Structured sparsity regularization

Structured sparsity regularization

Structured sparsity regularization is a class of methods, and an area of research in statistical learning theory, that extend and generalize sparsity regularization learning methods. Both sparsity and structured sparsity regularization methods seek to exploit the assumption that the output variable Y {\displaystyle Y} (i.e., response, or dependent variable) to be learned can be described by a reduced number of variables in the input space X {\displaystyle X} (i.e., the domain, space of features or explanatory variables). Sparsity regularization methods focus on selecting the input variables that best describe the output. Structured sparsity regularization methods generalize and extend sparsity regularization methods, by allowing for optimal selection over structures like groups or networks of input variables in X {\displaystyle X} . Common motivation for the use of structured sparsity methods are model interpretability, high-dimensional learning (where dimensionality of X {\displaystyle X} may be higher than the number of observations n {\displaystyle n} ), and reduction of computational complexity. Moreover, structured sparsity methods allow to incorporate prior assumptions on the structure of the input variables, such as overlapping groups, non-overlapping groups, and acyclic graphs. Examples of uses of structured sparsity methods include face recognition, magnetic resonance image (MRI) processing, socio-linguistic analysis in natural language processing, and analysis of genetic expression in breast cancer. == Definition and related concepts == === Sparsity regularization === Consider the linear kernel regularized empirical risk minimization problem with a loss function V ( y i , f ( x ) ) {\displaystyle V(y_{i},f(x))} and the ℓ 0 {\displaystyle \ell _{0}} "norm" as the regularization penalty: min w ∈ R d 1 n ∑ i = 1 n V ( y i , ⟨ w , x i ⟩ ) + λ ‖ w ‖ 0 , {\displaystyle \min _{w\in \mathbb {R} ^{d}}{\frac {1}{n}}\sum _{i=1}^{n}V(y_{i},\langle w,x_{i}\rangle )+\lambda \|w\|_{0},} where x , w ∈ R d {\displaystyle x,w\in \mathbb {R^{d}} } , and ‖ w ‖ 0 {\displaystyle \|w\|_{0}} denotes the ℓ 0 {\displaystyle \ell _{0}} "norm", defined as the number of nonzero entries of the vector w {\displaystyle w} . f ( x ) = ⟨ w , x i ⟩ {\displaystyle f(x)=\langle w,x_{i}\rangle } is said to be sparse if ‖ w ‖ 0 = s < d {\displaystyle \|w\|_{0}=s 0 {\displaystyle w_{j}>0} . However, as in this case groups may overlap, we take the intersection of the complements of those groups that are not set to zero. This intersection of complements selection criteria implies the modeling choice that we allow some coefficients within a particular group g {\displaystyle g} to be set to zero, while others within the same group g {\displaystyle g} may remain positive. In other words, coefficients within a group may differ depending on the several group memberships that each variable within the group may have. ==== Union of groups: latent group Lasso ==== A different approach is to consider union of groups for variable selection. This approach captures the modeling situation where variables can be selected as long as they belong at least to one group with positive coefficients. This modeling perspective implies that we want to preserve group structure. The formulation of the union of groups approach is also referred to as latent group Lasso, and requires to modify the group ℓ 2 {\displaystyle \ell _{2}} norm considered above and introduce the following regularizer R ( w ) = i n f { ∑ g ‖ w g ‖ g : w = ∑ g = 1 G w ¯ g } {\displaystyle R(w)=inf\left\{\sum _{g}\|w_{g}\|_{g}:w=\sum _{g=1}^{G}{\bar {w}}_{g}\right\}} where w ∈ R d {\displaystyle w\in {\mathbb {R^{d}} }} , w g ∈ G g {\displaystyle w_{g}\in G_{g}} is the vector of coefficients of group g, and w ¯ g ∈ R d {\displaystyle {\bar {w}}_{g}\in {\mathbb {R^{d}} }} is a vector with coefficients w g j {\displaystyle w_{g}^{j}} for all variables j {

