BioCreative

BioCreAtIvE (A critical assessment of text mining methods in molecular biology) consists in a community-wide effort for evaluating information extraction and text mining developments in the biological domain. It was preceded by the Knowledge Discovery and Data Mining (KDD) Challenge Cup for detection of gene mentions. == Community Challenges == === First edition (2004-2005) === Three main tasks were posed at the first BioCreAtIvE challenge: the entity extraction task, the gene name normalization task, and the functional annotation of gene products task. The data sets produced by this contest serve as a Gold Standard training and test set to evaluate and train Bio-NER tools and annotation extraction tools. === Second edition (2006-2007) === The second BioCreAtIvE challenge (2006-2007) had also 3 tasks: detection of gene mentions, extraction of unique idenfiers for genes and extraction information related to physical protein-protein interactions. It counted with participation of 44 teams from 13 countries. === Third edition (2011-2012) === The third edition of BioCreative included for the first time the InterActive Task (IAT), designed to evaluate the practical usability of text mining tools in real-world biocuration tasks. === Fifth edition (2016) === BioCreative V had 5 different tracks, including an interactive task (IAT) for usability of text mining systems and a track using the BioC format for curating information for BioGRID.

Rapid PHP Editor

rapid PHP Editor is a PHP Editor that incorporates many functions such as AutoComplete, Syntax checker, debugger and many other tools for fast PHP development. Rapid PHP Editor also contain other development tools for helping on HTML, CSS, JavaScript and many other languages. Is part of a family of products covering most aspects of modern web development integrating as well many other capabilities used by developers. Some features: (X)HTML to HTML5 CSS to CSS3 Code intelligence Powerful search and replace Support for several frameworks Code beautifier FTP Explorer (FTP/SFTP/FTPS) File explorer Database explorer Code snippets Validators and Debuggers FAST, real fast Many other tools available (many more to describe all here) == History == Rapid PHP Editor was built using the Delphi programming language.

Bisection (software engineering)

Bisection is a method used in software development to identify change sets that result in a specific behavior change. It is mostly employed for finding the patch that introduced a bug. Another application area is finding the patch that indirectly fixed a bug. == Overview == The process of locating the changeset that introduced a specific regression was described as "source change isolation" in 1997 by Brian Ness and Viet Ngo of Cray Research. Regression testing was performed on Cray's compilers in editions comprising one or more changesets. Editions with known regressions could not be validated until developers addressed the problem. Source change isolation narrowed the cause to a single changeset that could then be excluded from editions, unblocking them with respect to this problem, while the author of the change worked on a fix. Ness and Ngo outlined linear search and binary search methods of performing this isolation. Code bisection has the goal of minimizing the effort to find a specific change set. It employs a divide and conquer algorithm that depends on having access to the code history which is usually preserved by revision control in a code repository. == Bisection method == === Code bisection algorithm === Code history has the structure of a directed acyclic graph which can be topologically sorted. This makes it possible to use a divide and conquer search algorithm which: splits up the search space of candidate revisions tests for the behavior in question reduces the search space depending on the test result re-iterates the steps above until a range with at most one bisectable patch candidate remains === Algorithmic complexity === Bisection is in LSPACE having an algorithmic complexity of O ( log ⁡ N ) {\displaystyle O(\log N)} with N {\displaystyle N} denoting the number of revisions in the search space, and is similar to a binary search. === Desirable repository properties === For code bisection it is desirable that each revision in the search space can be built and tested independently. === Monotonicity === For the bisection algorithm to identify a single changeset which caused the behavior being tested to change, the behavior must change monotonically across the search space. For a Boolean function such as a pass/fail test, this means that it only changes once across all changesets between the start and end of the search space. If there are multiple changesets across the search space where the behavior being tested changes between false and true, then the bisection algorithm will find one of them, but it will not necessarily be the root cause of the change in behavior between the start and the end of the search space. The root cause could be a different changeset, or a combination of two or more changesets across the search space. To help deal with this problem, automated tools allow specific changesets to be ignored during a bisection search. == Automation support == Although the bisection method can be completed manually, one of its main advantages is that it can be easily automated. It can thus fit into existing test automation processes: failures in exhaustive automated regression tests can trigger automated bisection to localize faults. Ness and Ngo focused on its potential in Cray's continuous delivery-style environment in which the automatically isolated bad changeset could be automatically excluded from builds. The revision control systems Fossil, Git and Mercurial have built-in functionality for code bisection. The user can start a bisection session with a specified range of revisions from which the revision control system proposes a revision to test, the user tells the system whether the revision tested as "good" or "bad", and the process repeats until the specific "bad" revision has been identified. Other revision control systems, such as Bazaar or Subversion, support bisection through plugins or external scripts. Phoronix Test Suite can do bisection automatically to find performance regressions.

