In computer vision, photo-consistency determines whether a given voxel is occupied. A voxel is considered to be photo consistent when its color appears to be similar to all the cameras that can see it. Most voxel coloring or space carving techniques require using photo consistency as a check condition in Image-based modeling and rendering applications. == Usage == 3D Volumetric Reconstruction. Image registration. Multi-view reconstruction.
Graphics software
In computer graphics, graphics software refers to a program or collection of programs that enable a person to manipulate images or models visually on a computer. Computer graphics can be classified into two distinct categories: raster graphics and vector graphics, with further 2D and 3D variants. Many graphics programs focus exclusively on either vector or raster graphics, but there are a few that operate on both. It is simple to convert from vector graphics to raster graphics, but going the other way is harder. Some software attempts to do this. In addition to static graphics, there are animation and video editing software. Different types of software are often designed to edit different types of graphics such as video, photos, and vector-based drawings. The exact sources of graphics may vary for different tasks, but most can read and write files. Most graphics programs have the ability to import and export one or more graphics file formats, including those formats written for a particular computer graphics program. Such programs include, but are not limited to: GIMP, Adobe Photoshop, CorelDRAW, Microsoft Publisher, Picasa, etc. The use of a swatch is a palette of active colours that are selected and rearranged by the preference of the user. A swatch may be used in a program or be part of the universal palette on an operating system. It is used to change the colour of a text or image and in video editing. Vector graphics animation can be described as a series of mathematical transformations that are applied in sequence to one or more shapes in a scene. Raster graphics animation works in a similar fashion to film-based animation, where a series of still images produces the illusion of continuous movement. == History == SuperPaint was one of the earliest graphics software applications, first conceptualized in 1972 and achieving its first stable image in 1973 Fauve Matisse (later Macromedia xRes) was a pioneering program of the early 1990s, notably introducing layers in customer software. Currently Adobe Photoshop is one of the most used and best-known graphics programs in the Americas, having created more custom hardware solutions in the early 1990s, but was initially subject to various litigation. GIMP is a popular open-source alternative to Adobe Photoshop.
Multiple sequence alignment
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides. Multiple sequence alignments require more sophisticated methodologies than pairwise alignments, as they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. However, heuristic methods generally cannot guarantee high-quality solutions and have been shown to fail to yield near-optimal solutions on benchmark test cases. == Problem statement == Given m {\displaystyle m} sequences S i {\displaystyle S_{i}} , i = 1 , ⋯ , m {\displaystyle i=1,\cdots ,m} similar to the form below: S := { S 1 = ( S 11 , S 12 , … , S 1 n 1 ) S 2 = ( S 21 , S 22 , ⋯ , S 2 n 2 ) ⋮ S m = ( S m 1 , S m 2 , … , S m n m ) {\displaystyle S:={\begin{cases}S_{1}=(S_{11},S_{12},\ldots ,S_{1n_{1}})\\S_{2}=(S_{21},S_{22},\cdots ,S_{2n_{2}})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S_{m}=(S_{m1},S_{m2},\ldots ,S_{mn_{m}})\end{cases}}} A multiple sequence alignment is taken of this set of sequences S {\displaystyle S} by inserting any amount of gaps needed into each of the S i {\displaystyle S_{i}} sequences of S {\displaystyle S} until the modified sequences, S i ′ {\displaystyle S'_{i}} , all conform to length L ≥ max { n i ∣ i = 1 , … , m } {\displaystyle L\geq \max\{n_{i}\mid i=1,\ldots ,m\}} and no values in the sequences of S {\displaystyle S} of the same column consists of only gaps. The mathematical form of an MSA of the above sequence set is shown below: S ′ := { S 1 ′ = ( S 11 ′ , S 12 ′ , … , S 1 L ′ ) S 2 ′ = ( S 21 ′ , S 22 ′ , … , S 2 L ′ ) ⋮ S m ′ = ( S m 1 ′ , S m 2 ′ , … , S m L ′ ) {\displaystyle S':={\begin{cases}S'_{1}=(S'_{11},S'_{12},\ldots ,S'_{1L})\\S'_{2}=(S'_{21},S'_{22},\ldots ,S'_{2L})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S'_{m}=(S'_{m1},S'_{m2},\ldots ,S'_{mL})\end{cases}}} To return from each particular sequence S i ′ {\displaystyle S'_{i}} to S i {\displaystyle S_{i}} , remove all gaps. == Graphing approach == A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. When finding alignments via graph, a complete alignment is created in a weighted graph that contains a set of vertices and a set of edges. Each of the graph edges has a weight based on a certain heuristic that helps to score each alignment or subset of the original