Hostile Waters, released as Hostile Waters: Antaeus Rising in America, is a hybrid vehicle and strategy game developed and published by Rage Software for Microsoft Windows. It was inspired by Carrier Command (Realtime Games, 1988). It has won several awards and one unofficial award from Rock Paper Shotgun as a "lost classic" or "The best game you've never played". == Plot == Hostile Waters takes place in a Utopian future where war has been abolished. In the year 2012, a revolutionary war takes place between the corrupt and power-hungry politicians, leaders and businessmen (described as the "Old Guard") and the people. The Old Guard were defeated, with only a few of their leaders escaping. By 2032, the world has been rebuilt as a utopia, with the help of nano-technological assemblers, which are used in "creation engines" to create matter from energy and waste, for free. The newly united world is governed from a capital city known as Central. Missile attacks are suddenly launched against major cities all over the world from an unknown location. This is eventually discovered to be an island chain in the South Pacific Ocean. A response to the missile attacks was a special forces team sent in to investigate the area for preliminary investigations. The Ministry of Intelligence (MinIntel) loses contact with it shortly thereafter. The world government authorises a reactivation of the Antaeus program, a series of warships able to create any weapon of their choosing using their on-board nano-technological creation engine. Two of these were left on the seabed in the case of an emergency, capable of being re-activated and refloating itself. On board are a series of "soulcatcher" chips, a classified 1990s military program researched into for the storage of human brain functions on a silicon chip. The soulcatcher technology was used to store the minds of every crew member ever assigned to an Antaeus vessel. It is soon discovered that one of the cruisers does not respond to the awakening signal. The other cruiser, however, is refloated and re-activated, with heavy damage to vital ship components. A course is plotted for a nearby disused wet-dock. As the Antaeus progresses from the wet-dock, unusual biological life-forms are discovered amongst the enemy bases on the islands. The identity of the aggressor firing the missiles is confirmed as the leftovers of the old, pre-Central forces, known as the Cabal. Outnumbering Central's army a thousand to one, they are fighting with thousands of troops and weapons that they hid away when it was apparent that the war was lost. The Antaeus is deployed into the chicane to stop the Cabal's operations there. It's later discovered that along with their superior numbers, they have also biologically engineered a species of organic machines, designed in the popular likeness of extraterrestrials, which they intend to use to create the fear of an alien invasion, to facilitate their taking over the world and the removal of the public use of creation engines. The Cabal later lose control of the species, which eventually turns on its masters, destroying them. The species starts spreading, modifying the planetary climate and geographical features in an attempt to exterminate humanity and make the planet more hospitable to itself. Having exterminated its creators, the species resolves to cleanse humanity as a whole from the planet using a massive 'disassembler cannon', only to be stopped by the Antaeus. The species subsequently attempts to flee into the cosmos and colonise the surrounding planets and stars, by launching a massive number of 'culture stones' (information devices that also double as creation engines) into space from an enormous, artificially-grown organic "island", the final staging point. Central's only option is to bind the Antaeus' creation engine and the disassembler cannon stolen from the aliens together to create a makeshift bomb, and detonate it at the central "column" containing the culture stones. The plan succeeds, and the Antaeus is sacrificed to save the world. The final cinematic show the organic disassembler cannon and the Antaeus' creation engine moving closer together and fusing, creating something new. A post-credits scene also shows that two of the species' culture stones have managed to get into space. == Gameplay == Each Mission takes place on and or near a fortified enemy island containing various forms of anti-air and ground defence, with scattered unit-production complexes powered by oil-derricks and fuel containers (which are dependent on the oil-derricks) that the player can destroy to keep the enemy from replacing destroyed forces. Vehicles are built on the Antaeus and, if desired, land vehicles can be delivered to a location by the air-lifting "magpie". Units are created by providing Antaeus with a number of resources which are obtained at the beginning of the level and debris which are taken from destroyed enemy units and structures. Transport helicopters such as the "Pegasus" can fly to an object and airlift it to the ship-board recycling system with little resources required. The carrier can analyse objects it disassembles at the rear of the Antaeus cruiser, and several of the game's vehicles and items are unlocked by "sampling" them in this fashion. The game has a number of vehicles that are progressively unlocked as the missions progress. Vehicles contain a number of slots for equipment and a selection of different types of weapons to use in the vehicle. A variety of vehicle equipment combinations can be designed. Vehicles have an individual damage multiplier such that different vehicles with the same weapon will do different damage. In addition to this, each soul-chip personality specializes in one unit along with specific equipment, which, if equipped will gain them a bonus in efficiency. == Development == The game was developed by 12 people. == Reception == The game received "favourable" reviews according to the review aggregation website Metacritic. Carla Harker of NextGen said, "You'll feel like a real battlefield general when you take to the field in Antaeus Rising." Jake The Snake of GamePro said, "If the usual game categories leave you unscathed, get bloodied in these Hostile Waters."