Digital artifact

Digital artifact in information science, is any undesired or unintended alteration in data introduced in a digital process by an involved technique and/or technology. Digital artifact can be of any content types including text, audio, video, image, animation or a combination. == Information science == In information science, digital artifacts result from: Hardware malfunction: In computer graphics, visual artifacts may be generated whenever a hardware component such as the processor, memory chip, cabling malfunctions, etc., corrupts data. Examples of malfunctions include physical damage, overheating, insufficient voltage and GPU overclocking. Common types of hardware artifacts are texture corruption and T-vertices in 3D graphics, and pixelization in MPEG compressed video. Software malfunction: Artifacts may be caused by algorithm flaws such as decoding/encoding audio or video, or a poor pseudo-random number generator that would introduce artifacts distinguishable from the desired noise into statistical models. Compression: Controlled amounts of unwanted information may be generated as a result of the use of lossy compression techniques. One example is the artifacts seen in JPEG and MPEG compression algorithms that produce compression artifacts. Quantization: Digital imprecision generated in the process of converting analog information into digital space, is due to the limited granularity of digital numbering space. In computer graphics, quantization is seen as pixelation. Aliasing: As a consequence of sampling or sample-rate conversion, energy from frequencies outside of the signal frequency band of interest are folded across multiples of the Nyquist frequency. This is typically mitigated by using an anti-aliasing filter. Filtering: The process of filtering a signal, such as using an anti-aliasing filter, causes undesired alterations to the signal due to imperfections in the frequency response magnitude and phase, and due to the time domain impulse response. Rolling shutter, the line scanning of an object that is moving too fast for the image sensor to capture a unitary image. Error diffusion: poorly-weighted kernel coefficients result in undesirable visual artifacts.

Snap rounding

Snap rounding is a method of approximating line segment locations by creating a grid and placing each point in the centre of a cell (pixel) of the grid. The method preserves certain topological properties of the arrangement of line segments. Drawbacks include the potential interpolation of additional vertices in line segments (lines become polylines), the arbitrary closeness of a point to a non-incident edge, and arbitrary numbers of intersections between input line-segments. The 3 dimensional case is worse, with a polyhedral subdivision of complexity n becoming complexity O(n4). There are more refined algorithms to cope with some of these issues, for example iterated snap rounding guarantees a "large" separation between points and non-incident edges. == Algorithm == ... (please edit). See, and https://www.cgal.org/ () == Properties == Canonicity: Efficiency; A number of efficient implementations exist. Conversely there are undesirable properties: Non-idempotence: Repeated applications can cause arbitrary drift of points. Exception on "Stable snap rounding" algorithms, see https://doi.org/10.1016/j.comgeo.2012.02.011

