Gary Bryce Fogel (born 1968) is an American biologist and computer scientist. He is the Chief Executive Officer of Natural Selection, Inc. He is most known for his applications of computational intelligence and machine learning to bioinformatics, computational biology, and industrial optimization. == Education and Research == Fogel was born and raised in La Jolla, California, graduating from La Jolla High School. He received a B.A. in biology with a minor in earth sciences from the University of California, Santa Cruz in 1991 and a Ph.D. in biology from the University of California, Los Angeles in 1998. Fogel has published over 150 peer-reviewed publications in conferences and journals, 2 edited books, and 11 patents. As CEO of Natural Selection, Inc., his research focuses on the application of computational intelligence, machine learning, and predictive analytics in areas not limited to: Viral evolution, cellular differentiation, drug discovery, RNA structure, cis-regulatory elements, cancer, and evolutionary game theory as well as the development of evolutionary algorithms and other approaches. == Service == Between 2008–2018 Gary Fogel was editor-in-chief of the Elsevier journal BioSystems. He has served previously as an associate editor for IEEE Transactions on Artificial Intelligence, IEEE Computational Intelligence Magazine (2005–2010), IEEE Transactions on Evolutionary Computation (2001–2013), IEEE Transactions on Emerging Topics in Computational Intelligence (2016–2018), IEEE/ACM Transactions on Computational Biology and Bioinformatics (2004–2008), International Journal of Bioinformatics Research and Applications (2004–2007), International Journal of Data Mining and Bioinformatics (2005–2007), as a consulting editor for the Journal of Computational Intelligence in Bioinformatics (2006–2007), and as an editorial board member of Ecological Informatics (2005–2009) and BMC Big Data Analytics (2015–2020). Within the IEEE Computational Intelligence Society, Fogel founded the Bioinformatics and Bioengineering Technical Committee and established the IEEE Computational Intelligence in Bioinformatics and Computational Biology conference series, chairing the first two meetings in 2004 and 2005 in San Diego. He co-founded the IEEE Conference on Artificial Intelligence in 2023. Fogel served on the IEEE Computational Intelligence Society Administrative Committee (2004–2009, 2014–2022) and served as IEEE CIS Vice President of Conferences (2010–2013, 2019). == Teaching == Gary Fogel also serves as adjunct faculty at San Diego State University in the department of aerospace engineering as well as in the Computational Science Research Center. He has authored four books and numerous articles on the history of early aviation focusing on motorless flight. He is an associate fellow of the American Institute of Aeronautics and Astronautics and serves on the AIAA History Committee. == Awards == 2023 – Outstanding Contribution to Aerospace Education Award, AIAA San Diego Section 2022 – Elected Fellow of the Asia-Pacific Artificial Intelligence Association 2019 – Top 100 AI Leaders in Drug Discovery and Advanced Healthcare by Deep Knowledge Analytics 2019 – Outstanding Contribution to Aerospace Education Award, AIAA San Diego Section 2016 – Meritorious Service Award, IEEE Computational Intelligence Society 2016 – Outstanding Contribution to the Community Award, AIAA San Diego Section 2015 – Outstanding Enhancement of the Image of the Aerospace Profession Award, AIAA San Diego Section 2012 – Medal for Significant Achievement, San Diego Chapter of Sigma Xi 2012 – Fellow of the Institute of Electrical and Electronics Engineers for contributions to computational intelligence and its application to biology, chemistry, and medicine. == Aeromodeling == Gary Fogel has established national and world records for model aircraft. He helped establish the National Model Aviation Heritage program for the Academy of Model Aeronautics. He is a leader member, contest director, and fellow of the Academy of Model Aeronautics, and was inducted into the Academy of Model Aeronautics Hall of Fame in 2025.
List of 3D rendering software
3D rendering software products are the dedicated engines used for rendering computer-generated imagery. This is not the same as 3D modeling software, which involves the creation of 3D models, for which the software listed below can produce realistically rendered visualisations.General-purpose packages which can have their own built-in rendering capabilities are not listed here; these can be found in the list of 3D computer graphics software and list of 3D animation software. See 3D computer graphics software for more discussion about the distinctions.
AI Code Generators: Free vs Paid (2026)
Looking for the best AI code generator? An AI code generator is software that uses machine learning to help you get more done — it can save you hours every week by automating repetitive work. Most options offer a generous free tier, with paid plans unlocking higher limits, faster processing, and team features. Whether you are a beginner or a pro, the right AI code generator slots into your workflow and pays for itself fast. Read on for hands-on impressions, pricing tiers, and the standout features that matter.