JSGF
JSGF stands for Java Speech Grammar Format or the JSpeech Grammar Format (in a W3C Note). Developed by Sun Microsystems, it is a textual representation of grammars for use in speech recognition for technologies like XHTML+Voice. JSGF adopts the style and conventions of the Java programming language in addition to use of traditional grammar notations. The Speech Recognition Grammar Specification was derived from this specification. == Example == The following JSGF grammar will recognize the words coffee, tea, and milk.
Is an Conversational AI Platform Worth It in 2026?
Looking for the best conversational AI platform? An conversational AI platform 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 conversational AI platform slots into your workflow and pays for itself fast. This guide breaks down the top picks, their pros and cons, and who each one is best for.
Ziad Obermeyer
Ziad Obermeyer (Arabic: زياد أوبرماير) is a Lebanese American physician and researcher whose work focuses on machine learning, health policy, and clinical decision-making in medicine. He is the Blue Cross of California Distinguished Associate Professor at the UC Berkeley School of Public Health, a Chan Zuckerberg Biohub investigator, and a research associate at the National Bureau of Economic Research. He is known for his research on racial bias in health care algorithms and the use of artificial intelligence in health care. == Early life and education == Obermeyer was born in Beirut, Lebanon, and raised in Cambridge, Massachusetts. He earned a Bachelor of Arts degree from Harvard College and a Master of Philosophy (M.Phil.) in History and Science from the University of Cambridge. He received his Doctor of Medicine (M.D.) from Harvard Medical School in 2008. Before pursuing medicine, Obermeyer worked as a consultant at McKinsey & Company, advising pharmaceutical and global health clients in New Jersey, Geneva, and Tokyo. After completing his medical degree, he trained as an emergency physician at Mass General Brigham (MGB) in Boston, Massachusetts. He later continued practicing emergency medicine at the Fort Defiance Indian Hospital on the Navajo Nation in Arizona. == Academic career == Obermeyer served as an Assistant Professor at Harvard Medical School from 2014 to 2020. In 2020, he joined the University of California, Berkeley as an Associate Professor and the Blue Cross of California Distinguished Professor at the School of Public Health. == Research focus == === Algorithmic racial bias in healthcare === In 2019, Obermeyer and economist Sendhil Mullainathan examined a commercial healthcare algorithm by UnitedHealth Group, used in hospitals and by insurers to identify patients with complex health needs. The study found that the algorithm underestimated the health needs of Black patients compared to white patients with similar conditions and that reformulating it would reduce racial bias. In 2020, Obermeyer analyzed an algorithm used to allocate CARE Act relief funding to hospitals. The study identified allocation patterns that favored hospitals with higher revenues over hospitals serving larger numbers of COVID-19 patients who are predominantly Black. === Clinical decision-making === In 2021, Obermeyer and colleagues examined physician decision-making in cardiac care using machine learning models. The study found that physicians misdiagnose cases when they rely on symptoms representative of a heart attack, such as chest pain, over other symptoms. === Pain assessment === Obermeyer developed a deep learning approach to investigate the severity of osteoarthritis in underserved communities. == Policy and regulatory work == Following the publication of the 2019 algorithmic racial bias study, the New York Department of Financial Services and Department of Health launched an investigation into UnitedHealth Group's algorithm, requesting that the company cease using it, citing discriminatory business