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Design in synthetic biology is typically goal-oriented: aiming to repurpose and optimize existing biological functions for new contexts, augmenting biology with new-to-nature capabilities, or creating life-like systems from scratch. While the field has seen many advances over the past two decades, bottlenecks in the complexity of the systems built are emerging and designs that function in the lab often fail when used in real-world contexts. Here, we propose an open-ended approach to biological design that aims to continuously generate innovative solutions capable of overcoming such hurdles. The fundamental principle we put forward is that the novelty of designed biology, be it a protein, genetic construct or organism, is at least as important as how well it fulfils its goal. Designing with novelty in mind, rather than a sole focus on optimization towards a single ``best'' design, may allow us to move beyond the diminishing returns we see in performance for most engineered biology to date. Research from the artificial life and evolutionary computing communities has demonstrated that embracing novelty can allow for the automatic generation of innovative and surprising solutions to challenging problems that move us beyond local optima. Synthetic biology now offers the ideal playground to test these ideas in living systems and explore more creative approaches to biological design.

Machine learning has been broadly implemented to investigate biological systems. In this regard, the field of phage biology has embraced machine learning to elucidate and predict phage-host interactions, based on receptor-binding proteins, (anti-)defense systems, prophage detection, and life cycle recognition. Here, we highlight the enormous potential of integrating information from omics data with insights from systems biology to better understand phage-host interactions. We conceptualize and discuss the potential of a multilayer model that mirrors the phage infection process, integrating adsorption, bacterial pan-immune components and hijacking of the bacterial metabolism to predict phage infectivity. In the future, this model can offer insights into the underlying mechanisms of the infection process, and digital phagograms can support phage cocktail design and phage engineering.

BackgroundDisability progression is a key milestone in the disease evolution of people with multiple sclerosis (PwMS). Prediction models of disability progression have not yet reached the level of trust needed to be adopted in the clinic. A common benchmark to assess model development in multiple sclerosis is also currently lacking.MethodsData of adult PwMS with a follow-up of at least three years from 146 MS centers, spread over 40 countries and collected by the MSBase consortium was used. With basic inclusion criteria for quality requirements, it represents a total of 15, 240 PwMS. External validation was performed and repeated five times to assess the significance of the results. TRIPOD guidelines were followed.Confirmed disability progression after two years was predicted, with a confirmation window of six months. Only routinely collected variables were used such as the expended disability status scale, treatment, relapse information, and MS course.To learn the probability of disability progression, state-of-the-art machine learning models were investigated. The discrimination performance of the models is evaluated on their area under the receiver operator curve (ROC-AUC) and under the precision recall curve (AUC-PR), and their calibration via the Brier score and the expected calibration error.FindingsA temporal attention model was the best model. It achieved a ROC-AUC of 0·71 ± 0·01, an AUC-PR of 0·26 ± 0·02, a Brier score of 0·1 ± 0·01 and an expected calibration error of 0·07 ± 0·04. The history of disability progression is more predictive for future disability progression than the treatment or relapses.InterpretationGood discrimination and calibration performance on an external validation set is achieved, using only routinely collected variables. This makes these models ready for a clinical impact study. All our preprocessing and model code is available at https://gitlab.com/edebrouwer/ms_benchmark, making this task an ideal benchmark for predicting disability progression in MS.

A major goal in synthetic biology is the engineering of synthetic gene circuits with a predictable, controlled and designed outcome. This creates a need for building blocks that can modulate gene expression without interference with the native cell system. A tool allowing forward engineering of promoters with predictable transcription initiation frequency is still lacking. Promoter libraries specific for σ

Researchers relying on electrochemical impedance spectroscopy need to decide which equivalent electrical circuit to use to analyze their measurements. Here, we present an identification algorithm based on gene expression programming to support this decision. It is accompanied by some measures to enhance the interpretability of the resulting circuits, such as the removal of redundant components to avoid overly complex circuits. We also provide the option to depart from an initial population of widely applied circuits, allowing for quick identification of known circuits that are capable of modeling the measurement data. As the number of measurements per experiment is typically rather limited in real-life experiments, we examine the number needed to find an adequate circuit topology for two example circuits. Next, the algorithm is tested on impedance simulations for a variety of circuits. Noise robustness is evaluated by subjecting the impedance measurements to increasing amounts of Gaussian noise, demonstrating that the algorithm still works well even for noise levels that are significantly higher than what is typically encountered in practice. Finally, we validate the algorithm by identifying the appropriate circuit for impedance measurements from a biological application.