Developmental robotics

Developmental robotics (DevRob), sometimes called epigenetic robotics, is a scientific field which aims at studying the developmental mechanisms, architectures and constraints that allow lifelong and open-ended learning of new skills and new knowledge in embodied machines. As in human children, learning is expected to be cumulative and of progressively increasing complexity, and to result from self-exploration of the world in combination with social interaction. The typical methodological approach consists in starting from theories of human and animal development elaborated in fields such as developmental psychology, neuroscience, developmental and evolutionary biology, and linguistics, then to formalize and implement them in robots, sometimes exploring extensions or variants of them. The experimentation of those models in robots allows researchers to confront them with reality, and as a consequence, developmental robotics also provides feedback and novel hypotheses on theories of human and animal development. Developmental robotics is related to but differs from evolutionary robotics (ER). ER uses populations of robots that evolve over time, whereas DevRob is interested in how the organization of a single robot's control system develops through experience, over time. DevRob is also related to work done in the domains of robotics and artificial life. == Background == Can a robot learn like a child? Can it learn a variety of new skills and new knowledge unspecified at design time and in a partially unknown and changing environment? How can it discover its body and its relationships with the physical and social environment? How can its cognitive capacities continuously develop without the intervention of an engineer once it is "out of the factory"? What can it learn through natural social interactions with humans? These are the questions at the center of developmental robotics. Alan Turing, as well as a number of other pioneers of cybernetics, already formulated those questions and the general approach in 1950, but it is only since the end of the 20th century that they began to be investigated systematically. Because the concept of adaptive intelligent machines is central to developmental robotics, it has relationships with fields such as artificial intelligence, machine learning, cognitive robotics or computational neuroscience. Yet, while it may reuse some of the techniques elaborated in these fields, it differs from them from many perspectives. It differs from classical artificial intelligence because it does not assume the capability of advanced symbolic reasoning and focuses on embodied and situated sensorimotor and social skills rather than on abstract symbolic problems. It differs from cognitive robotics because it focuses on the processes that allow the formation of cognitive capabilities rather than these capabilities themselves. It differs from computational neuroscience because it focuses on functional modeling of integrated architectures of development and learning. More generally, developmental robotics is uniquely characterized by the following three features: It targets task-independent architectures and learning mechanisms, i.e. the machine/robot has to be able to learn new tasks that are unknown by the engineer; It emphasizes open-ended development and lifelong learning, i.e. the capacity of an organism to acquire continuously novel skills. This should not be understood as a capacity for learning "anything" or even “everything”, but just that the set of skills that is acquired can be infinitely extended at least in some (not all) directions; The complexity of acquired knowledge and skills shall increase (and the increase be controlled) progressively. Developmental robotics emerged at the crossroads of several research communities including embodied artificial intelligence, enactive and dynamical systems cognitive science, connectionism. Starting from the essential idea that learning and development happen as the self-organized result of the dynamical interactions among brains, bodies and their physical and social environment, and trying to understand how this self-organization can be harnessed to provide task-independent lifelong learning of skills of increasing complexity, developmental robotics strongly interacts with fields such as developmental psychology, developmental and cognitive neuroscience, developmental biology (embryology), evolutionary biology, and cognitive linguistics. As many