Models of DNA evolution

Models of DNA evolution

A number of different Markov models of DNA sequence evolution have been proposed. These substitution models differ in terms of the parameters used to describe the rates at which one nucleotide replaces another during evolution. These models are frequently used in molecular phylogenetic analyses. In particular, they are used during the calculation of likelihood of a tree (in Bayesian and maximum likelihood approaches to tree estimation) and they are used to estimate the evolutionary distance between sequences from the observed differences between the sequences. == Introduction == These models are phenomenological descriptions of the evolution of DNA as a string of four discrete states. These Markov models do not explicitly depict the mechanism of mutation nor the action of natural selection. Rather they describe the relative rates of different changes. For example, mutational biases and purifying selection favoring conservative changes are probably both responsible for the relatively high rate of transitions compared to transversions in evolving sequences. However, the Kimura (K80) model described below only attempts to capture the effect of both forces in a parameter that reflects the relative rate of transitions to transversions. Evolutionary analyses of sequences are conducted on a wide variety of time scales. Thus, it is convenient to express these models in terms of the instantaneous rates of change between different states (the Q matrices below). If we are given a starting (ancestral) state at one position, the model's Q matrix and a branch length expressing the expected number of changes to have occurred since the ancestor, then we can derive the probability of the descendant sequence having each of the four states. The mathematical details of this transformation from rate-matrix to probability matrix are described in the mathematics of substitution models section of the substitution model page. By expressing models in terms of the instantaneous rates of change we can avoid estimating a large numbers of parameters for each branch on a phylogenetic tree (or each comparison if the analysis involves many pairwise sequence comparisons). The models described on this page describe the evolution of a single site within a set of sequences. They are often used for analyzing the evolution of an entire locus by making the simplifying assumption that different sites evolve independently and are identically distributed. This assumption may be justifiable if the sites can be assumed to be evolving neutrally. If the primary effect of natural selection on the evolution of the sequences is to constrain some sites, then models of among-site rate-heterogeneity can be used. This approach allows one to estimate only one matrix of relative rates of substitution, and another set of parameters describing the variance in the total rate of substitution across sites. == DNA evolution as a continuous-time Markov chain == === Continuous-time Markov chains === Continuous-time Markov chains have the usual transition matrices which are, in addition, parameterized by time, t {\displaystyle t} . Specifically, if E 1 , E 2 , E 3 , E 4 {\displaystyle E_{1},E_{2},E_{3},E_{4}} are the states, then the transition matrix P ( t ) = ( P i j ( t ) ) {\displaystyle P(t)={\big (}P_{ij}(t){\big )}} where each individual entry, P i j ( t ) {\displaystyle P_{ij}(t)} refers to the probability that state E i {\displaystyle E_{i}} will change to state E j {\displaystyle E_{j}} in time t {\displaystyle t} . Example: We would like to model the substitution process in DNA sequences (i.e. Jukes–Cantor, Kimura, etc.) in a continuous-time fashion. The corresponding transition matrices will look like: P ( t ) = ( p A A ( t ) p A G ( t ) p A C ( t ) p A T ( t ) p G A ( t ) p G G ( t ) p G C ( t ) p G T ( t ) p C A ( t ) p C G ( t ) p C C ( t ) p C T ( t ) p T A ( t ) p T G ( t ) p T C ( t ) p T T ( t ) ) {\displaystyle P(t)={\begin{pmatrix}p_{\mathrm {AA} }(t)&p_{\mathrm {AG} }(t)&p_{\mathrm {AC} }(t)&p_{\mathrm {AT} }(t)\\p_{\mathrm {GA} }(t)&p_{\mathrm {GG} }(t)&p_{\mathrm {GC} }(t)&p_{\mathrm {GT} }(t)\\p_{\mathrm {CA} }(t)&p_{\mathrm {CG} }(t)&p_{\mathrm {CC} }(t)&p_{\mathrm {CT} }(t)\\p_{\mathrm {TA} }(t)&p_{\mathrm {TG} }(t)&p_{\mathrm {TC} }(t)&p_{\mathrm {TT} }(t)\end{pmatrix}}} where the top-left and bottom-right 2 × 2 blocks correspond to transition probabilities and the top-right and bottom-left 2 × 2 blocks corresponds to transversion