Receptor-binding proteins (RBPs) of bacteriophages initiate the infection of their corresponding bacterial host and act as the primary determinant for host specificity. The ever-increasing amount of sequence data enables the development of predictive models for the automated identification of RBP sequences. However, the development of such models is challenged by the inconsistent or missing annotation of many phage proteins. Recently developed tools have started to bridge this gap but are not specifically focused on RBP sequences, for which many different annotations are available. We have developed two parallel approaches to alleviate the complex identification of RBP sequences in phage genomic data. The first combines known RBP-related hidden Markov models (HMMs) from the Pfam database with custom-built HMMs to identify phage RBPs based on protein domains. The second approach consists of training an extreme gradient boosting classifier that can accurately discriminate between RBPs and other phage proteins. We explained how these complementary approaches can reinforce each other in identifying RBP sequences. In addition, we benchmarked our methods against the recently developed PhANNs tool. Our best performing model reached a precision-recall area-under-the-curve of 93.8% and outperformed PhANNs on an independent test set, reaching an F1-score of 84.0% compared to 69.8%.

Water potential explains water transport in the soil–plant–atmosphere continuum (SPAC), and is gaining interest as connecting variable between ‘pedo-, bio- and atmosphere’. It is primarily used to simulate hydraulics in the SPAC, and is thus essential for studying drought effects. Recent implementations of hydraulics in large-scale terrestrial biosphere models (TBMs) improved their performance under water-limited conditions, while hydraulic features of recent detailed functional–structural plant models (FSPMs) open new possibilities for dissecting complex traits for drought tolerance. These developments in models across scales deserve a critical appraisal to evaluate its potential for wider use in FSPMs, but also in crop systems models (CSMs), where hydraulics are currently still absent. After refreshing the physical basis, we first address models where water potential is primarily used for describing water transport along the transpiration pathway from the soil to the leaves, through the roots, the xylem and the leaf mesophyll. Then, we highlight models for three ecophysiological processes, which have well-recognized links to water potential: phloem transport, stomatal conductance and organ growth. We identify water potential as the bridge between soil, root and shoot models, as the physiological variable integrating below- and above-ground abiotic drivers, but also as the link between water status and growth. Models making these connections enable identifying crucial traits for ecosystem resilience to drought and for breeding towards improved drought tolerance in crops. Including hydraulics often increases model complexity, and thus requires experimental data on soil and plant hydraulics. Nevertheless, modelling hydraulics is insightful at different scales (FSPMs, CSMs and TBMs).

Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guide sampling target prioritisation, but the predictions from any given model might be highly uncertain; moreover, systematic model validation is rare, and the drivers of model performance are consequently under-documented. Here, we use the bat hosts of betacoronaviruses as a case study for the data-driven process of comparing and validating predictive models of probable reservoir hosts. In early 2020, we generated an ensemble of eight statistical models that predicted host-virus associations and developed priority sampling recommendations for potential bat reservoirs of betacoronaviruses and bridge hosts for SARS-CoV-2. During a time frame of more than a year, we tracked the discovery of 47 new bat hosts of betacoronaviruses, validated the initial predictions, and dynamically updated our analytical pipeline. We found that ecological trait-based models performed well at predicting these novel hosts, whereas network methods consistently performed approximately as well or worse than expected at random. These findings illustrate the importance of ensemble modelling as a buffer against mixed-model quality and highlight the value of including host ecology in predictive models. Our revised models showed an improved performance compared with the initial ensemble, and predicted more than 400 bat species globally that could be undetected betacoronavirus hosts. We show, through systematic validation, that machine learning models can help to optimise wildlife sampling for undiscovered viruses and illustrates how such approaches are best implemented through a dynamic process of prediction, data collection, validation, and updating. © 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.

Summary In combinatorial biotechnology, it is crucial for screening experiments to sufficiently cover the design space. In the BioCCP.jl package (Julia), we provide functions for minimum sample size determination based on the mathematical framework coined the Coupon Collector Problem. Availability and implementation BioCCP.jl, including source code, documentation and Pluto notebooks, is available at https://github.com/kirstvh/BioCCP.jl.

Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms., SDA acknowledges funding from CNRS for her sabbatical in 2018–2020. JOI acknowledges funding from the Belmont Forum, grant ANR-18-BELM-0003-01. This work is a contribution to the scientific program of Québec Océan and the Takuvik Joint International Laboratory (UMI3376; CNRS - Université Laval). FM was supported by an NSERC Discovery Grant (RGPIN-2014-05433). MS is supported by the Research Foundation - Flanders (FWO17/PDO/067). FB received support from ETH Zürich. MDO is supported by the Gordon and Betty Moore Foundation and the U.S. National Science Foundation. ECB is supported by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) under the grant agreement no. 88882.438735/2019-01. TB is supported by the French National Research Agency (ANR-19-CE01-0006). NVP is supported by the Spanish State Research Agency, Ministry of Science and Innovation (PTA2016-12822-I). FL is supported by the Institut Universitaire de France (IUF). HMS was supported by the Simons Foundation (561126) and the U.S. National Science Foundation (CCF-1539256, OCE-1655686). LS was supported by the Chair VISION from CNRS/Sorbonne Université.

Phage lytic proteins are a clinically advanced class of novel enzyme-based antibiotics, so-called enzybiotics. A growing community of researchers develops phage lytic proteins with the perspective of their use as enzybiotics. A successful translation of enzybiotics to the market requires well-considered selections of phage lytic proteins in early research stages. Here, we introduce PhaLP, a database of phage lytic proteins, which serves as an open portal to facilitate the development of phage lytic proteins. PhaLP is a comprehensive, easily accessible and automatically updated database (currently 16,095 entries). Capitalizing on the rich content of PhaLP, we have mapped the high diversity of natural phage lytic proteins and conducted analyses at three levels to gain insight in their host-specific evolution. First, we provide an overview of the modular diversity. Secondly, datamining and interpretable machine learning approaches were adopted to reveal host-specific design rules for domain architectures in endolysins. Lastly, the evolution of phage lytic proteins on the protein sequence level was explored, revealing host-specific clusters. In sum, PhaLP can act as a starting point for the broad community of enzybiotic researchers, while the steadily improving evolutionary insights will serve as a natural inspiration for protein engineers.

Shannon’s entropy measure is a popular means for quantifying ecological diversity. We explore how one can use information-theoretic measures (that are often called indices in ecology) on joint ensembles to study the diversity of species interaction networks. We leverage the little-known balance equation to decompose the network information into three components describing the species abundance, specificity, and redundancy. This balance reveals that there exists a fundamental trade-off between these components. The decomposition can be straightforwardly extended to analyse networks through time as well as space, leading to the corresponding notions for alpha, beta, and gamma diversity. Our work aims to provide an accessible introduction for ecologists. To this end, we illustrate the interpretation of the components on numerous real networks. The corresponding code is made available to the community in the specialised Julia package EcologicalNetworks.jl.

Many disciplines rely on testing combinations of compounds, materials, proteins, or bacterial species to drive scientific discovery. It is time-consuming and expensive to determine experimentally, via trial-and-error or random selection approaches, which of the many possible combinations will lead to desirable outcomes. Hence, there is a pressing need for more rational and efficient experimental design approaches to reduce experimental effort. In this work, we demonstrate the potential of machine learning methods for the in silico selection of promising co-culture combinations in the application of bioaugmentation. We use the example of pollutant removal in drinking water treatment plants, which can be achieved using co-cultures of a specialized pollutant degrader with combinations of bacterial isolates. To reduce the experimental effort needed to discover high-performing combinations, we propose a data-driven experimental design. Based on a dataset of mineralization performance for all pairs of 13 bacterial species co-cultured with MSH1, we built a Gaussian process regression model to predict the Gompertz mineralization parameters of the co-cultures of two and three species, based on the single-strain parameters. We subsequently used this model in a Bayesian optimization scheme to suggest potentially high-performing combinations of bacteria. We achieved good performance with this approach, both for predicting mineralization parameters and for selecting effective co-cultures, despite the limited dataset. As a novel application of Bayesian optimization in bioremediation, this experimental design approach has promising applications for highlighting co-culture combinations for in vitro testing in various settings, to lessen the experimental burden and perform more targeted screenings.

