Multi-utility Learning: Structured-output Learning with Multiple Annotation-specific Loss Functions

Structured-output learning is a challenging problem; particularly so because of the difficulty in obtaining large datasets of fully labelled instances for training. In this paper we try to overcome this difficulty by presenting a multi-utility learning framework for structured prediction that can learn from training instances with different forms of supervision. We propose a unified technique for inferring the loss functions most suitable for quantifying the consistency of solutions with the given weak annotation. We demonstrate the effectiveness of our framework on the challenging semantic image segmentation problem for which a wide variety of annotations can be used. For instance, the popular training datasets for semantic segmentation are composed of images with hard-to-generate full pixel labellings, as well as images with easy-to-obtain weak annotations, such as bounding boxes around objects, or image-level labels that specify which object categories are present in an image. Experimental evaluation shows that the use of annotation-specific loss functions dramatically improves segmentation accuracy compared to the baseline system where only one type of weak annotation is used

Enabling remote design and troubleshooting experiments using the ilab shared architecture

12th Biennial International Conference on Engineering, Construction, and Operations in Challenging Environments; and Fourth NASA/ARO/ASCE Workshop on Granular Materials in Lunar and Martian Exploration Honolulu, Hawaii, United States March 14-17, 2010The MIT iLab Project is dedicated to the goal of increasing laboratory experimentation opportunities for engineering students worldwide. Since its inception in 1998, the project has furthered this goal through the development of individual remote laboratories, or iLabs, as well as a distributed software infrastructure designed to streamline the implementation and sharing of remote laboratories. iLabs are designed to complement traditional, hands-on laboratories by providing practical educational experiences where they would not otherwise be available. Such remote labs, developed and hosted by MIT and other institutions within the iLab Consortium, have been successfully used by instructors at schools across the educational spectrum and around the world. While certainly valuable, many of the original experiments available through the iLab platform provide a limited experience in that they are observational in nature. They only provide students the ability to study the behavior of a pre-defined system under test. Such labs have proven to be valuable additions to engineering curricula, but do not have the flexibility that is inherent in a traditional laboratory experience. To address this, the MIT iLab Project has begun focusing on the development of iLabs that provide students with the ability to design or troubleshoot experimental systems. Through two particular remote labs, focusing on electronic control system analysis and basic electronics test and measurement respectively, the project is designing remote labs that provide a more flexible learning experience for students and are more attractive to instructors in a broad set of disciplines.National Science Foundation (U.S.) (award 0702735)Singapore-MIT Alliance for Research and Technology CenterMicrosoft CorporationCarnegie Corporation of New YorkMaricopa County Community College District. Maricopa Advanced Technology Education Cente

Effect of HSV-2 Suppressive Therapy on Genital Tract HIV-1 RNA Shedding among Women on HAART: A Pilot Randomized Controlled Trial

Background. The role of suppressive HSV therapy in women coinfected with HSV-2 and HIV-1 taking highly active antiretroviral therapy (HAART) is unclear. Methods. 60 women with HIV-1/HSV-2 coinfection on HAART with plasma HIV-1 viral load (PVL) ≤75 copies/mL were randomized to receive acyclovir (N = 30) or no acyclovir (N = 30). PVL, genital tract (GT) HIV-1, and GT HSV were measured every 4 weeks for one year. Results. Detection of GT HIV-1 was not significantly different in the two arms (OR 1.23, P = 0.67), although this pilot study was underpowered to detect this difference. When PVL was undetectable, the odds of detecting GT HIV were 0.4 times smaller in the acyclovir arm than in the control arm, though this was not statistically significant (P = 0.07). The odds of detecting GT HSV DNA in women receiving acyclovir were significantly lower than in women in the control group, OR 0.38, P < 0.05. Conclusions. Chronic suppressive therapy with acyclovir in HIV-1/HSV-2-positive women on HAART significantly reduces asymptomatic GT HSV shedding, though not GT HIV shedding or PVL. PVL was strongly associated with GT HIV shedding, reinforcing the importance of HAART in decreasing HIV sexual transmission

Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics

Microorganisms play a fundamental role in the cycling of nutrients and energy on our planet. A common strategy for many microorganisms mediating biogeochemical cycles in anoxic environments is syntrophy, frequently necessitating close spatial proximity between microbial partners. We are only now beginning to fully appreciate the diversity and pervasiveness of microbial partnerships in nature, the majority of which cannot be replicated in the laboratory. One notable example of such cooperation is the interspecies association between anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria. These consortia are globally distributed in the environment and provide a significant sink for methane by substantially reducing the export of this potent greenhouse gas into the atmosphere. The interdependence of these currently uncultured microbes renders them difficult to study, and our knowledge of their physiological capabilities in nature is limited. Here, we have developed a method to capture select microorganisms directly from the environment, using combined fluorescence in situ hybridization and immunomagnetic cell capture. We used this method to purify syntrophic anaerobic methane oxidizing ANME-2c archaea and physically associated microorganisms directly from deep-sea marine sediment. Metagenomics, PCR, and microscopy of these purified consortia revealed unexpected diversity of associated bacteria, including Betaproteobacteria and a second sulfate-reducing Deltaproteobacterial partner. The detection of nitrogenase genes within the metagenome and subsequent demonstration of 15N2 incorporation in the biomass of these methane-oxidizing consortia suggest a possible role in new nitrogen inputs by these syntrophic assemblages

A Graph Theoretic Approach for Object Shape Representation in Compositional Hierarchies Using a Hybrid Generative-Descriptive Model

A graph theoretic approach is proposed for object shape representation in a hierarchical compositional architecture called Compositional Hierarchy of Parts (CHOP). In the proposed approach, vocabulary learning is performed using a hybrid generative-descriptive model. First, statistical relationships between parts are learned using a Minimum Conditional Entropy Clustering algorithm. Then, selection of descriptive parts is defined as a frequent subgraph discovery problem, and solved using a Minimum Description Length (MDL) principle. Finally, part compositions are constructed by compressing the internal data representation with discovered substructures. Shape representation and computational complexity properties of the proposed approach and algorithms are examined using six benchmark two-dimensional shape image datasets. Experiments show that CHOP can employ part shareability and indexing mechanisms for fast inference of part compositions using learned shape vocabularies. Additionally, CHOP provides better shape retrieval performance than the state-of-the-art shape retrieval methods.Comment: Paper : 17 pages. 13th European Conference on Computer Vision (ECCV 2014), Zurich, Switzerland, September 6-12, 2014, Proceedings, Part III, pp 566-581. Supplementary material can be downloaded from http://link.springer.com/content/esm/chp:10.1007/978-3-319-10578-9_37/file/MediaObjects/978-3-319-10578-9_37_MOESM1_ESM.pd

Improving Global Multi-target Tracking with Local Updates

Conference dates: September 6-7 & 12, 2014We propose a scheme to explicitly detect and resolve ambiguous situations in multiple target tracking. During periods of uncertainty, our method applies multiple local single target trackers to hypothesise short term tracks. These tracks are combined with the tracks obtained by a global multi-target tracker, if they result in a reduction in the global cost function. Since tracking failures typically arise when targets become occluded, we propose a local data association scheme to maintain the target identities in these situations. We demonstrate a reduction of up to 50% in the global cost function, which in turn leads to superior performance on several challenging benchmark sequences. Additionally, we show tracking results in sports videos where poor video quality and frequent and severe occlusions between multiple players pose difficulties for state-of-the-art trackers.Anton Milan, Rikke Gade, Anthony Dick, Thomas B. Moeslund, and Ian Rei

Interactive effects of iron and light limitation on the molecular physiology of the Southern Ocean diatom Fragilariopsis kerguelensis