probabilities. Assumption: If at some time t 0 {\displaystyle t_{0}} , the Markov chain is in state E i {\displaystyle E_{i}} , then the probability that at time t 0 + t {\displaystyle t_{0}+t} , it will be in state E j {\displaystyle E_{j}} depends only upon i {\displaystyle i} , j {\displaystyle j} and t {\displaystyle t} . This then allows us to write that probability as p i j ( t ) {\displaystyle p_{ij}(t)} . Theorem: Continuous-time transition matrices satisfy: P ( t + τ ) = P ( t ) P ( τ ) {\displaystyle P(t+\tau )=P(t)P(\tau )} Note: There is here a possible confusion between two meanings of the word transition. (i) In the context of Markov chains, transition is the general term for the change between two states. (ii) In the context of nucleotide changes in DNA sequences, transition is a specific term for the exchange between either the two purines (A ↔ G) or the two pyrimidines (C ↔ T) (for additional details, see the article about transitions in genetics). By contrast, an exchange between one purine and one pyrimidine is called a transversion. === Deriving the dynamics of substitution === Consider a DNA sequence of fixed length m evolving in time by base replacement. Assume that the processes followed by the m sites are Markovian independent, identically distributed and that the process is constant over time. For a particular site, let E = { A , G , C , T } {\displaystyle {\mathcal {E}}=\{A,\,G,\,C,\,T\}} be the set of possible states for the site, and p ( t ) = ( p A ( t ) , p G ( t ) , p C ( t ) , p T ( t ) ) {\displaystyle \mathbf {p} (t)=(p_{A}(t),\,p_{G}(t),\,p_{C}(t),\,p_{T}(t))} their respective probabilities at time t {\displaystyle t} . For two distinct x , y ∈ E {\displaystyle x,y\in {\mathcal {E}}} , let μ x y {\displaystyle \mu _{xy}\ } be the transition rate from state x {\displaystyle x} to state y {\displaystyle y} . Similarly, for any x {\displaystyle x} , let the total rate of change from x {\displaystyle x} be μ x = ∑ y ≠ x μ x y . {\displaystyle \mu _{x}=\sum _{y\neq x}\mu _{xy}\,.} The changes in the probability distribution p A ( t ) {\displaystyle p_{A}(t)} for small increments of time Δ t {\displaystyle \Delta t} are given by p A ( t + Δ t ) = p A ( t ) − p A ( t ) μ A Δ t + ∑ x ≠ A p x ( t ) μ x A Δ t . {\displaystyle p_{A}(t+\Delta t)=p_{A}(t)-p_{A}(t)\mu _{A}\Delta t+\sum _{x\neq A}p_{x}(t)\mu _{xA}\Delta t\,.} In other words, (in frequentist language), the frequency of A {\displaystyle A} 's at time t + Δ t {\displaystyle t+\Delta t} is equal to the frequency at time t {\displaystyle t} minus the frequency of the lost A {\displaystyle A} 's plus the frequency of the newly created A {\displaystyle A} 's. Similarly for the probabilities p G ( t ) {\displaystyle p_{G}(t)} , p C ( t ) {\displaystyle p_{C}(t)} and p T ( t ) {\displaystyle p_{T}(t)} . These equations can be written compactly as p ( t + Δ t ) = p ( t ) + p ( t ) Q Δ t , {\displaystyle \mathbf {p} (t+\Delta t)=\mathbf {p} (t)+\mathbf {p} (t)Q\Delta t\,,} where Q = ( − μ A μ A G μ A C μ A T μ G A − μ G μ G C μ G T μ C A μ C G − μ C μ C T μ T A μ T G μ T C − μ T ) {\displaystyle Q={\begin{pmatrix}-\mu _{A}&\mu _{AG}&\mu _{AC}&\mu _{AT}\\\mu _{GA}&-\mu _{G}&\mu _{GC}&\mu _{GT}\\\mu _{CA}&\mu _{CG}&-\mu _{C}&\mu _{CT}\\\mu _{TA}&\mu _{TG}&\mu _{TC}&-\mu _{T}\end{pmatrix}}} is known as the rate matrix. Note that, by definition, the sum of the entries in each row of Q {\displaystyle Q} is equal to zero. It follows that p ′ ( t ) = p ( t ) Q . {\displaystyle \mathbf {p} '(t)=\mathbf {p} (t)Q\,.} For a stationary process, where Q {\displaystyle Q} does not depend on time t, this differential equation can be solved. First, P ( t ) = exp ⁡ ( t Q ) , {\displaystyle P(t)=\exp(tQ),} where exp ⁡ ( t Q ) {\displaystyle \exp(tQ)} denotes the exponential of the matrix t Q {\displaystyle tQ} . As a result, p ( t ) = p ( 0 ) P ( t ) = p ( 0 ) exp ⁡ ( t Q ) . {\displaystyle \mathbf {p} (t)=\mathbf {p} (0)P(t)=\mathbf {p} (0)\exp(tQ)\,.} === Ergodicity === If the Markov chain is irreducible, i.e. if it is always possible to go from a state x {\displaystyle x} to a state y {\displaystyle y} (possibly in several steps), then it is also ergodic. As a result, it has a unique stationary distribution π = { π x , x ∈ E } {\displaystyle {\boldsymbol {\pi }}=\{\pi _{x},\,x\in {\mathcal {E}}\}} , where π x {\displaystyle \pi _{x}} corresponds to the proportion of time spent in state x {\displaystyle x} after the Markov chain has run for an infinite amount of time. In DNA evo