Reverse correlation technique

The reverse correlation technique is a data driven study method used primarily in psychological and neurophysiological research. This method earned its name from its origins in neurophysiology, where cross-correlations between white noise stimuli and sparsely occurring neuronal spikes could be computed quicker when only computing it for segments preceding the spikes. The term has since been adopted in psychological experiments that usually do not analyze the temporal dimension, but also present noise to human participants. In contrast to the original meaning, the term is here thought to reflect that the standard psychological practice of presenting stimuli of defined categories to the participants is "reversed": Instead, the participant's mental representations of categories are estimated from interactions of the presented noise and the behavioral responses. It is used to create composite pictures of individual and/or group mental representations of various items (e.g. faces, bodies, and the self) that depict characteristics of said items (e.g. trustworthiness and self-body image). This technique is helpful when evaluating the mental representations of those with and without mental illnesses. == Terms == This technique utilizes spike-triggered average to explain what areas of signal and noise in an image are valuable for the given research question. Signal is information used to produce objects of value that help explain and connect the world around us. Noise is commonly referred to as unwanted signal that obscures the information that the signal is trying to present. Most importantly for reverse correlation studies, noise is randomly varying information. To determine the areas of importance using reverse correlation, noise is applied to a base image and then evaluated by observers. A base image is any image void of noise that relates to the research question. A base image that has noise superimposed on top is the stimuli that is presented to and evaluated by participants. Each time a new set of stimuli is presented to a participant, this is known as a trial. After a participant has responded to hundreds to thousands of trials, a researcher is ready to create a classification image. A classification image (abbreviated as "CI" in some studies) is a single image that represents the average noise patterns in the images selected by participants. A classification image can also be computed for groups by averaging the individuals’ classification images. These classification images are what researchers use to interpret the data and draw conclusions. As a whole, the reverse correlation method is a process that results in a composite image (from an individual or group) that can be used to estimate and interpret mental representations. == Basic study layout == The reverse correlation method is typically executed as an in-lab computer experiment. This method follows four broad steps. Each of the following steps are described in greater detail below. After creating a research question and determining that the reverse correlation method is the most suitable technique to answer the question, a researcher must (1) design randomly varying stimuli. After the stimuli have been prepared, a researcher should (2) collect data from participants who will see and respond to approximately 300 -1,000 trials. Each trial will either consist of one or two images (side by side) derived from the same base image with noise superimposed on top. Participant responses will depend on the chosen study design; if a researcher presents only one image at a time, participants rate the image on a 4pt scale, but when two images are shown, the participant is asked to choose which best aligns with the given category (e.g. choose the image that looks the most aggressive). Once all of the data is collected, the researcher will (3) compute classification images for each participant and using those images compute group classification images. Finally, with the classification images available, the researcher will (4) evaluate the images and draw conclusions about their results. === Step 1: making stimuli === When designing the stimuli for a reverse correlation study, the two primary factors that one should consider are (1) the base image and (2) the noise that will be used. While not all bases are images per se, the majority are and for this reason the base is typically referred to as a base image. The base image should represent whatever the research question is addressing. For example, if you are interested in peoples’ mental representations of Chinese people, it would not make sense to use a base image of a Spanish or Caucasian person. Again, if you are interested in the mental representations of male vocal patterns, it would make the most sense to use a base vocal pattern that has been produced by a male. Having a base is important because it provides a kind of anchor for participants to work from. When there is no base image, the number of trials that are required increases dramatically, thus making it harder to collect data. While there are studies that have excluded a base image, (e.g. the S study), for more elaborate and nuanced research questions, it is important to have a base image that is a fair representation of what participants are being asked to categorize. Photographs of faces are generally the most popular base image. Although the reverse correlation method is capable of investigating a wide variety of research questions, the most common application of the method is for evaluating faces on a single trait. Reverse correlation studies that address evaluations of the face are sometimes referred to as being a face space reverse correlation model (FSRCM). Thankfully, there are existing databases for face images of varying demographics and emotion that work well as base images. The reverse correlation method can also be used to help researchers identify what areas of an image (e.g. the areas on the face) have diagnostic value. In order to identify these areas of value, researchers start by minimizing the space a participant can pull information from. By imposing a “mask” on an image (e.g. blur an image while leaving random areas un-blurred), this reduces the information individuals might see, and forces them to focus on certain areas. Then, if/when participants are able to correctly identify an image with a trait repeatedly, we can draw conclusions about what areas have diagnostic value. While faces and visual stimuli are the most popular, this is not the only stimuli that can be used in a reverse correlation study. This method was originally designed for auditory stimuli which allows researchers to investigate how perceivers interpret auditory information and create trait based attributions to different sound patterns. For example, by segmenting a vocal recording of a single word (total sound time 426 ms) into six segments (71 ms each), and varying each segment's pitch using Gaussian distributions, researchers were able to uncover what vocal patterns people associated with certain traits. Specifically, this study investigated how listeners rated sound clips of the word “really” as sounding more interrogative (i.e. like the more common reverse correlation studies this study had participants listen to two sound clips per trial, choose which fit the category the best, and then created an average of the pitch contours). Beyond face and auditory perception, research utilizing the reverse correlation method has expanded to investigate how individuals see three-dimensional objects in images with noise (but no signal). After selecting your base image, regardless of what the image is, it is helpful to apply a Gaussian blur to smooth noise in the image. While noise will be applied later, it is helpful to reduce existing noise in the photo before applying your chosen noise. There are three primary choices when it comes to noise: white noise, sine-wave noise, and Gabor noise. The latter two of these constrain the configurations that the noise can have, and because of this white noise is usually the most commonly used. Regardless of the type of noise that is chosen, it is crucial that the noise randomly varies. === Step 2: data collection === Once the stimuli for the study has been developed, the researcher must make a few decisions before actually collecting the data. The researcher must come to a conclusion on how many stimuli will be presented at a time and how many trials the participants will see. In terms of stimuli presentation, a researcher can choose from either a 2-Image Forced Choice (2IFC) or a 4-Alternative Forced Choice (4AFC). The 2IFC presents two images at once (side by side) and requires participants to choose between the two on a specified category (e.g. which image looks the most like a male). Typically the noise from the left image is the mathematical inverse of the noise from the right image. This method was developed to better answer questions that could n