Combining drugs, a phenomenon often referred to as polypharmacy, can induce additional adverse effects. The identification of adverse combinations is a key task in pharmacovigilance. In this context, in silico approaches based on machine learning are promising as they can learn from a limited number of combinations to predict for all. In this work, we identify various subtasks in predicting effects caused by drug–drug interaction. Predicting drug–drug interaction effects for drugs that already exist is very different from predicting outcomes for newly developed drugs, commonly called a cold-start problem. We propose suitable validation schemes for the different subtasks that emerge. These validation schemes are critical to correctly assess the performance. We develop a new model that obtains AUC-ROC =0.843 for the hardest cold-start task up to AUC-ROC =0.957 for the easiest one on the benchmark dataset of Zitnik et al. Finally, we illustrate how our predictions can be used to improve post-market surveillance systems or detect drug–drug interaction effects earlier during drug development.

International audience; Network analysis is an indispensable part of ecological studies. Specifically, networks have played a pivotal role in studying the diversity, dynamics and functionality of pollination systems. Recording plant-pollinator interaction networks is a laborious task, prone to missing or false negative interactions. Several methods enable the assessment of sampling completeness of the network with the use of species accumulation curves or Chao estimators. However, these methods do not provide a way to identify which interactions might be missed in the field. Methods that enable a more directed and focused field sampling are needed. Such methods would greatlybenefit plant-pollinator studies and network studies in general.We additively decomposed the information of an interaction matrix into three parts: the difference in importance of the species, the specificity of the interactions, and the generality of the interactions. This information is exploited by a previously proposed linear filtering method to re-score absent interactions, thus pinpointing the likely missing interactions. We evaluated this approach using null models, intensive cross-validation, as well as external validation with the Web of Life database.By means of a case study, we provide insight into the structure of the network using an information-theoretic approach. We show how to use linear filtering to suggest missing interactions. A thorough evaluation shows that these results are both statistically stable and useful to guide the search for missing interactions in real-world networks.The non-uniformity of pollination interactions can be quantified using information theory and extracted using linear filtering. Our work can be valuable as a way to study different interaction networks as well as a tool to help identifying missing interactions.

The study of the dynamic responses of plants to short-term environmental changes is becoming increasingly important in basic plant science, phenotyping, breeding, crop management, and modelling. These short-term variations are crucial in plant adaptation to new environments and, consequently, in plant fitness and productivity. Scalable, versatile, accurate, and low-cost data-logging solutions are necessary to advance these fields and complement existing sensing platforms such as high-throughput phenotyping. However, current data logging and sensing platforms do not meet the requirements to monitor these responses. Therefore, a new modular data logging platform was designed, named Gloxinia. Different sensor boards are interconnected depending upon the needs, with the potential to scale to hundreds of sensors in a distributed sensor system. To demonstrate the architecture, two sensor boards were designed&mdash, one for single-ended measurements and one for lock-in amplifier based measurements, named Sylvatica and Planalta, respectively. To evaluate the performance of the system in small setups, a small-scale trial was conducted in a growth chamber. Expected plant dynamics were successfully captured, indicating proper operation of the system. Though a large scale trial was not performed, we expect the system to scale very well to larger setups. Additionally, the platform is open-source, enabling other users to easily build upon our work and perform application-specific optimisations.

Despite global investment in One Health disease surveillance, it remains difficult—and often very costly—to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can be used to guide sampling prioritization, but predictions from any given model may be highly uncertain; moreover, systematic model validation is rare, and the drivers of model performance are consequently under-documented. Here, we use bat hosts of betacoronaviruses as a case study for the data-driven process of comparing and validating predictive models of likely reservoir hosts. In the first quarter of 2020, we generated an ensemble of eight statistical models that predict host-virus associations and developed priority sampling recommendations for potential bat reservoirs and potential bridge hosts for SARS-CoV-2. Over more than a year, we tracked the discovery of 40 new bat hosts of betacoronaviruses, validated initial predictions, and dynamically updated our analytic pipeline. We find that ecological trait-based models perform extremely well at predicting these novel hosts, whereas network methods consistently perform roughly as well or worse than expected at random. These findings illustrate the importance of ensembling as a buffer against variation in model quality and highlight the value of including host ecology in predictive models. Our revised models show improved performance and predict over 400 bat species globally that could be undetected hosts of betacoronaviruses. Although 20 species of horseshoe bats (Rhinolophus spp.) are known to be the primary reservoir of SARS-like viruses, we find at least three-fourths of plausible betacoronavirus reservoirs in this bat genus might still be undetected. Our study is the first to demonstrate through systematic validation that machine learning models can help optimize wildlife sampling for undiscovered viruses and illustrates how such approaches are best implemented through a dynamic process of prediction, data collection, validation, and updating.