of the theories coming from these sciences are verbal and/or descriptive, this implies a crucial formalization and computational modeling activity in developmental robotics. These computational models are then not only used as ways to explore how to build more versatile and adaptive machines but also as a way to evaluate their coherence and possibly explore alternative explanations for understanding biological development. == Research directions == === Skill domains === Due to the general approach and methodology, developmental robotics projects typically focus on having robots develop the same types of skills as human infants. A first category that is important being investigated is the acquisition of sensorimotor skills. These include the discovery of one's own body, including its structure and dynamics such as hand-eye coordination, locomotion, and interaction with objects as well as tool use, with a particular focus on the discovery and learning of affordances. A second category of skills targeted by developmental robots are social and linguistic skills: the acquisition of simple social behavioural games such as turn-taking, coordinated interaction, lexicons, syntax and grammar, and the grounding of these linguistic skills into sensorimotor skills (sometimes referred as symbol grounding). In parallel, the acquisition of associated cognitive skills are being investigated such as the emergence of the self/non-self distinction, the development of attentional capabilities, of categorization systems and higher-level representations of affordances or social constructs, of the emergence of values, empathy, or theories of mind. === Mechanisms and constraints === The sensorimotor and social spaces in which humans and robot live are so large and complex that only a small part of potentially learnable skills can actually be explored and learnt within a life-time. Thus, mechanisms and constraints are necessary to guide developmental organisms in their development and control of the growth of complexity. There are several important families of these guiding mechanisms and constraints which are studied in developmental robotics, all inspired by human development: Motivational systems, generating internal reward signals that drive exploration and learning, which can be of two main types: extrinsic motivations push robots/organisms to maintain basic specific internal properties such as food and water level, physical integrity, or light (e.g. in phototropic systems); intrinsic motivations push robot to search for novelty, challenge, compression or learning progress per se, thus generating what is sometimes called curiosity-driven learning and exploration, or alternatively active learning and exploration; Social guidance: as humans learn a lot by interacting with their peers, developmental robotics investigates mechanisms that can allow robots to participate to human-like social interaction. By perceiving and interpreting social cues, this may allow robots both to learn from humans (through diverse means such as imitation, emulation, stimulus enhancement, demonstration, etc. ...) and to trigger natural human pedagogy. Thus, social acceptance of developmental robots is also investigated; Statistical inference biases and cumulative knowledge/skill reuse: biases characterizing both representations/encodings and inference mechanisms can typically allow considerable improvement of the efficiency of learning and are thus studied. Related to this, mechanisms allowing to infer new knowledge and acquire new skills by reusing previously learnt structures is also an essential field of study; The properties of embodiment, including geometry, materials, or innate motor primitives/synergies often encoded as dynamical systems, can considerably simplify the acquisition of sensorimotor or social skills, and is sometimes referred as morphological computation. The interaction of these constraints with other constraints is an important axis of investigation; Maturational constraints: In human infants, both the body and the neural system grow progressively, rather than being full-fledged already at birth. This implies, for example, that new degrees of freedom, as well as increases of the volume and resolution of available sensorimotor signals, may appear as learning and development unfold. Transposing these mechanisms in developmental robots, and understanding how it may hinder or on the contrary ease the acquisition of novel complex skills is a central questi