practices. Also related to this study, in December 2019, Democratic Senators Cory Booker and Ron Wyden released letters to the Federal Trade Commission and Centers for Medicare and Medicaid Services asking to investigate potential discrimination in decision-making algorithms against marginalized communities in healthcare. The senators also wrote to major healthcare companies, including Aetna and Blue Cross Blue Shield, about their internal safeguards against racial bias in their technology. In 2021, Obermeyer and colleagues at the University of Chicago Booth School of Business released the Algorithmic Bias Playbook, a resource for policymakers and technical teams working in healthcare on how to measure and mitigate algorithmic racial bias. Obermeyer testified before the U.S. Senate Financial Committee in February 2024 on artificial intelligence in healthcare, recommending transparency requirements for AI developers and independent algorithm evaluations. In December 2025, he testified before the United States House Committee on Oversight and Government Reform on the role of AI in affordable healthcare and the impact of its integration on the workforce. == Organizations == In 2021, Obermeyer cofounded Nightingale Open Science, a non-profit that creates new medical imaging datasets available for research, and Dandelion Health, a health data analytics company. In June 2023, the company launched a program to audit and evaluate the performance of algorithms to identify potential racial, ethnic, and geographic bias, funded by the Gordon and Betty Moore Foundation and the SCAN Foundation. Dandelion Health partnered with the American Heart Association in 2025 to power an AI assessment lab for cardiovascular algorithms. Obermeyer is a founding faculty member of the University of California, Berkeley–University of California, San Francisco joint program in computational precision health. == Recognition == TIME magazine named Obermeyer one of the 100 most influential people in artificial intelligence in 2023. He has served as a Chan Zuckerberg Biohub Investigator since 2022, and as a Research Associate at the National Bureau of Economic Research since 2023. He was designated an Emerging Leader by the National Academy of Medicine in 2020. Obermeyer's racial bias study received the Willard G. Manning Memorial Award for the Best Research in Health Econometrics from the American Society of Health Economists (ASHEcon) in 2021 and the Responsible Business Education Award from the Financial Times in 2022.
Büchi automaton
In computer science and automata theory, a deterministic Büchi automaton is a theoretical machine which either accepts or rejects infinite inputs. Such a machine has a set of states and a transition function, which determines which state the machine should move to from its current state when it reads the next input character. Some states are accepting states and one state is the start state. The machine accepts an input if and only if it will pass through an accepting state infinitely many times as it reads the input. A non-deterministic Büchi automaton, later referred to just as a Büchi automaton, has a transition function which may have multiple outputs, leading to many possible paths for the same input; it accepts an infinite input if and only if some possible path is accepting. Deterministic and non-deterministic Büchi automata generalize deterministic finite automata and nondeterministic finite automata to infinite inputs. Each are types of ω-automata. Büchi automata recognize the ω-regular languages, the infinite word version of regular languages. They are named after the Swiss mathematician Julius Richard Büchi, who invented them in 1962. Büchi automata are often used in model checking as an automata-theoretic version of a formula in linear temporal logic. == Formal definition == Formally, a deterministic Büchi automaton is a tuple A = ( Q , Σ , δ , q 0 , F ) {\textstyle A=(Q,\Sigma ,\delta ,q_{0},\mathbf {F} )} that consists of the following components: Q {\textstyle Q} is a finite set. The elements of Q {\textstyle Q} are called the states of A {\textstyle A} . Σ {\textstyle \Sigma } is a finite set called the alphabet of A {\textstyle A} . δ : Q × Σ → Q {\textstyle \delta \colon Q\times \Sigma \to Q} is a function, called the transition function of A {\textstyle A} . q 0 {\textstyle q_{0}} is an element of Q {\textstyle Q} , called the initial state of A {\textstyle A} . F ⊆ Q {\textstyle \mathbf {F} \subseteq Q} is the acceptance condition. A run i _ = i 0 i 1 i 2 ⋯ ∈ Σ ω {\displaystyle {\underline {i}}=i_{0}i_{1}i_{2}\cdots \in \Sigma ^{\omega }} is an infinite string of inputs of A {\displaystyle A} . By calling δ {\displaystyle \delta } recursively, we can extend it to a function δ ω : Σ ω → Q ω {\displaystyle \delta ^{\omega }:\Sigma ^{\omega }\to Q^{\omega }} . A state q ∈ Q {\displaystyle q\in Q} is said to occur infinitely often for a run i _ {\displaystyle {\underline {i}}} when the set { n ∈ N ∣ δ ω ( i _ ) n = q } {\displaystyle \{n\in \mathbb {N} \mid \delta ^{\omega }({\underline {i}})_{n}=q\}} is infinite. Let I n f ( i _ ) {\displaystyle \mathrm {Inf} ({\underline {i}})} be the set of states occurring infinitely often for i _ {\displaystyle {\underline {i}}} . The language of A {\displaystyle A} is then the set of runs of A {\displaystyle A} in which at least one of the infinitely-often occurring states is in F {\textstyle \mathbf {F} } ; in symbols: L ( A ) = { i _ ∈ Σ ω ∣ I n f ( i _ ) ∩ F ≠ ∅ } . {\displaystyle L(A)=\{{\underline {i}}\in \Sigma ^{\omega }\mid \mathrm {Inf} ({\underline {i}})\cap \mathbf {F} \neq \varnothing \}.} In a (non-deterministic) Büchi automaton, the transition function δ {\textstyle \delta } is replaced with a transition relation Δ {\textstyle \Delta } that returns a set of states, and the single initial state q 0 {\textstyle q_{0}} is replaced by a set I {\textstyle I} of initial states. Generally, the term Büchi automaton without qualifier refers to non-deterministic Büchi automata. For more comprehensive formalism see also ω-automaton. == Closure properties == The set of Büchi automata is closed under the following operations. Let A = ( Q A , Σ , Δ A , I A , F A ) {\displaystyle A=(Q_{A},\Sigma ,\Delta _{A},I_{A},{F}_{A})} and B = ( Q B , Σ , Δ B , I B , F B ) {\displaystyle B=(Q_{B},\Sigma ,\Delta _{B},I_{B},{F}_{B})} be Büchi automata and C = ( Q C , Σ , Δ C , I C , F C ) {\displaystyle C=(Q_{C},\Sigma ,\Delta _{C},I_{C},{F}_{C})} be a finite automaton. Union: There is a Büchi automaton that recognizes the language L ( A ) ∪ L ( B ) . {\displaystyle L(A)\cup L(B).} Proof: If we assume, w.l.o.g., Q A ∩ Q B {\displaystyle Q_{A}\cap Q_{B}} is empty then L ( A ) ∪ L ( B ) {\displaystyle L(A)\cup L(B)} is recognized by the Büchi automaton ( Q A ∪ Q B , Σ ∪ Σ , Δ A ∪ Δ B , I A ∪ I B , F A ∪ F B ) . {\displaystyle (Q_{A}\cup Q_{B},\Sigma \cup \Sigma ,\Delta _{A}\cup \Delta _{B},I_{A}\cup I_{B},{F}_{A}\cup {F}_{B}).} Intersection: There is a Büchi automaton that recognizes the language L ( A ) ∩ L ( B ) . {\displaystyle L(A)\cap L(B).} Proof: The Büchi automaton A ′ = ( Q ′ , Σ , Δ ′ , I ′ , F ′ ) {\displaystyle A'=(Q',\Sigma ,\Delta ',I',F')} recognizes L ( A ) ∩ L ( B ) , {\displaystyle L(A)\cap L(B),} where Q ′ = Q A × Q B × { 1 , 2 } {\displaystyle Q'=Q_{A}\times Q_{B}\times \{1,2\}} Δ ′ = Δ 1 ∪ Δ 2 {\displaystyle \Delta '=\Delta _{1}\cup \Delta _{2}} Δ 1 = { ( ( q A , q B , 1 ) , a , ( q A ′ , q B ′ , i ) ) | ( q A , a , q A ′ ) ∈ Δ A and ( q B , a , q B ′ ) ∈ Δ B and if q A ∈ F A then i = 2 else i = 1 } {\displaystyle \Delta _{1}=\{((q_{A},q_{B},1),a,(q'_{A},q'_{B},i))|(q_{A},a,q'_{A})\in \Delta _{A}{\text{ and }}(q_{B},a,q'_{B})\in \Delta _{B}{\text{ and if }}q_{A}\in F_{A}{\text{ then }}i=2{\text{ else }}i=1\}} Δ 2 = { ( ( q A , q B , 2 ) , a , ( q A ′ , q B ′ , i ) ) | ( q A , a , q A ′ ) ∈ Δ A and ( q B , a , q B ′ ) ∈ Δ B and if q B ∈ F B then i = 1 else i = 2 } {\displaystyle \Delta _{2}=\{((q_{A},q_{B},2),a,(q'_{A},q'_{B},i))|(q_{A},a,q'_{A})\in \Delta _{A}{\text{ and }}(q_{B},a,q'_{B})\in \Delta _{B}{\text{ and if }}q_{B}\in F_{B}{\text{ then }}i=1{\text{ else }}i=2\}} I ′ = I A × I B × { 1 } {\displaystyle I'=I_{A}\times I_{B}\times \{1\}} F ′ = { ( q A , q B , 2 ) | q B ∈ F B } {\displaystyle F'=\{(q_{A},q_{B},2)|q_{B}\in F_{B}\}} By construction, r ′ = ( q A 0 , q B 0 , i 0 ) , ( q A 1 , q B 1 , i 1 ) , … {\displaystyle r'=(q_{A}^{0},q_{B}^{0},i^{0}),(q_{A}^{1},q_{B}^{1},i^{1}),\dots } is a run of automaton A' on input word w {\textstyle w} if r A = q A 0 , q A 1 , … {\displaystyle r_{A}=q_{A}^{0},q_{A}^{1},\dots } is run of A {\textstyle A} on w {\textstyle w} and r B = q B 0 , q B 1 , … {\displaystyle r_{B}=q_{B}^{0},q_{B}^{1},\dots } is run of B {\textstyle B} on w {\textstyle w} . r A {\textstyle r_{A}} is accepting and r B {\textstyle r_{B}} is accepting if r ′ {\textstyle r'} is concatenation of an infinite series of finite segments of 1-states (states with third component 1) and 2-states (states with third component 2) alternatively. There is such a series of segments of r ′ {\textstyle r'} if r ′ {\textstyle r'} is accepted by A ′ {\textstyle A'} . Concatenation: There is a Büchi automaton that recognizes the language L ( C ) ⋅ L ( A ) . {\displaystyle L(C)\cdot L(A).} Proof: If we assume, w.l.o.g., Q C ∩ Q A {\displaystyle Q_{C}\cap Q_{A}} is empty then the Büchi automaton A ′ = ( Q C ∪ Q A , Σ , Δ ′ , I ′ , F A ) {\displaystyle A'=(Q_{C}\cup Q_{A},\Sigma ,\Delta ',I',F_{A})} recognizes L ( C ) ⋅ L ( A ) {\displaystyle L(C)\cdot L(A)} , where Δ ′ = Δ A ∪ Δ C ∪ { ( q , a , q ′ ) | q ′ ∈ I A and ∃ f ∈ F C . ( q , a , f ) ∈ Δ C } {\displaystyle \Delta '=\Delta _{A}\cup \Delta _{C}\cup \{(q,a,q')|q'\in I_{A}{\text{ and }}\exists f\in F_{C}.(q,a,f)\in \Delta _{C}\}} if I C ∩ F C is empty then I ′ = I C otherwise I ′ = I C ∪ I A {\displaystyle {\text{ if }}I_{C}\cap F_{C}{\text{ is empty then }}I'=I_{C}{\text{ otherwise }}I'=I_{C}\cup I_{A}} ω-closure: If L ( C ) {\displaystyle L(C)} does not contain the empty word then there is a Büchi automaton that recognizes the language L ( C ) ω . {\displaystyle L(C)^{\omega }.} Proof: The Büchi automaton that recognizes L ( C ) ω {\displaystyle L(C)^{\omega }} is constructed in two stages. First, we construct a finite automaton A ′ {\textstyle A'} such that A ′ {\textstyle A'} also recognizes L ( C ) {\displaystyle L(C)} but there are no incoming transitions to initial states of A ′ {\textstyle A'} . So, A ′ = ( Q C ∪ { q new } , Σ , Δ ′ , { q new } , F C ) , {\displaystyle A'=(Q_{C}\cup \{q_{\text{new}}\},\Sigma ,\Delta ',\{q_{\text{new}}\},F_{C}),} where Δ ′ = Δ C ∪ { ( q new , a , q ′ ) | ∃ q ∈ I C . ( q , a , q ′ ) ∈ Δ C } . {\displaystyle \Delta '=\Delta _{C}\cup \{(q_{\text{new}},a,q')|\exists q\in I_{C}.(q,a,q')\in \Delta _{C}\}.} Note that L ( C ) = L ( A ′ ) {\displaystyle L(C)=L(A')} because L ( C ) {\displaystyle L(C)} does not contain the empty string. Second, we will construct the Büchi automaton A ″ {\textstyle A''} that recognize L ( C ) ω {\displaystyle L(C)^{\omega }} by adding a loop back to the initial state of A ′ {\textstyle A'} . So, A ″ = ( Q C ∪ { q new } , Σ , Δ ″ , { q new } , { q new } ) {\displaystyle A''=(Q_{C}\cup \{q_{\text{new}}\},\Sigma ,\Delta '',\{q_{\text{new}}\},\{q_{\text{new}}\})} , where Δ ″ = Δ ′ ∪ { ( q , a , q new ) | ∃ q ′ ∈ F C . ( q , a , q ′ ) ∈ Δ ′ } . {\displaystyle \Delta ''=\Delta '\cup \{(q,a,q_{\text{new}})|\exists q'\in F_{C}.(q,a,q')\in \Delta '\}.} Complementation:
Cognition Network Technology