Background Acoustic emission (AE) sensing is in use since the late 1960s in drought-induced embolism research as a non-invasive and continuous method. It is very well suited to assess a plant’s vulnerability to dehydration. Over the last couple of years, AE sensing has further improved due to progress in AE sensors, data acquisition methods and analysis systems. Despite these recent advances, it is still challenging to detect drought-induced embolism events in the AE sources registered by the sensors during dehydration, which sometimes questions the quantitative potential of AE sensing. Results In quest of a method to separate embolism-related AE signals from other dehydration-related signals, a 2-year-old potted Fraxinus excelsior L. tree was subjected to a drought experiment. Embolism formation was acoustically measured with two broadband point-contact AE sensors while simultaneously being visualized by X-ray computed microtomography (µCT). A machine learning method was used to link visually detected embolism formation by µCT with corresponding AE signals. Specifically, applying linear discriminant analysis (LDA) on the six AE waveform parameters amplitude, counts, duration, signal strength, absolute energy and partial power in the range 100–200 kHz resulted in an embolism-related acoustic vulnerability curve (VCAE-E) better resembling the standard µCT VC (VCCT), both in time and in absolute number of embolized vessels. Interestingly, the unfiltered acoustic vulnerability curve (VCAE) also closely resembled VCCT, indicating that VCs constructed from all registered AE signals did not compromise the quantitative interpretation of the species’ vulnerability to drought-induced embolism formation. Conclusion Although machine learning could detect similar numbers of embolism-related AE as µCT, there still is insufficient model-based evidence to conclusively attribute these signals to embolism events. Future research should therefore focus on similar experiments with more in-depth analysis of acoustic waveforms, as well as explore the possibility of Fast Fourier transformation (FFT) to remove non-embolism-related AE signals.

Assuring compliance of intermediate and final quality attributes in a continuous pharmaceutical manufacturing campaign is of utmost importance. Application of corrective actions might be required in real-time. This work exemplifies the steps needed to identify a linear pulse transfer function for the dynamic behavior of the granule liquid-to-solid ratio (%w/w) at the end of the granulation unit of a commercial ConsiGma(TM)-25 production line. Near-infrared spectroscopy was used to monitor the granule composition in-line. The outcome for both the tracking and regulator problem using either conventional or model predictive control was implemented and evaluated. Dynamic setpoints were correctly followed and an RMSE of 0.25%w/w with respect to the setpoint was obtained when inducing artificial disturbances. Important practical challenges were also tackled. Examples are fouling, computational limitations, and the limited flexibility of the automation software. Applying the proposed advanced process control solution offers an answer to upstream material flow rate deviations. (c) 2018 American Institute of Chemical Engineers AIChE J, 64: 2500-2514, 2018

Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction or network inference problems. During the last decade kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify existing kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency and spectral filtering properties. Our theoretical results provide valuable insights in assessing the advantages and limitations of existing pairwise learning methods., arXiv admin note: text overlap with arXiv:1606.04275