AFNLP

AFNLP (Asian Federation of Natural Language Processing Associations) is the organization for coordinating the natural language processing related activities and events in the Asia-Pacific region. == Foundation == AFNLP was founded on 4 October 2000. == Member Associations == ALTA – Australasian Language Technology Association ANLP Japan Association of Natural Language Processing ROCLING Taiwan ROC Computational Linguistics Society SIG-KLC Korea SIG-Korean Language Computing of Korea Information Science Society == Existing Asian Initiatives == NLPRS: Natural Language Processing Pacific Rim Symposium IRAL: International Workshop on Information Retrieval with Asian Languages PACLING: Pacific Association for Computational Linguistics PACLIC: Pacific Asia Conference on Language, Information and Computation PRICAI: Pacific Rim International Conference on AI ICCPOL: International Conference on Computer Processing of Oriental Languages ROCLING: Research on Computational Linguistics Conference == Conferences == IJCNLP-04: The 1st International Joint Conference on Natural Language Processing in Hainan Island, China IJCNLP-05: The 2nd International Joint Conference on Natural Language Processing in Jeju Island, Korea IJCNLP-08: The 3rd International Joint Conference on Natural Language Processing in Hyderabad, India ACL-IJCNLP-2009: Joint Conference of the 47th Annual Meeting of the Association for Computational Linguistics (ACL) and 4th International Joint Conference on Natural Language Processing (IJCNLP) in Singapore IJNCLP-11: The 5th International Joint Conference on Natural Language Processing in Chiang Mai, Thailand