Iterative Viterbi decoding
Iterative Viterbi decoding is an algorithm that spots the subsequence S of an observation O = {o1, ..., on} having the highest average probability (i.e., probability scaled by the length of S) of being generated by a given hidden Markov model M with m states. The algorithm uses a modified Viterbi algorithm as an internal step. The scaled probability measure was first proposed by John S. Bridle. An early algorithm to solve this problem, sliding window, was proposed by Jay G. Wilpon et al., 1989, with constant cost T = mn2/2. A faster algorithm consists of an iteration of calls to the Viterbi algorithm, reestimating a filler score until convergence. == The algorithm == A basic (non-optimized) version, finding the sequence s with the smallest normalized distance from some subsequence of t is: // input is placed in observation s[1..n], template t[1..m], // and [[distance matrix]] d[1..n,1..m] // remaining elements in matrices are solely for internal computations (int, int, int) AverageSubmatchDistance(char s[0..(n+1)], char t[0..(m+1)], int d[1..n,0..(m+1)]) { // score, subsequence start, subsequence end declare int e, B, E t'[0] := t'[m+1] := s'[0] := s'[n+1] := 'e' e := random() do e' := e for i := 1 to n do d'[i,0] := d'[i,m+1] := e (e, B, E) := ViterbiDistance(s', t', d') e := e/(E-B+1) until (e == e') return (e, B, E) } The ViterbiDistance() procedure returns the tuple (e, B, E), i.e., the Viterbi score "e" for the match of t and the selected entry (B) and exit (E) points from it. "B" and "E" have to be recorded using a simple modification to Viterbi. A modification that can be applied to CYK tables, proposed by Antoine Rozenknop, consists in subtracting e from all elements of the initial matrix d.
Lex (software)
Lex is a computer program that generates lexical analyzers ("scanners" or "lexers"). It is commonly used with the yacc parser generator and is the standard lexical analyzer generator on many Unix and Unix-like systems. An equivalent tool is specified as part of the POSIX standard. Lex reads an input stream specifying the lexical analyzer and writes source code which implements the lexical analyzer in the C programming language. In addition to C, some old versions of Lex could generate a lexer in Ratfor. == History == Lex was originally written by Mike Lesk and Eric Schmidt and described in 1975. In the following years, Lex became the standard lexical analyzer generator on many Unix and Unix-like systems. In 1983, Lex was one of several UNIX tools available for Charles River Data Systems' UNOS operating system under the Bell Laboratories license. Although originally distributed as proprietary software, some versions of Lex are now open-source. Open-source versions of Lex, based on the original proprietary code, are now distributed with open-source operating systems such as OpenSolaris and Plan 9 from Bell Labs. One popular open-source version of Lex, called flex, or the "fast lexical analyzer", is not derived from proprietary coding. == Structure of a Lex file == The structure of a Lex file is intentionally similar to that of a yacc file: files are divided into three sections, separated by lines that contain only two percent signs, as follows: The definitions section defines macros and imports header files written in C. It is also possible to write any C code here, which will be copied verbatim into the generated source file. The rules section associates regular expression patterns with C statements. When the lexer sees text in the input matching a given pattern, it will execute the associated C code. The C code section contains C statements and functions that are copied verbatim to the generated source file. These statements presumably contain code called by the rules in the rules section. In large programs it is more convenient to place this code in a separate file linked in at compile time. == Example of a Lex file == The following is an example Lex file for the flex version of Lex. It recognizes strings of numbers (positive integers) in the input, and simply prints them out. If this input is given to flex, it will be converted into a C file, lex.yy.c. This can be compiled into an executable which matches and outputs strings of integers. For example, given the input: abc123z.!&2gj6 the program will print: Saw an integer: 123 Saw an integer: 2 Saw an integer: 6 == Using Lex with other programming tools == === Using Lex with parser generators === Lex, as with other lexical analyzers, limits rules to those which can be described by regular expressions. Due to this, Lex can be implemented by a finite-state automata as shown by the Chomsky hierarchy of languages. To recognize more complex languages, Lex is often used with parser generators such as Yacc or Bison. Parser generators use a formal grammar to parse an input stream. It is typically preferable to have a parser, one generated by Yacc for instance, accept a stream of tokens (a "token-stream") as input, rather than having to process a stream of characters (a "character-stream") directly. Lex is often used to produce such a token-stream. Scannerless parsing refers to parsing the input character-stream directly, without a distinct lexer. === Lex and make === make is a utility that can be used to maintain programs involving Lex. Make assumes that a file that has an extension of .l is a Lex source file. The make internal macro LFLAGS can be used to specify Lex options to be invoked automatically by make.
TAPPS2
TAPPS2 (Technische Alternative Planungs- und Programmier-System) is a tool used for developing the program logic for the universal, heating and solar thermal controllers by Austrian manufacturer Technische Alternative. Its primary usecase is defining the exact reaction of the controller to a certain event. Other than its predecessor, TAPPS, which could only be used to program controllers of type UVR1611, TAPPS2 is mainly used to program the UVR16x2 and RSM610 controllers, as well as several extension modules. == Development == Development in TAPPS2 is done on a vector-based drawing surface using components that can be placed via drag and drop. The components, which can be separated into inputs, functions and outputs are then being connected according to their individual features. Available components vary according to the current solar thermal control unit.