Mathematical knowledge management

Mathematical knowledge management (MKM) is the study of how society can effectively make use of the vast and growing literature on mathematics. It studies approaches such as databases of mathematical knowledge, automated processing of formulae and the use of semantic information, and artificial intelligence. Mathematics is particularly suited to a systematic study of automated knowledge processing due to the high degree of interconnectedness between different areas of mathematics.

Affectiva

Affectiva is an artificial intelligence software development company. In 2021, the company was acquired by SmartEye. The company claimed its AI understood human emotions, cognitive states, activities and the objects people use, by analyzing facial and vocal expressions. The offshoot of MIT Media Lab, Affectiva created a new technological category of artificial emotional intelligence, namely, Emotion AI. == History == Affectiva was co-founded by Rana el Kaliouby, who became chief executive officer as of May 25, 2016, and Rosalind W. Picard, who worked as chairman and Chief Scientist until 2013. Both of Affectiva's early products grew out of collaborative research at the MIT's Media Lab to help people on the autism spectrum. Affectiva was acquired for a mostly-stock deal of $73.5m by Swedish SmartEye, a former competitor. == Technology == The company has expanded its Emotion AI technology to detect more than facial expressions, reactions and emotions. Affectiva's software detects complex and nuanced emotions, cognitive states, such as drowsiness and distraction, certain activities and the objects people use. It does that by analyzing the human face, vocal intonations and body posture. Affectiva's AI is built with deep learning, computer vision, and large amounts of data that has been collected in real-world scenarios. The AI uses an optical sensor like a webcam or smartphone camera to identify a human face in real-time. Then, computer vision algorithms identify key features on the face, which are analyzed by deep learning algorithms to classify facial expressions. These facial expressions are then mapped back to emotions. One journal paper found the Affectiva iMotions Facial Expression Analysis Software results are comparable to results using facial Electromyography. Affectiva also uses computer vision to detect objects like a cellphone and car seat, as well as body key points, which track body joints to determine movement and location. Affectiva has collected massive amounts of data that are used to train and test the company's deep learning algorithms, and provide insight into human emotional reactions and engagement. The company has analyzed more than 10 million face videos from 90 countries, making it one of the largest data repositories of its kind. Affectiva has also collected more than 19,000 hours of automotive in-cabin data from 4,000 unique individuals. This automotive data is used to adapt its algorithms to varying camera angles, lighting and other environmental conditions in a vehicle. === Applications === Affectiva's AI had many applications, but the company's primary focus is on Media Analytics. Other uses of Affectiva's AI includes applications in automotive, healthcare and mental health, robotics, conversational interfaces, education, gaming, and more. ==== Media analytics ==== Affectiva's technology was first deployed in media analytics, for market research purposes. The company had since then tested more than 53,000 ads in 90 countries. Brands, advertising agencies and insights firms used the company's Emotion AI to measure the unfiltered and unbiased emotional responses consumers have when viewing video ads and movie trailers. These insights helped improve brand and media content, and predict key metrics in advertising such as sales lift, purchase intent and virality. Affectiva's technology was also used in qualitative research. Affectiva had partnered with leading insights firms such as Kantar, LRW, Added Value and Unruly. Through these collaborations, 28 percent of the Fortune Global 500 companies, and 70 percent of the world's largest advertisers, used Affectiva's Emotion AI. On September 5, 2019, Affectiva announced the appointment of Graham Page, a seasoned Kantar executive, as Global Managing Director of Media Analytics to expand on the company's existing footprint in the media analytics space. ==== Automotive ==== On March 21, 2018, Affectiva launched Affectiva Automotive AI, the first multi-modal in-cabin sensing solution to understand what is happening with people in a vehicle. It used cameras in the car to measure in real time, the state of the driver, the state of the occupants and the state of the vehicle interior (i.e. cabin). This insight helped car manufacturers, fleet management companies and rideshare providers improve road safety and build better driver monitoring systems, by understanding dangerous driver behavior such as drowsiness, distraction and anger. It was also used to create more comfortable and enjoyable transportation experiences, by understanding how passengers react to the environment, such as content they can consume in the back of the car. In addition to understanding driver and occupant emotional and cognitive states, Affectiva Automotive AI could also detect contextual cabin information such as the number of passengers, where they are sitting and if an object is present. Affectiva worked with a number of leading car manufacturers and transportation technology companies, including Aptiv, Cerence, Hyundai Kia, Faurecia, Porsche, BMW, GreenRoad Technologies, and Veoneer. == Acquisition == In June 2021 Smart Eye acquired Affectiva.

