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This paper revisits building machine learning algorithms that involve interactions between entities, such as those between financial assets in an actively managed portfolio, or interactions between users in a social network. Our goal is to forecast the future evolution of ensembles of multivariate time series in such applications (e.g., the future return of a financial asset or the future popularity of a Twitter account). Designing ML algorithms for such systems requires addressing the challenges of high-dimensional interactions and non-linearity. Existing approaches usually adopt an ad-hoc approach to integrating high-dimensional techniques into non-linear models and re- cent studies have shown these approaches have questionable efficacy in time-evolving interacting systems. To this end, we propose a novel framework, which we dub as the additive influence model. Under our modeling assump- tion, we show that it is possible to decouple the learning of high-dimensional interactions from the learning of non-linear feature interactions. To learn the high-dimensional interac- tions, we leverage kernel-based techniques, with provable guarantees, to embed the entities in a low-dimensional latent space. To learn the non-linear feature-response interactions, we generalize prominent machine learning techniques, includ- ing designing a new statistically sound non-parametric method and an ensemble learning algorithm optimized for vector re- gressions. Extensive experiments on two common applica- tions demonstrate that our new algorithms deliver significantly stronger forecasting power compared to standard and recently proposed methods. 

Chemotrophic microorganisms face the steep challenge of limited energy resources in natural environments. This observation has important implications for interpreting and modeling the kinetics and thermodynamics of microbial reactions. Current modeling frameworks treat microbes as autocatalysts, and simulate microbial energy conservation and growth with fixed kinetic and thermodynamic parameters. However, microbes are capable of acclimating to the environment and modulating their parameters in order to gain competitive fitness. Here we constructed an optimization model and described microbes as self-adapting catalysts by linking microbial parameters to intracellular metabolic resources. From the optimization results, we related microbial parameters to the substrate concentration and the energy available in the environment, and simplified the relationship between the kinetics and the thermodynamics of microbial reactions. We took as examples Methanosarcina and Methanosaeta – the methanogens that produce methane from acetate – and showed how the acclimation model extrapolated laboratory observations to natural environments and improved the simulation of methanogenesis and the dominance of Methanosaeta over Methanosarcina in lake sediments. These results highlight the importance of physiological acclimation in shaping the kinetics and thermodynamics of microbial reactions and in determining the outcome of microbial interactions. 

Chemotrophic microorganisms face the steep challenge of limited energy resources in natural environments. This observation has important implications for interpreting and modeling the kinetics and thermodynamics of microbial reactions. Current modeling frameworks treat microbes as autocatalysts, and simulate microbial energy conservation and growth with fixed kinetic and thermodynamic parameters. However, microbes are capable of acclimating to the environment and modulating their parameters in order to gain competitive fitness. Here we constructed an optimization model and described microbes as self-adapting catalysts by linking microbial parameters to intracellular metabolic resources. From the optimization results, we related microbial parameters to the substrate concentration and the energy available in the environment, and simplified the relationship between the kinetics and the thermodynamics of microbial reactions.We took as examples Methanosarcina and Methanosaeta – the methanogens that produce methane from acetate – and showed how the acclimation model extrapolated laboratory observations to natural environments and improved the simulation of methanogenesis and the dominance of Methanosaeta over Methanosarcina in lake sediments. These results highlight the importance of physiological acclimation in shaping the kinetics and thermodynamics of microbial reactions and in determining the outcome of microbial interactions. 

ABSTRACT The Monod equation has been widely applied as the general rate law of microbial growth, but its applications are not always successful. By drawing on the frameworks of kinetic and stoichiometric metabolic models and metabolic control analysis, the modeling reported here simulated the growth kinetics of a methanogenic microorganism and illustrated that different enzymes and metabolites control growth rate to various extents and that their controls peak at either very low, intermediate, or very high substrate concentrations. In comparison, with a single term and two parameters, the Monod equation only approximately accounts for the controls of rate-determining enzymes and metabolites at very high and very low substrate concentrations, but neglects the enzymes and metabolites whose controls are most notable at intermediate concentrations. These findings support a limited link between the Monod equation and methanogen growth, and unify the competing views regarding enzyme roles in shaping growth kinetics. The results also preclude a mechanistic derivation of the Monod equation from methanogen metabolic networks and highlight a fundamental challenge in microbiology: single-term expressions may not be sufficient for accurate prediction of microbial growth. IMPORTANCE The Monod equation has been widely applied to predict the rate of microbial growth, but its application is not always successful. Using a novel metabolic modeling approach, we simulated the growth of a methanogen and uncovered a limited mechanistic link between the Monod equation and the methanogen’s metabolic network. Specifically, the equation provides an approximation to the controls by rate-determining metabolites and enzymes at very low and very high substrate concentrations, but it is missing the remaining enzymes and metabolites whose controls are most notable at intermediate concentrations. These results support the Monod equation as a useful approximation of growth rates and highlight a fundamental challenge in microbial kinetics: single-term rate expressions may not be sufficient for accurate prediction of microbial growth. 