The polar diatom Fragilariopsis kerguelensis is ubiquitous in Southern Ocean waters and is a major responder to iron fertilization, encountering large gradients in iron concentrations and light availability. We performed a comparative transcriptomic analysis of F. kerguelensis grown under varying iron and light conditions in order to investigate the molecular underpinnings that may explain its physiological response to iron and light limitation. Low iron reduced growth rates more than low light, but there was not an additive effect of low iron and low light on growth rate. Low iron treatments (saturating and low light) had the largest transcriptomic response; however, expression patterns were more similar in low light treatments (high and low iron). Under iron and light limitation, carbon fixation and amino acid, ribosome, and sulfur metabolisms were overrepresented relative to the control (iron replete, saturating light). Transcripts of genes encoding for the proteins aquaporin, proteorhodopsin, plastocyanin, and flavodoxin were overrepresented to the greatest extent in the low iron/low light treatment, indicating there may be an additive effect of iron/light colimitation at the molecular level. Iron and light replete cells demonstrated increased expression of genes encoding for the proteins ferritin, carbonic anhydrase, and numerous iron-dependent proteins relative to the growth-limiting treatments. This transcriptome analysis reveals mechanisms that may underpin the ecological success of this diatom in low iron and light environments, highlighting the important role of diversified photosynthetic isoforms, iron acquisition, unique detoxification mechanisms of reactive oxygen species, and metabolic shifts in amino acid recycling and carbon metabolism

Socio-Economic Instability and the Scaling of Energy Use with Population Size

The size of the human population is relevant to the development of a sustainable world, yet the forces setting growth or declines in the human population are poorly understood. Generally, population growth rates depend on whether new individuals compete for the same energy (leading to Malthusian or density-dependent growth) or help to generate new energy (leading to exponential and super-exponential growth). It has been hypothesized that exponential and super-exponential growth in humans has resulted from carrying capacity, which is in part determined by energy availability, keeping pace with or exceeding the rate of population growth. We evaluated the relationship between energy use and population size for countries with long records of both and the world as a whole to assess whether energy yields are consistent with the idea of an increasing carrying capacity. We find that on average energy use has indeed kept pace with population size over long time periods. We also show, however, that the energy-population scaling exponent plummets during, and its temporal variability increases preceding, periods of social, political, technological, and environmental change. We suggest that efforts to increase the reliability of future energy yields may be essential for stabilizing both population growth and the global socio-economic system

Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Environmental Microbiology 16 (2014): 2815-2830, doi:10.1111/1462-2920.12254.A considerable fraction of the Earth's organic carbon exists in dissolved form in seawater. To investigate the roles of planktonic marine microbes in the biogeochemical cycling of this dissolved organic matter (DOM), we performed controlled seawater incubation experiments and followed the responses of an oligotrophic surface water microbial assemblage to perturbations with DOM derived from an axenic culture of Prochlorococcus, or high-molecular weight DOM concentrated from nearby surface waters. The rapid transcriptional responses of both Prochlorococcus and Pelagibacter populations suggested the utilization of organic nitrogen compounds common to both DOM treatments. Along with these responses, both populations demonstrated decreases in gene transcripts associated with nitrogen stress, including those involved in ammonium acquisition. In contrast, responses from low abundance organisms of the NOR5/OM60 gammaproteobacteria were observed later in the experiment, and included elevated levels of gene transcripts associated with polysaccharide uptake and oxidation. In total, these results suggest that numerically dominant oligotrophic microbes rapidly acquire nitrogen from commonly available organic sources, and also point to an important role for carbohydrates found within the DOM pool for sustaining the less abundant microorganisms in these oligotrophic systems.This work was supported by a National Science Foundation Science and Technology Center Award EF0424599 (E.F.D and D.M.K.), grants to D.M.K., D.J.R and E.F.D from the Gordon and Betty Moore Foundation, a gift from the Agouron Institute (to E.F.D.) and a fellowship (202180) to A.K.S. from the Canadian Institutes of Health Research (CIHR)