graph. === Tracing alignments === When determining the best suited alignments for each MSA, a trace is usually generated. A trace is a set of realized, or corresponding and aligned, vertices that has a specific weight based on the edges that are selected between corresponding vertices. When choosing traces for a set of sequences it is necessary to choose a trace with a maximum weight to get the best alignment of the sequences. == Alignment methods == There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. Each is usually based on a certain heuristic with an insight into the evolutionary process. Most try to replicate evolution to get the most realistic alignment possible to best predict relations between sequences. === Dynamic programming === A direct method for producing an MSA uses the dynamic programming technique to identify the globally optimal alignment solution. For proteins, this method usually involves two sets of parameters: a gap penalty and a substitution matrix assigning scores or probabilities to the alignment of each possible pair of amino acids based on the similarity of the amino acids' chemical properties and the evolutionary probability of the mutation. For nucleotide sequences, a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global alignment, but must be both positive and negative, in the case of a local alignment. For n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. The search space thus increases exponentially with increasing n and is also strongly dependent on sequence length. Expressed with the big O notation commonly used to measure computational complexity, a naïve MSA takes O(LengthNseqs) time to produce. To find the global optimum for n sequences this way has been shown to be an NP-complete problem. In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a practical method that uses pairwise alignments to constrain the n-dimensional search space. In this approach pairwise dynamic programming alignments are performed on each pair of sequences in the query set, and only the space near the n-dimensional intersection of these alignments is searched for the n-way alignment. The MSA program optimizes the sum of all of the pairs of characters at each position in the alignment (the so-called sum of pair score) and has been implemented in a software program for constructing multiple sequence alignments. In 2019, Hosseininasab and van Hoeve showed that by using decision diagrams, MSA may be modeled in polynomial space complexity. === Progressive alignment construction === The most widely used approach to multiple sequence alignments uses a heuristic search known as progressive technique (also known as the hierarchical or tree method) developed by Da-Fei Feng and Doolittle in 1987. Progressive alignment builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly related. All progressive alignment methods require two stages: a first stage in which the relationships between the sequences are represented as a phylogenetic tree, called a guide tree, and a second step in which the MSA is built by adding the sequences sequentially to the growing MSA according to the guide tree. The initial guide tree is determined by an efficient clustering method such as neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA), and may use distances based on the number of identical two-letter sub-sequences (as in FASTA rather than a dynamic programming alignment). Progressive alignments are not guaranteed to be globally optimal. The primary problem is that when errors are made at any stage in growing the MSA, these errors are then propagated through to the final result. Performance is also particularly bad when all of the sequences in the set are rather distantly related. Most modern progressive methods modify their scoring function with a secondary weighting function that assigns scaling factors to individual members of the query set in a nonlinear fashion based on their phylogenetic distance from their nearest neighbors. This corrects for non-random selection of the sequences given to the alignment program. Progressive alignment methods are efficient enough to implement on a large scale for many (100s to 1000s) sequences. A popular progressive alignment method has been the Clustal family. ClustalW is used extensively for phylogenetic tree construction, in spite of the author's explicit warnings that unedited alignments should not be used in such studies and as input for protein structure prediction by homology modeling. European Bioinformatics Institute (EMBL-EBI) announced that CLustalW2 will expire in August 2015. They recommend Clustal Omega which performs based on seeded guide trees and HMM profile-profile techniques for protein alignments. An alternative tool for progressive DNA alignments is multiple alignment using fast Fourier transform (MAFFT). Another common progressive alignment method named T-Coffee is slower than Clustal and its derivatives but generally produces more accurate alignments for distantly related sequence sets. T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence. It uses the output from Clustal as well as another local alignment program LALIGN, which finds multiple regions of local alignment between two sequences. The resulting alignment and phylogenetic tree are used as a guide to produce new and more accurate w