The Monodequationhasbeenwidelyappliedasthegeneralratelaw of microbialgrowth,butitsapplicationsarenotalwayssuccessful.Bydrawingon the frameworksofkineticandstoichiometricmetabolicmodelsandmetaboliccon- trol analysis,themodelingreportedheresimulatedthegrowthkineticsofametha- nogenic microorganismandillustratedthatdifferentenzymesandmetabolitescon- trol growthratetovariousextentsandthattheircontrolspeakateitherverylow, intermediate, orveryhighsubstrateconcentrations.Incomparison,withasingle term andtwoparameters,theMonodequationonlyapproximatelyaccountsforthe controls ofrate-determiningenzymesandmetabolitesatveryhighandverylow substrate concentrations,butneglectstheenzymesandmetaboliteswhosecontrols are mostnotableatintermediateconcentrations.These findings supportalimited link betweentheMonodequationandmethanogengrowth,andunifythecompet- ing viewsregardingenzymerolesinshapinggrowthkinetics.Theresultsalsopre- clude amechanisticderivationoftheMonodequationfrommethanogenmetabolic networks andhighlightafundamentalchallengeinmicrobiology:single-termexpres- sions maynotbesufficient foraccuratepredictionofmicrobialgrowth. 

The Q10 coefficient is the ratio of reaction rates at two temperatures 10°C apart, and has been widely applied to quantify the temperature sensitivity of organic matter decomposition. However, biogeochemists and ecologists have long recognized that a constant Q10 coefficient does not describe the temperature sensitivity of organic matter decomposition accurately. To examine the consequences of the constant Q10 assumption, we built a biogeochemical reaction model to simulate anaerobic organic matter decomposition in peatlands in the Upper Peninsula of Michigan, USA, and compared the simulation results to the predictions with Q10 coefficients. By accounting for the reactions of extracellular enzymes, mesophilic fermenting and methanogenic microbes, and their temperature responses, the biogeochemical reaction model reproduces the observations of previous laboratory incubation experiments, including the temporal variations in the concentrations of dissolved organic carbon, acetate, dihydrogen, carbon dioxide, and methane, and confirms that fermentation limits the progress of anaerobic organic matter decomposition. The modeling results illustrate the oversimplification inherent in the constant Q10 assumption and how the assumption undermines the kinetic prediction of anaerobic organic matter decomposition. In particular, the model predicts that between 5°C and 30°C, the decomposition rate increases almost linearly with increasing temperature, which stands in sharp contrast to the exponential relationship given by the Q10 coefficient. As a result, the constant Q10 approach tends to underestimate the rates of organic matter decomposition within the temperature ranges where Q10 values are determined, and overestimate the rates outside the temperature ranges. The results also show how biogeochemical reaction modeling, combined with laboratory experiments, can help uncover the temperature sensitivity of organic matter decomposition arising from underlying catalytic mechanisms. 

Existing topic modeling and text segmentation methodologies generally require large datasets for training, limiting their capabilities when only small collections of text are available. In this work, we reexamine the inter-related problems of “topic identification” and “text segmentation” for sparse document learning, when there is a single new text of interest. In developing a methodology to handle single documents, we face two major challenges. First is sparse information : with access to only one document, we cannot train traditional topic models or deep learning algorithms. Second is significant noise : a considerable portion of words in any single document will produce only noise and not help discern topics or segments. To tackle these issues, we design an unsupervised, computationally efficient methodology called Biclustering Approach to Topic modeling and Segmentation (BATS). BATS leverages three key ideas to simultaneously identify topics and segment text: (i) a new mechanism that uses word order information to reduce sample complexity, (ii) a statistically sound graph-based biclustering technique that identifies latent structures of words and sentences, and (iii) a collection of effective heuristics that remove noise words and award important words to further improve performance. Experiments on six datasets show that our approach outperforms several state-of-the-art baselines when considering topic coherence, topic diversity, segmentation, and runtime comparison metrics. 

Poly[ n ]catenanes are a class of polymers that are composed entirely of interlocked rings. One synthetic route to these polymers involves the formation of a metallosupramolecular polymer (MSP) that consists of alternating units of macrocyclic and linear thread components. Ring closure of the thread components has been shown to yield a mixture of cyclic, linear, and branched poly[ n ]catenanes. Reported herein are investigations into this synthetic methodology, with a focus on a more detailed understanding of the crude product distribution and how the concentration of the MSP during the ring closing reaction impacts the resulting poly[ n ]catenanes. In addition to a better understanding of the molecular products obtained in these reactions, the results show that the concentration of the reaction can be used to tune the size and type of poly[ n ]catenanes accessed. At low concentrations the interlocked product distribution is limited to primarily oligomeric and small cyclic catenanes . However, the same reaction at increased concentration can yield branched poly[ n ]catenanes with an ca. 21 kg mol −1 , with evidence of structures containing as many as 640 interlocked rings (1000 kg mol −1 ).