow-up, complete statistical analysis and intention-to-treat analysis.Scopu

An Essential Farnesylated Kinesin in Trypanosoma brucei

Kinesins are a family of motor proteins conserved throughout eukaryotes. In our present study we characterize a novel kinesin, KinesinCaaX, orthologs of which are only found in the kinetoplastids and not other eukaryotes. KinesinCaaX has the CVIM amino acids at the C-terminus, and CVIM was previously shown to be an ideal signal for protein farnesylation in T. brucei. In this study we show KinesinCaaX is farnesylated using radiolabeling studies and that farnesylation is dependent on the CVIM motif. Using RNA interference, we show KinesinCaaX is essential for T. brucei proliferation. Additionally RNAi KinesinCaaX depleted T. brucei are 4 fold more sensitive to the protein farneysltransferase (PFT) inhibitor LN-59, suggesting that KinesinCaaX is a target of PFT inhibitors' action to block proliferation of T. brucei. Using tetracycline-induced exogenous tagged KinesinCaaX and KinesinCVIMdeletion (non-farnesylated Kinesin) expression lines in T. brucei, we demonstrate KinesinCaaX is farnesylated in T. brucei cells and this farnesylation has functional effects. In cells expressing a CaaX-deleted version of Kinesin, the localization is more diffuse which suggests correct localization depends on farnesylation. Through our investigation of cell cycle, nucleus and kinetoplast quantitation and immunofluorescence assays an important role is suggested for KinesinCaaX in the separation of nuclei and kinetoplasts during and after they have been replicated. Taken together, our work suggests KinesinCaaX is a target of PFT inhibition of T. brucei cell proliferation and KinesinCaaX functions through both the motor and farnesyl groups

Excited State Nucleon Spectrum with Two Flavors of Dynamical Fermions

Highly excited states for isospin 1/2 baryons are calculated for the first time using lattice QCD with two flavors of dynamical quarks. Anisotropic lattices are used with two pion masses: 416(36) MeV and 578(29) MeV. The lowest four energies are reported in each of the six irreducible representations of the octahedral group at each pion mass. The lattices used have dimensions 24^3x64, spatial lattice spacing a_s = 0.11 fm and temporal lattice spacing a_t = 1/3 a_s. Clear evidence is found for a 5/2^-state in the pattern of negative-parity excited states. This agrees with the pattern of physical states and spin 5/2 has been realized for the first time on the lattice.Comment: 21 pages, 12 figure

Accelerating the annotation of sparse named entities by dynamic sentence selection

Background: Previous studies of named entity recognition have shown that a reasonable level of recognition accuracy can be achieved by using machine learning models such as conditional random fields or support vector machines. However, the lack of training data (i.e. annotated corpora) makes it difficult for machine learning-based named entity recognizers to be used in building practical information extraction systems. Results: This paper presents an active learning-like framework for reducing the human effort required to create named entity annotations in a corpus. In this framework, the annotation work is performed as an iterative and interactive process between the human annotator and a probabilistic named entity tagger. Unlike active learning, our framework aims to annotate all occurrences of the target named entities in the given corpus, so that the resulting annotations are free from the sampling bias which is inevitable in active learning approaches. Conclusion: We evaluate our framework by simulating the annotation process using two named entity corpora and show that our approach can reduce the number of sentences which need to be examined by the human annotator. The cost reduction achieved by the framework could be drastic when the target named entities are sparse. © 2008 Tsuruoka et al; licensee BioMed Central Ltd

Beneficial effects of physical activity in an HIV-infected woman with lipodystrophy: a case report

<p>Abstract</p> <p>Introduction</p> <p>Lipodystrophy is common in patients infected with human immunodeficiency virus receiving highly active antiretroviral therapy, and presents with morphologic changes and metabolic alterations that are associated with depressive behavior and reduced quality of life. We examined the effects of exercise training on morphological changes, lipid profile and quality of life in a woman with human immunodeficiency virus presenting with lipodystrophy.</p> <p>Case presentation</p> <p>A 31-year-old Latin-American Caucasian woman infected with human immunodeficiency virus participated in a 12-week progressive resistance exercise training program with an aerobic component. Her weight, height, skinfold thickness, body circumferences, femur and humerus diameter, blood lipid profile, maximal oxygen uptake volume, exercise duration, strength and quality of life were assessed pre-exercise and post-exercise training. After 12 weeks, she exhibited reductions in her total subcutaneous fat (18.5%), central subcutaneous fat (21.0%), peripheral subcutaneous fat (10.7%), waist circumference (WC) (4.5%), triglycerides (9.9%), total cholesterol (12.0%) and low-density lipoprotein cholesterol (8.6%). She had increased body mass (4.6%), body mass index (4.37%), humerus and femur diameter (3.0% and 2.3%, respectively), high-density lipoprotein cholesterol (16.7%), maximal oxygen uptake volume (33.3%), exercise duration (37.5%) and strength (65.5%). Quality of life measures improved mainly for psychological and physical measures, independence and social relationships.</p> <p>Conclusions</p> <p>These findings suggest that supervised progressive resistance exercise training is a safe and effective treatment for evolving morphologic and metabolic disorders in adults infected with HIV receiving highly active antiretroviral therapy, and improves their quality of life.</p

Recombinant Human Growth Hormone and Rosiglitazone for Abdominal Fat Accumulation in HIV- Infected Patients with Insulin Resistance: A Randomized, Double-Blind, Placebo-Controlled, Factorial Trial

Background: Recombinant human growth hormone (rhGH) reduces visceral adipose tissue (VAT) volume in HIV-infected patients but can worsen glucose homeostasis and lipoatrophy. We aimed to determine if adding rosiglitazone to rhGH would abrogate the adverse effects of rhGH on insulin sensitivity (SI) and subcutaneous adipose tissue (SAT) volume. Methodology/Principal Findings: Randomized, double-blind, placebo-controlled, multicenter trial using a 262 factorial design in which HIV-infected subjects with abdominal obesity and insulin resistance were randomized to rhGH 3 mg daily, rosiglitazone 4 mg twice daily, combination rhGH + rosiglitazone, or double placebo (control) for 12 weeks. The primary endpoint was change in SI by frequently sampled intravenous glucose tolerance test from entry to week 12. Body composition was assessed by whole body magnetic resonance imaging (MRI) and dual Xray absorptiometry (DEXA). Seventy-seven subjects were randomized of whom 72 initiated study drugs. Change in SI from entry to week 12 differed across the 4 arms by 1-way ANCOVA (P = 0.02); by pair-wise comparisons, only rhGH (decreasing SI; P = 0.03) differed significantly from control. Changes from entry to week 12 in fasting glucose and glucose area under the curve on 2- hour oral glucose tolerance test differed across arms (1-way ANCOVA P = 0.004), increasing in the rhGH arm relative to control. VAT decreased significantly in the rhGH arms (217.5% in rhGH/rosiglitazone and 222.7% in rhGH) but not in the rosiglitazone alone (22.5%) or control arms (21.9%). SAT did not change significantly in any arm. DEXA results were consistent with the MRI data. There was no significant rhGH x rosiglitazone interaction for any body composition parameter. Conclusions/Significance: The addition of rosiglitazone abrogated the adverse effects of rhGH on insulin sensitivity and glucose tolerance while not significantly modifying the lowering effect of rhGH on VAT