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Node2vec
node2vec is an algorithm to generate vector representations of nodes on a graph. The node2vec framework learns low-dimensional representations for nodes in a graph through the use of random walks through a graph starting at a target node. It is useful for a variety of machine learning applications. node2vec follows the intuition that random walks through a graph can be treated like sentences in a corpus. Each node in a graph is treated like an individual word, and a random walk is treated as a sentence. By feeding these "sentences" into a skip-gram, or by using the continuous bag of words model, paths found by random walks can be treated as sentences, and traditional data-mining techniques for documents can be used. The algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and argues that the added flexibility in exploring neighborhoods is the key to learning richer representations of nodes in graphs. The algorithm is considered one of the best graph classifiers.
Distinguishable interfaces
Distinguishable interfaces use computer graphic principles to automatically generate easily distinguishable appearance for computer data. Although the desktop metaphor revolutionized user interfaces, there is evidence that a spatial layout alone does little to help in locating files and other data; distinguishable appearance is also required. Studies have shown that average users have considerable difficulty finding files on their personal computers, even ones that they created the same day. Search engines do not always help, since it has been found that users often know of the existence of a file without being able to specify relevant search terms. On the contrary, people appear to incrementally search for files using some form of context. Recently researchers and web developers have argued that the problem is the lack of distinguishable appearance: in the traditional computer interface most objects and locations appear identical. This problem rarely occurs in the real world, where both objects and locations generally have easily distinguishable appearance. Discriminability was one of the recommendations in the ISO 9241-12 recommendation on presentation of information on visual displays (part of the overall report on Ergonomics of Human System Interaction), however it was assumed in that report that this would be achieved by manual design of graphical symbols. == VisualIDs, semanticons, and identicons == The mass availability of computer graphics supported the introduction of approaches that make better use of the brain's "visual hardware", by providing individual files and other abstract data with distinguishable appearance. This idea initially appeared in strictly academic VisualIDs and Semanticons works, but the web community has explored and rapidly adopted similar ideas, such as the Identicon. The VisualIDs project automatically generated icons for files or other data based on a hash of the data identifier, so the icons had no relation to the content or meaning of the data. It was argued not only that generating meaningful icons is unnecessary (their user study showed rapid learning of the arbitrary icons), but also that basing icons on content is actually incorrect ("contrasting visualization with visual identifiers"). The Semanticons project developed by Setlur et al. demonstrated an algorithm to create icons that reflect the content of files. In this work the name, location and content of a file are parsed and used to retrieve related image(s) from an image database. These are then processed using a Non-photorealistic rendering technique in order to generate graphical icons. Developer Don Park introduced the identicon library for making a visual icon from a hash of a data identifier. This initial public implementation has spawned a large number of implementations for various environments. In particular, identicons are now being used as default visual user identifiers (avatars) for several widely used systems. They are also used as a complement to Gravatars, which are pre-existing avatar images created or chosen by users, instead of automatically generated images. (see #External links). == Current research == While current web practice has followed the semantics-free approach of VisualIDs, recent research has followed the semantics-based approach of Semanticons. Examples include using data mining principles to automatically create "intelligent icons" that reflect the contents of files and creating icons for music files that reflect audio characteristics or affective content.
AI Clip Makers: Free vs Paid (2026)
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