Mutualistic bee–plant interaction networks are a vital part of terrestrial ecosystems. They frequently arise through co-evolutionary processes, which match the traits of both partners, facilitating their interaction. Insights in these interaction mechanisms are vital to be able to manage changing ecosystems. This entails the need for models to predict species interaction networks in general and pollination networks in particular. We show how kernel-based pairwise learning can predict bee–plant interactions based on the traits and the phylogeny of the plant and bee species. The traits and the phylogeny of the plant and bee species proved to be highly predictive. Although the traits were slightly more informative compared to the phylogeny, the best results were obtained by combining both the traits and the phylogeny in the model Notably, the model performance varied greatly depending on whether the goal was to pinpoint missing interactions in the network or to predict interactions for new bee species, new plant species, or both. This issue highlights the importance of proper stratification when fitting biological network prediction models. Our model, however, showed the capacity to generalize beyond the original dataset provided by FlorAbeilles. The model was validated by predicting potentially interacting plant species for the invasive bee species Megachile sculpturalis. Four out of the five plant species identified by the model could be validated based on literature. Our results indicate that pairwise learning has potential as a general method for supervised species interaction prediction. Caution should be taken to validate such models correctly.

The diet of seabirds can yield important insights into the status of economically and ecologically important fish. By analyzing the otoliths found in the birds’ droppings, researchers can observe which fish the birds eat in which abundances. However, identifying the species based on an otolith image is quite labor-intensive and requires particular expertise. In this work, we show that a deep convolutional neural network can identify six fish species with high accuracy. We show that this deep learning approach outperforms more traditional methods and is also more accessible to set up in practice. By exploiting the hierarchy in the species labels, we impose a structure on the prediction probabilities, leading to a remarkable improvement compared to a conventional artificial neural network. Importantly, we can attain good results using only a modest dataset, demonstrating that such approaches are feasible for small-scale and specialized projects.

Plants’ dynamic eco-physiological responses are vital to their productivity in continuously fluctuating conditions, such as those in agricultural fields. However, it is currently still very difficult to capture these responses at the field scale for phenotyping purposes. Advanced hyperspectral imaging tools are increasingly used in phenotyping, and have been applied to detect changes in plants in response to a specific treatment, phenological state or monitor its growth and development. Phenotyping has to evolve towards capturing dynamic behaviour under more subtle fluctuations in environmental conditions, without the presence of clear treatments or stresses. Therefore, we investigated the potential of hyperspectral imaging to capture dynamic behaviour of plants in stress-free conditions at a temporal resolution of seconds. Two growth chamber experiments were set up, in which strawberry plants and four different background materials, serving as controls, were monitored by a snapshot hyperspectral camera in variable conditions of light, temperature and relative humidity. The sampling period was set to three seconds, triggering image acquisition and gas exchange measurements. Different background materials were used to assess the influence of the environment and the camera in both experiments. To separate the plant and background data, static masks were determined. Two datasets were created, which encompass both experiments. One dataset was constructed after averaging over the entire mask to acquire one value per spectral band. These values were then used to calculate a set of vegetation indices. The other dataset used spatial subsampling to retain spatial information. From both datasets, linear models were constructed using ridge regression, which estimated the measured eco-physiological and environmental data. Leaf temperature and vapour pressure deficit based on leaf temperature are the two main eco-physiological characteristics that could be predicted successfully. Stomatal conductance, photosynthesis and transpiration rate show less promising results. We suspect that limited variation, and low spectral resolution and range are the main causes of the inability of the models to extract meaningful predictions. Furthermore, the models that were only trained on background data also showed good predictive performance. This is probably because the main drivers for good performing eco-physiological variables are temperature and incident light intensity. Environmental characteristics that have good performance are photosynthetically active radiation and air temperature. Current hyperspectral sensing technologies are not yet able to uncover most plant dynamic eco-physiological responses when plants are cultivated in stress-free conditions.

Background Completing recipes is a non-trivial task, as the success of ingredient combinations depends on a multitude of factors such as taste, smell and texture. Scope and approach In this article, we illustrate that machine learning methods can be applied for this purpose. Non-negative matrix factorization and two-step regularized least squares are presented as two alternative methods and their ability to build models to complete recipes is evaluated. The former method exploits information captured in existing recipes to complete a recipe, while the latter one is able to also incorporate information on flavor profiles of ingredients. The performance of the resulting models is evaluated on real-life data. Key findings and conclusions The two machine learning methods can be used to build models to complete a recipe. Both models are able to retrieve an eliminated ingredient from a recipe and the two-step RLS model is also capable of completing an ingredient set to create a complete recipe. By applying machine learning methods on existing recipes, it is not necessary to model the complexity of good ingredient combinations to be able to complete a recipe.