Prompt engineering

Prompt engineering is the process of structuring natural language inputs (known as prompts) to produce specified outputs from a generative artificial intelligence (GenAI) model. Context engineering is the related area of software engineering that focuses on the management of non-prompt contexts supplied to the GenAI model, such as metadata, API tools, and tokens. It can also be defined as the practice of designing and refining input instructions given to a generative AI model to produce more accurate, relevant, or useful outputs. Effective prompt engineering involves understanding how a model interprets language, and may include techniques such as few-shot prompting, chain-of-thought prompting, and role assignment. It is increasingly considered a skill for working with large language models (LLMs) in both research and professional contexts. During the 2020s AI boom, prompt engineering became regarded as a business capability across corporations and industries. Employees with the title prompt engineer were hired to create prompts that would increase productivity and efficacy, although the individual title has since lost traction amid AI models that produce better prompts than humans and corporate training in prompting for general employees. Common prompting techniques include multi-shot, chain-of-thought, and tree-of-thought prompting, as well as the use of assigning roles to the model. Automated prompt generation methods, such as retrieval-augmented generation (RAG), provide for greater accuracy and a wider scope of functions for prompt engineers. Prompt injection is a type of cybersecurity attack that targets machine learning models through malicious prompts. == Terminology == The Oxford English Dictionary defines prompt engineering as "The action or process of formulating and refining prompts for an artificial intelligence program, algorithm, etc., in order to optimize its output or to achieve a desired outcome; the discipline or profession concerned with this." In 2023, prompt ("an instruction given to an artificial intelligence program, algorithm, etc., which determines or influences the content it generates") was the runner-up to Oxford's word of the year. === Prompt === A prompt is some natural language text that describes and prescribes the task that an artificial intelligence (AI) should perform. A prompt for a text-to-text language model can be a query, a command, or a longer statement referencing context, instructions, and conversation history. The process of prompt engineering may involve designing clear queries, refining wording, providing relevant context, specifying the style of output, and assigning a character for the AI to mimic in order to guide the model toward more accurate, useful, and consistent responses. When communicating with a text-to-image or a text-to-audio model, a typical prompt contains a description of a desired output such as "a high-quality photo of an astronaut riding a horse" or "Lo-fi slow BPM electro chill with organic samples". Prompt engineering may be applied to text-to-image models to achieve a desired subject, style, layout, lighting, and aesthetic. === Techniques === Common terms used to describe various specific prompt engineering techniques include chain-of-thought, tree-of-thought, and retrieval-augmented generation (RAG). A 2024 survey of the field identified over 50 distinct text-based prompting techniques, 40 multimodal variants, and a vocabulary of 33 terms used across prompting research, highlighting a present lack of standardised terminology for prompt engineering. Vibe coding is an AI-assisted software development method where a user prompts an LLM with a description of what they want and lets it generate or edit the code. In 2025, "vibe coding" was the Collins Dictionary word of the year. === Context engineering === Context engineering is a related process that focuses on the context elements that accompany user prompts, which include system instructions, retrieved knowledge, tool definitions, conversation summaries, and task metadata. Context engineering is performed to improve reliability, provenance and token efficiency in production LLM systems. The concept emphasises operational practices such as token budgeting, provenance tags, versioning of context artifacts, observability (logging which context was supplied), and context regression tests to ensure that changes to supplied context do not silently alter system behaviour. == Rationale == Research has found that the performance of large language models (LLMs) is highly sensitive to choices such as the ordering of examples, the quality of demonstration labels, and even small variations in phrasing. In some cases, reordering examples in a prompt produced accuracy shifts of more than 40 percent. === In-context learning === A model's ability to temporarily learn from prompts is known as in-context learning. In-context learning is an emergent ability of large language models. It is an emergent property of model scale, meaning that breaks in scaling laws occur, leading to its efficacy increasing at a different rate in larger models than in smaller models. Unlike training and fine-tuning, which produce lasting changes, in-context learning is temporary. Training models to perform in-context learning can be viewed as a form of meta-learning, or "learning to learn". === Prompting to estimate model sensitivity === Research consistently demonstrates that LLMs are highly sensitive to subtle variations in prompt formatting, structure, and linguistic properties. Some studies have shown up to 76 accuracy points across formatting changes in few-shot settings. Linguistic features significantly influence prompt effectiveness—such as morphology, syntax, and lexico-semantic changes—which meaningfully enhance task performance across a variety of tasks. Clausal syntax, for example, improves consistency and reduces uncertainty in knowledge retrieval. This sensitivity persists even with larger model sizes, additional few-shot examples, or instruction tuning. To address sensitivity of models and make them more robust, several evaluative methods have been proposed. FormatSpread facilitates systematic analysis by evaluating a range of plausible prompt formats, offering a more comprehensive performance interval. Similarly, PromptEval estimates performance distributions across diverse prompts, enabling robust metrics such as performance quantiles and accurate evaluations under constrained budgets. == Prompting techniques == === Multi-shot === A prompt may include a few examples for a model to learn from in context, an approach called few-shot learning. For example, the prompt may ask the model to complete "maison → house, chat → cat, chien →", with the expected response being dog. === Chain-of-thought === Chain-of-thought (CoT) prompting is a technique that allows large language models (LLMs) to solve a problem as a series of intermediate steps before giving a final answer. In 2022, Google Brain reported that chain-of-thought prompting improves reasoning ability by inducing the model to answer a multi-step problem with steps of reasoning that mimic a train of thought. Chain-of-thought techniques were developed to help LLMs handle multi-step reasoning tasks, such as arithmetic or commonsense reasoning questions. When applied to PaLM, a 540 billion parameter language model, according to Google, CoT prompting significantly aided the model, allowing it to perform comparably with task-specific fine-tuned models on several tasks, achieving state-of-the-art results at the time on the GSM8K mathematical reasoning benchmark. It is possible to fine-tune models on CoT reasoning datasets to enhance this capability further and stimulate better interpretability. As originally proposed by Google, each CoT prompt is accompanied by a set of input/output examples—called exemplars—to demonstrate the desired model output, making it a few-shot prompting technique. However, according to a later paper from researchers at Google and the University of Tokyo, simply appending the words "Let's think step-by-step" was also effective, which allowed for CoT to be employed as a zero-shot technique. ==== Self-consistency ==== Self-consistency performs several chain-of-thought rollouts, then selects the most commonly reached conclusion out of all the rollouts. === Tree-of-thought === Tree-of-thought prompting generalizes chain-of-thought by generating multiple lines of reasoning in parallel, with the ability to backtrack or explore other paths. It can use tree search algorithms like breadth-first, depth-first, or beam. === Text-to-image prompting === In 2022, text-to-image models like DALL-E 2, Stable Diffusion, and Midjourney were released to the public. These models take text prompts as input and use them to generate images. Early text-to-image models typically do not understand negation, grammar and sentence structure in the same way as large language models, and may thus requi