Very large database

A very large database, (originally written very large data base) or VLDB, is a database that contains a very large amount of data, so much that it can require specialized architectural, management, processing and maintenance methodologies. == Definition == The vague adjectives of very and large allow for a broad and subjective interpretation, but attempts at defining a metric and threshold have been made. Early metrics were the size of the database in a canonical form via database normalization or the time for a full database operation like a backup. Technology improvements have continually changed what is considered very large. One definition has suggested that a database has become a VLDB when it is "too large to be maintained within the window of opportunity… the time when the database is quiet". == Sizes of a VLDB database == There is no absolute amount of data that can be cited. For example, one cannot say that any database with more than 1 TB of data is considered a VLDB. This absolute amount of data has varied over time as computer processing, storage and backup methods have become better able to handle larger amounts of data. That said, VLDB issues may start to appear when 1 TB is approached, and are more than likely to have appeared as 30 TB or so is exceeded. == VLDB challenges == Key areas where a VLDB may present challenges include configuration, storage, performance, maintenance, administration, availability and server resources. === Configuration === Careful configuration of databases that lie in the VLDB realm is necessary to alleviate or reduce issues raised by VLDB databases. === Administration === The complexities of managing a VLDB can increase exponentially for the database administrator as database size increases. === Availability and maintenance === When dealing with VLDB operations relating to maintenance and recovery such as database reorganizations and file copies which were quite practical on a non-VLDB take very significant amounts of time and resources for a VLDB database. In particular it typically infeasible to meet a typical recovery time objective (RTO), the maximum expected time a database is expected to be unavailable due to interruption, by methods which involve copying files from disk or other storage archives. To overcome these issues techniques such as clustering, cloned/replicated/standby databases, file-snapshots, storage snapshots or a backup manager may help achieve the RTO and availability, although individual methods may have limitations, caveats, license, and infrastructure requirements while some may risk data loss and not meet the recovery point objective (RPO). For many systems only geographically remote solutions may be acceptable. ==== Backup and recovery ==== Best practice is for backup and recovery to be architectured in terms of the overall availability and business continuity solution. === Performance === Given the same infrastructure there may typically be a decrease in performance, that is increase in response time as database size increases. Some accesses will simply have more data to process (scan) which will take proportionally longer (linear time); while the indexes used to access data may grow slightly in height requiring perhaps an extra storage access to reach the data (sub-linear time). Other effects can be caching becoming less efficient because proportionally less data can be cached and while some indexes such as the B+ automatically sustain well with growth others such as a hash table may need to be rebuilt. Should an increase in database size cause the number of accessors of the database to increase then more server and network resources may be consumed, and the risk of contention will increase. Some solutions to regaining performance include partitioning, clustering, possibly with sharding, or use of a database machine. ==== Partitioning ==== Partitioning may be able assist the performance of bulk operations on a VLDB including backup and recovery., bulk movements due to information lifecycle management (ILM), reducing contention as well as allowing optimization of some query processing. === Storage === In order to satisfy needs of a VLDB the database storage needs to have low access latency and contention, high throughput, and high availability. === Server resources === The increasing size of a VLDB may put pressure on server and network resources and a bottleneck may appear that may require infrastructure investment to resolve. == Relationship to big data == VLDB is not the same as big data, but the storage aspect of big data may involve a VLDB database. That said some of the storage solutions supporting big data were designed from the start to support large volumes of data, so database administrators may not encounter VLDB issues that older versions of traditional RDBMS's might encounter.

