Open Vocabulary Learning on Source Code with a Graph-Structured Cache

Machine learning models that take computer program source code as input typically use Natural Language Processing (NLP) techniques. However, a major challenge is that code is written using an open, rapidly changing vocabulary due to, e.g., the coinage of new variable and method names. Reasoning over such a vocabulary is not something for which most NLP methods are designed. We introduce a Graph-Structured Cache to address this problem; this cache contains a node for each new word the model encounters with edges connecting each word to its occurrences in the code. We find that combining this graph-structured cache strategy with recent Graph-Neural-Network-based models for supervised learning on code improves the models' performance on a code completion task and a variable naming task --- with over $100\%$ relative improvement on the latter --- at the cost of a moderate increase in computation time.Comment: Published in the International Conference on Machine Learning (ICML 2019), 13 page

A dynamic fluid landscape mediates the spread of bacteria

Microbial interactions regulate their spread and survival in competitive environments. It is not clear if the physical parameters of the environment regulate the outcome of these interactions. In this work, we show that the opportunistic pathogen Pseudomonas aeruginosa occupies a larger area on the substratum in the presence of yeast such as Cryptococcus neoformans , than without it. At the microscopic level, bacterial cells show an enhanced activity in the vicinity of yeast cells. We observe this behaviour even when the live yeast cells are replaced with heat-killed cells or with spherical glass beads of similar morphology, which suggests that the observed behaviour is not specific to the biology of microbes. Upon careful investigation, we find that a fluid pool is formed around yeast cells which facilitates the swimming of the flagellated P. aeruginosa , causing their enhanced motility. Using mathematical modeling we demonstrate how this local enhancement of bacterial motility leads to the enhanced spread observed at the level of the plate. We find that the dynamics of the fluid landscape around the bacteria, mediated by the growing yeast lawn, affects the spreading. For instance, when the yeast lawn grows faster, a bacterial colony prefers a lower initial loading of yeast cells for optimum enhancement in the spread. We confirm our predictions using Candida albicans and C. neoformans, at different initial compositions. In summary, our work shows the importance of considering the dynamically changing physical environment while studying bacterial motility in complex environments.Comment: 14 pages of main text, 5 figures, 4 pages of SI adde

Specific collagens maintain the cuticle permeability barrier in Caenorhabditis elegans

Collagen-enriched cuticle forms the outermost layer of skin in nematode Caenorhabditis elegans. The nematode’s genome encodes 177 collagens, but little is known about their role in maintaining the structure or barrier function of the cuticle. In this study, we found six permeability determining (PD) collagens. Loss of any of these PD collagens—DPY-2, DPY-3, DPY-7, DPY-8, DPY-9, and DPY-10—led to enhanced susceptibility of nematodes to paraquat (PQ) and antihelminthic drugs- levamisole and ivermectin. Upon exposure to PQ, PD collagen mutants accumulated more PQ and incurred more damage and death despite the robust activation of antioxidant machinery. We find that BLMP-1, a zinc finger transcription factor, maintains the barrier function of the cuticle by regulating the expression of PD collagens. We show that the permeability barrier maintained by PD collagens acts in parallel to FOXO transcription factor DAF-16 to enhance survival of insulin-like receptor mutant, daf-2. In all, this study shows that PD collagens regulate cuticle permeability by maintaining the structure of C. elegans cuticle and thus provide protection against exogenous toxins.</p

Contrasting seed biology of two ornamental palms: Pygmy Date Palm (Phoenix roebelenii O’Brien) and Fishtail Palm (Caryota urens L.) and implications for their long-term conservation

477-484The Arecaceae family includes palm trees of economic importance both as a source of agricultural produce and as ornamental components in landscaping projects. Pygmy date palm (Phoenix roebelenii) and solitary fishtail palm (Caryota urens) are well known landscaping plants today. Both species have their origin in Southeast Asia and, especially C. urens is widespread in peninsular India and Sri Lanka. They are multipurpose species with a variety of applications and thus very heavily utilized. Knowledge of palm seed storage biology will improve their conservation prospects. In present studies, fresh seed moisture content in P. roebelenii was recorded to be 30% with germinability of 98%. After desiccation to 8% moisture germinability was reduced to 90% and the seeds survived cryo-exposure. Fresh seeds of C. urens, with initial moisture content of 34% and 95% germinability could be desiccated to lowest level of only 29% moisture content, with complete loss of germinability. Fresh as well as desiccated seeds of this species did not survive cryo-exposure. While the seeds of C. urens stored at room temperature lost their germinability by 110 days, seeds of P. roebelenii could germinate even after 9 months of storage. P. roebelenii is proven to exhibit orthodox seed storage behaviour while C. urens is found to exhibit recalcitrant seed storage behaviour. Long-term ex situ cryo-conservation in the form of seed gene banks would be suitable for seed propagated orthodox palm species and a few germplasm centres may be established for recalcitrant Indian palms in suitable bio-geographic regions as a complimentary ex situ conservation