Cognition Network Technology (CNT), also known as Definiens Cognition Network Technology, is an object-based image analysis method developed by Nobel laureate Gerd Binnig together with a team of researchers at Definiens AG in Munich, Germany. It serves for extracting information from images using a hierarchy of image objects (groups of pixels), as opposed to traditional pixel processing methods. To emulate the human mind's cognitive powers, Definiens used patented image segmentation and classification processes, and developed a method to render knowledge in a semantic network. CNT examines pixels not in isolation, but in context. It builds up a picture iteratively, recognizing groups of pixels as objects. It uses the color, shape, texture and size of objects as well as their context and relationships to draw conclusions and inferences, similar to human analysis. == History == In 1994 Professor Gerd Binnig founded Definiens. CNT was first available with the launch of the eCognition software in May 2000. In June 2010, Trimble Navigation Ltd (NASDAQ: TRMB) acquired Definiens business asset in earth sciences markets, including eCognition software, and also licensed Definiens' patented CNT. In 2014, Definiens was acquired by MedImmune, the global biologics research and development arm of AstraZeneca, for an initial consideration of $150 million. == Software == Definiens Tissue Studio Definiens Tissue Studio is a digital pathology image analysis software application based on CNT. The intended use of Definiens Tissue Studio is for biomarker translational research in formalin-fixed, paraffin-embedded tissue samples which have been treated with immunohistochemical staining assays, or hematoxylin and eosin (H&E). The central concept behind Definiens Tissue Studio is a user interface that facilitates machine learning from example digital histopathology images to derive an image analysis solution suitable for the measurement of biomarkers and/or histological features within pre-defined regions of interest on a cell-by-cell basis, and within sub-cellular compartments. The derived image analysis solution is then automatically applied to subsequent digital images to objectively measure defined sets of multiparametric image features. These data sets are used for further understanding the underlying biological processes that drive cancer and other diseases. Image processing and data analysis are performed either on a local desktop computer workstation, or on a server grid. eCognition The eCognition suite offers three components that can be used stand-alone or in combination to solve image analysis tasks. eCognition Developer is a development environment for object-based image analysis. It is used in earth sciences to develop rule sets (or applications) for the analysis of remote sensing data. eCognition Architect enables non-technical users to configure, calibrate and execute image analysis workflows created in eCognition Developer. eCognition Server software provides a processing environment for batch execution of image analysis jobs. eCognition software is utilized in numerous remote sensing and geospatial application scenarios and environments, using a variety of data types: Generic: Rapid Mapping, Change Detection, Object Recognition By environment: Diverse Landcover Mapping, Urban Analysis (i.e. impervious surface area analysis for taxation, property assessment for insurance, inventory of green infrastructure), Forestry (i.e. biomass measurement, species identification, firescar measurement), Agriculture (i.e. regional planning, precision farming, crisis response), Marine and Riparian (i.e. ecosystem evaluation, disaster management, harbor monitoring). Other: Defense, security, atmosphere and climate The online eCognition community was launched in July 2009 and had 2813 members as of July 9, 2010. Membership is distributed globally and user conferences are held regularly, the last having taken place in November 2009 in Munich, Germany. The bi-annual GEOBIA (Geographic Object-Based Image Analysis) conference is heavily attended by eCognition users, with the majority of presentations based on eCognition software.
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