Automated penetration testing

Automated penetration testing (also known as autonomous penetration testing or automated offensive security) is the application of software-driven workflows and orchestration to simulate cyberattack techniques. These methods are used to identify, validate, and exploit security vulnerabilities in IT assets such as networks, applications, and cloud infrastructure. Automated penetration testing is the use of software to simulate cyberattacks in order to rapidly identify exploitable vulnerabilities across systems without relying solely on human testers. In technical literature, the term describes a spectrum of activities ranging from scripted exploit orchestration to experimental systems designed for fully autonomous attack planning. Automated Penetration Testing falls short of testing using manual experts in terms of discovery of deep complex vulnerabilities and contextual business logic vulnerabilities. == Terminology and scope == The label “automated penetration testing” appears frequently in vendor and practitioner writing but lacks a single, neutral, standards-based definition. In the literature the term’s scope varies: some authors use it to mean automation of specific penetration-testing tasks (scanning, exploitation attempts, evidence collection), others to describe integrated, repeatable assessment pipelines, and a smaller body of work investigates autonomous decision-making agents that select attack steps algorithmically. To avoid implying consensus, this article describes common techniques and architectures reported in the literature and industry, and it notes where claims are primarily found in practitioner publications or early-stage research. Its important to note the differences between automated penetration testing and traditional penetration testing using human skill. The most important difference is scope and speed. Automated penetration testing generally fails at discovering exposures and weakness associated with business logic due to a lack of contextual understanding. The benefit of Automated Penetration testing is speed at which it can be conducted. Traditional penetration testing also is expected to be accurate and contain no false positives. This is due to the human validation aspect of the test. Automated approaches are expected to contain mistakes and false positives which need to be validated upon completion of the test. == History == Automated offensive techniques build on decades of tools and scripting that aided vulnerability discovery and exploitation. Early vulnerability scanners and community scripting in the 1990s and 2000s created the first layers of automation. Later, modular exploitation frameworks (notably Metasploit) integrated scanning and exploitation modules and made automated proof-of-concept attacks more accessible. Over the 2010s–2020s, as cloud platforms, APIs and continuous delivery practices increased the need for frequent validation, academic and industry interest in formalizing automated approaches also grew. == Methodologies and architectures == Descriptions in the literature and technical reports cluster automated capabilities into several overlapping models: Scripted/engineered playbooks (task automation): Predefined workflows or playbooks encode common attack paths (for example, web application exploit sequences or lateral-movement chains). These playbooks are designed to reproduce known techniques in a controlled way to validate exploitability and reduce manual repetition. Exploit-oriented orchestration: Automation orchestrates exploitation modules from established frameworks to perform controlled proof-of-concept attacks that confirm exploitability rather than simply flagging potential weaknesses. This approach can reduce false positives versus passive scanning when tests are run in an appropriately controlled environment. Orchestrated multi-tool pipelines: A coordinated toolchain integrates reconnaissance, vulnerability scanning, credential testing, exploitation modules and reporting. Data and state persist across stages so that multi-step workflows (e.g., discover → escalate → pivot) can be executed repeatably, approximating manual penetration-test methodologies at larger scale. Continuous / CI-integrated testing: Automation embedded in build or deployment pipelines (CI/CD) triggers assessments automatically on new builds, configuration changes, or on a schedule, supporting frequent, repeatable validation aligned with DevOps practices. Academic theses and experimental work describe CI/CD-integrated proof-of-concept systems for web applications and internal networks. Research on autonomous planning and learning: Recent academic work explores machine learning and reinforcement-learning approaches to select or prioritise attack steps, generate attack sequences, or optimize the testing path; these approaches are largely experimental and raise distinct validation and safety questions. == Tools and vendors == Automated penetration testing is provided by a mix of open-source projects, commercial platforms, and professional services. These often follow the penetration testing as a service (PTaaS) model, which integrates automated scanning with manual validation by security analysts. Examples of widely known tools and vendors in the space include exploitation frameworks such as Metasploit, commercial automated platforms and PTaaS providers, and specialist vendors that offer breach-and-attack simulation (BAS) or continuous testing capabilities. == Applications and deployment models == In industry practice, some organizations deploy automated techniques through dedicated security validation platforms rather than bespoke toolchains. These platforms are typically used for continuous or scheduled validation in pre-production or controlled environments and are often positioned alongside, rather than in place of, human-led penetration testing. Examples discussed in secondary literature include platforms such as Pentera, which are commonly classified under breach-and-attack simulation or automated security validation rather than as standalone penetration-testing methodologies.