Open Vocabulary Learning on Source Code with a Graph-Structured Cache

Machine learning models that take computer program source code as input typically use Natural Language Processing (NLP) techniques. However, a major challenge is that code is written using an open, rapidly changing vocabulary due to, e.g., the coinage of new variable and method names. Reasoning over such a vocabulary is not something for which most NLP methods are designed. We introduce a Graph-Structured Cache to address this problem; this cache contains a node for each new word the model encounters with edges connecting each word to its occurrences in the code. We find that combining this graph-structured cache strategy with recent Graph-Neural-Network-based models for supervised learning on code improves the models’ performance on a code completion task and a variable naming task — with over 100% relative improvement on the latter — at the cost of a moderate increase in computation time

Contrasting seed biology of two ornamental palms: Pygmy Date Palm (Phoenix roebelenii O’Brien) and Fishtail Palm (Caryota urens L.)

The Arecaceae family includes palm trees of economic importance both as a source of agricultural produce and asornamental components in landscaping projects. Pygmy date palm (Phoenix roebelenii) and solitary fishtail palm (Caryotaurens) are well known landscaping plants today. Both species have their origin in Southeast Asia and, especially C. urens iswidespread in peninsular India and Sri Lanka. They are multipurpose species with a variety of applications and thus veryheavily utilized. Knowledge of palm seed storage biology will improve their conservation prospects. In present studies, freshseed moisture content in P. roebelenii was recorded to be 30% with germinability of 98%. After desiccation to 8% moisturegerminability was reduced to 90% and the seeds survived cryo-exposure. Fresh seeds of C. urens, with initial moisturecontent of 34% and 95% germinability could be desiccated to lowest level of only 29% moisture content, with complete lossof germinability. Fresh as well as desiccated seeds of this species did not survive cryo-exposure. While the seeds of C. urensstored at room temperature lost their germinability by 110 days, seeds of P. roebelenii could germinate even after 9 monthsof storage. P. roebelenii is proven to exhibit orthodox seed storage behaviour while C. urens is found to exhibit recalcitrantseed storage behaviour. Long-term ex situ cryo-conservation in the form of seed gene banks would be suitable for seedpropagated orthodox palm species and a few germplasm centres may be established for recalcitrant Indian palms in suitablebio-geographic regions as a complimentary ex situ conservation

Foraging Signals Promote Swarming in Starving <i>Pseudomonas aeruginosa</i>

The opportunistic human pathogen Pseudomonas aeruginosa is known for exhibiting diverse forms of collective behaviors, like swarming motility and bio-film formation. Swarming in P. aeruginosa is a collective movement of the bacterial population over a semisolid surface, but specific swarming signals are not clear. We hypothesize that specific environmental signals induce swarming in P. aeruginosa. We show that under nutrient-limiting conditions, a low concentration of ethanol provides a strong ecological motivation for swarming in P. aeruginosa strain PA14. Ethanol serves as a signal and not a source of carbon under these conditions. Moreover, ethanol-driven swarming relies on the ability of the bacteria to metabolize ethanol to acetaldehyde using a periplasmic quinoprotein alcohol dehydrogenase, ExaA. We found that ErdR, an orphan response regulator linked to ethanol oxidation, is necessary for the transcriptional regulation of a cluster of 17 genes, including exaA, during swarm lag. Further, we show that P. aeruginosa displays characteristic foraging motility on a lawn of Cryptococcus neoformans, a yeast species, in a manner dependent on the ethanol dehydrogenase ErdR and on rhamnolipids. Finally, we show that ethanol, as a volatile, could induce swarming in P. aeruginosa at a distance, suggesting long-range spatial effects of ethanol as a signaling molecule.</p