Thompson's construction
In computer science, Thompson's construction algorithm, also called the McNaughton–Yamada–Thompson algorithm, is a method of transforming a regular expression into an equivalent nondeterministic finite automaton (NFA). This NFA can be used to match strings against the regular expression. This algorithm is credited to Ken Thompson. Regular expressions and nondeterministic finite automata are two representations of formal languages. For instance, text processing utilities use regular expressions to describe advanced search patterns, but NFAs are better suited for execution on a computer. Hence, this algorithm is of practical interest, since it can compile regular expressions into NFAs. From a theoretical point of view, this algorithm is a part of the proof that they both accept exactly the same languages, that is, the regular languages. An NFA can be made deterministic by the powerset construction and then be minimized to get an optimal automaton corresponding to the given regular expression. However, an NFA may also be interpreted directly. To decide whether two given regular expressions describe the same language, each can be converted into an equivalent minimal deterministic finite automaton via Thompson's construction, powerset construction, and DFA minimization. If, and only if, the resulting automata agree up to renaming of states, the regular expressions' languages agree. == The algorithm == The algorithm works recursively by splitting an expression into its constituent subexpressions, from which the NFA will be constructed using a set of rules. More precisely, from a regular expression E, the obtained automaton A with the transition function Δ respects the following properties: A has exactly one initial state q0, which is not accessible from any other state. That is, for any state q and any letter a, Δ ( q , a ) {\displaystyle \Delta (q,a)} does not contain q0. A has exactly one final state qf, which is not co-accessible from any other state. That is, for any letter a, Δ ( q f , a ) = ∅ {\displaystyle \Delta (q_{f},a)=\emptyset } . Let c be the number of concatenation of the regular expression E and let s be the number of symbols apart from parentheses — that is, |, , a and ε. Then, the number of states of A is 2s − c (linear in the size of E). The number of transitions leaving any state is at most two. Since an NFA of m states and at most e transitions from each state can match a string of length n in time O(emn), a Thompson NFA can do pattern matching in linear time, assuming a fixed-size alphabet. === Rules === The following rules are depicted according to Aho et al. (2007), p. 122. In what follows, N(s) and N(t) are the NFA of the subexpressions s and t, respectively. The empty-expression ε is converted to A symbol a of the input alphabet is converted to The union expression s|t is converted to State q goes via ε either to the initial state of N(s) or N(t). Their final states become intermediate states of the whole NFA and merge via two ε-transitions into the final state of the NFA. The concatenation expression st is converted to The initial state of N(s) is the initial state of the whole NFA. The final state of N(s) becomes the initial state of N(t). The final state of N(t) is the final state of the whole NFA. The Kleene star expression s is converted to An ε-transition connects initial and final state of the NFA with the sub-NFA N(s) in between. Another ε-transition from the inner final to the inner initial state of N(s) allows for repetition of expression s according to the star operator. The parenthesized expression (s) is converted to N(s) itself. With these rules, using the empty expression and symbol rules as base cases, it is possible to prove with structural induction that any regular expression may be converted into an equivalent NFA. == Example == Two examples are now given, a small informal one with the result, and a bigger with a step by step application of the algorithm. === Small Example === The picture below shows the result of Thompson's construction on (ε|ab). The purple oval corresponds to a, the teal oval corresponds to a, the green oval corresponds to b, the orange oval corresponds to ab, and the blue oval corresponds to ε. === Application of the algorithm === As an example, the picture shows the result of Thompson's construction algorithm on the regular expression (0|(1(01(00)0)1)) that denotes the set of binary numbers that are multiples of 3: { ε, "0", "00", "11", "000", "011", "110", "0000", "0011", "0110", "1001", "1100", "1111", "00000", ... }. The upper right part shows the logical structure (syntax tree) of the expression, with "." denoting concatenation (assumed to have variable arity); subexpressions are named a-q for reference purposes. The left part shows the nondeterministic finite automaton resulting from Thompson's algorithm, with the entry and exit state of each subexpression colored in magenta and cyan, respectively. An ε as transition label is omitted for clarity — unlabelled transitions are in fact ε transitions. The entry and exit state corresponding to the root expression q is the start and accept state of the automaton, respectively. The algorithm's steps are as follows: An equivalent minimal deterministic automaton is shown below. == Relation to other algorithms == Thompson's is one of several algorithms for constructing NFAs from regular expressions; an earlier algorithm was given by McNaughton and Yamada. Converse to Thompson's construction, Kleene's algorithm transforms a finite automaton into a regular expression. Glushkov's construction algorithm is similar to Thompson's construction, once the ε-transitions are removed. == Use in string pattern matching == Regular expressions are often used to specify patterns that software is then asked to match. Generating an NFA by Thompson's construction, and using an appropriate algorithm to simulate it, it is possible to create pattern-matching software with performance that is O ( m n ) {\displaystyle O(mn)} , where m is the length of the regular expression and n is the length of the string being matched. This is much better than is achieved by many popular programming-language implementations; however, it is restricted to purely regular expressions and does not support patterns for non-regular languages like backreferences.