Ecoinformatics

Ecoinformatics, or ecological informatics, is the science of information in ecology and environmental science. It integrates environmental and information sciences to define entities and natural processes with language common to both humans and computers. However, this is a rapidly developing area in ecology and there are alternative perspectives on what constitutes ecoinformatics. A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses. Ecoinformatics is related to the concept of ecosystem services. Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web. Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are National Science Foundation Datanet projects, DataONE, Data Conservancy, and Artificial Intelligence for Environment & Sustainability. == Software Development Lifecycle == Central to the concept of ecoinformatics is the Software Development Lifecycle (SDLC), a systematic framework for writing, implementing, and maintaining software products. Typically in Ecoinformatics projects, the development pipeline includes data collection, usually from several different environmental data sources, then integrating these data sources together, and then analyzing the data. Here, each step of the SDLC is described in the context of ecoinformatics, per Michener et al. It is important to note that the plan, collect, assure, describes and preserve steps refer to the data collection entity, which can be individual researchers or large data-collection networks, while the discover, integrate, and analyze steps typically refer to the individual researcher. Plan: Ecoinformatics projects require data from several databases. Each database holds different data, and therefore researchers should identify what types of environmental or ecological data they will need to answer their research question. Collect: Data is collected in several different ways. In ecoinformatics, this is usually restricted to manually entering data into a spreadsheet, and parsing data from an existing database. The growth of relational databases has made it easier for ecologists to download relevant data and integrate datasets together Assure: Data entries should be checked thoroughly to validate their accuracy and usability, such as to check for outliers and erroneous points. The same principle applies to data downloaded from datasets. This responsibility falls on both the ecologist downloading the data, and the entity that sets up the data collection system. Describe: An accurate description of the metadata of a dataset that is used in a study should include enough information to deduce the data collection and processing methodology, when the data were collected, why the data were collected, and how the data were stored. This is important for reproducibility, especially for projects that build on each other and may recycle data Preserve: After data is collected by an institutional entity, it should be archived such that it is easily accessible. Ideally, this is in databases that are maintained and not at risk of deprecation Discover: While there are good practices for discovering data to start a research project, this process is often marred by a lack of usable, published data, as researchers may collect data specific to their study, but may not publish this data for wider use. On the data collection end, this can be addressed by better data-sharing practices, such as by linking datasets when publishing papers or studies. On the data procurement end, this can be addressed by more precise data searching, such as using key words to find relevant datasets. Integrate: Synthesizing datasets together can be difficult and labor-intensive, largely due to the methodological differences in data collection. There are several approaches to this, but the best practices typically involve computational approaches, namely using R or Python, to automate the processes and prevent errors Analyze: Data analysis can take several forms, and should be tailored to the specific ecological project. However, all data analysis methods should be well-documented, including the procedure for analysis, justification for analysis methods, and any shortcomings in a specific approach. == Applications of Ecoinformatics Across Ecology == === Ecosystem Ecology === Source: Ecosystem studies, by definition, encompass interactions across the entire life sciences spectrum, from microscopic biochemical reactions to large-scale geological phenomena. As a result, big databases may not be designed specifically for any particular research question, but should be inclusive enough to support most studies. Since ecosystem-level questions require a broad perspective, data-related ecosystem projects would likely incorporate data from several databases. A common framework for incorporating data into ecosystem-level studies is the network science model, in which data collection mechanisms and resources are treated like a large, interconnected network instead of individual entities. The network may include several data collection stations within one databases, or may span across multiple databases. Currently there are several large-scale networks, but they do not generate data on the scale to consider ecology as a big data science. A current challenge for ecoinformatics in ecosystem ecology is that most funding is prioritized for generating new data rather than maintaining existing data infrastructures. Integrating data across the different spatial scales can also be difficult, since each dataset may hold different types of data. === Urban Ecology === Source: The current push for smart cities, and sensor network integration into infrastructure, has positioned as a major source of data for ecological studies. Typical urban ecology questions address the effects of urbanization on the local ecosystem, and how to drive future development to promote urban biodiversity. While sensor networks in cities typically collect environmental data to optimize city processes, they may also be used for ecological initiatives, especially with respect to understanding the complex, multi-layered relationship between cities and their local ecosystem. It can also be used to better understand the current landscape of cities, and identify avenues for rewinding of cities. For example, analyzing mobility patterns can identify areas that may lend themselves well to building parks and green spaces. Bird watching data can also be used to identify the types of bird species in a local area. === Infectious Disease === Source: Like other disciplines of ecology, emerging infectious disease and epidemiology span multiple scales, from understanding the genetics that drive disease trends to large-scale spatiotemporal analyses. As a result, infectious disease studies can incorporate everything from bioinformatics, genetic sequences, amino acid sequences, and environmental observation data. On the micro-scale, these data can then be used to predict infectivity/transmissibility, drug resistance, drug candidates, and mutation sites. On the macro-scale, it can be used to identify societal trends or environmental factors that lend themselves to spillover, locations of infection, and practices that cause disease transmission. == Databases == Source: USGS National Streamflow sensor network GBIF Neotoma Paleobiology database European Vegetation Archive USDA Forest Inventory Analysis TRY BIEN AmeriFlux TEAM iNaturalist NEON GLEON LTER CZO TERN SAEON