Information space analysis

Within the field of information science, information space analysis is a deterministic method, enhanced by machine intelligence, for locating and assessing resources for team-centric efforts. Organizations need to be able to quickly assemble teams backed by the support services, information, and material to do the job. To do so, these teams need to find and assess sources of services that are potential participants in the team effort. To support this initial team and resource development, information needs to be developed via analysis tools that help make sense of sets of data sources in an Intranet or Internet. Part of the process is to characterize them, partition them, and sort and filter them. These tools focus on three key issues in forming a collaborative team: Help individuals responsible for forming the team understand what is available. Assist team members in identifying the structure and categorize the information available to them in a manner specifically suited to the task at hand. Aid team members to understand the mappings of their information between their organization and that used by others who might participate. Information space analysis tools combine multiple methods to assist in this task. This causes the tools to be particularly well-suited to integrating additional technologies in order to create specialized systems.

Spike-and-slab regression

Spike-and-slab regression is a type of Bayesian linear regression in which a particular hierarchical prior distribution for the regression coefficients is chosen such that only a subset of the possible regressors is retained. The technique is particularly useful when the number of possible predictors is larger than the number of observations. The idea of the spike-and-slab model was originally proposed by Mitchell & Beauchamp (1988). The approach was further significantly developed by Madigan & Raftery (1994) and George & McCulloch (1997). A recent and important contribution to this literature is Ishwaran & Rao (2005). == Model description == Suppose we have P possible predictors in some model. Vector γ has a length equal to P and consists of zeros and ones. This vector indicates whether a particular variable is included in the regression or not. If no specific prior information on initial inclusion probabilities of particular variables is available, a Bernoulli prior distribution is a common default choice. Conditional on a predictor being in the regression, we identify a prior distribution for the model coefficient, which corresponds to that variable (β). A common choice on that step is to use a normal prior with a mean equal to zero and a large variance calculated based on ( X T X ) − 1 {\displaystyle (X^{T}X)^{-1}} (where X {\displaystyle X} is a design matrix of explanatory variables of the model). A draw of γ from its prior distribution is a list of the variables included in the regression. Conditional on this set of selected variables, we take a draw from the prior distribution of the regression coefficients (if γi = 1 then βi ≠ 0 and if γi = 0 then βi = 0). βγ denotes the subset of β for which γi = 1. In the next step, we calculate a posterior probability for both inclusion and coefficients by applying a standard statistical procedure. All steps of the described algorithm are repeated thousands of times using the Markov chain Monte Carlo (MCMC) technique. As a result, we obtain a posterior distribution of γ (variable inclusion in the model), β (regression coefficient values) and the corresponding prediction of y. The model got its name (spike-and-slab) due to the shape of the two prior distributions. The "spike" is the probability of a particular coefficient in the model to be zero. The "slab" is the prior distribution for the regression coefficient values. An advantage of Bayesian variable selection techniques is that they are able to make use of prior knowledge about the model. In the absence of such knowledge, some reasonable default values can be used; to quote Scott and Varian (2013): "For the analyst who prefers simplicity at the cost of some reasonable assumptions, useful prior information can be reduced to an expected model size, an expected R2, and a sample size ν determining the weight given to the guess at R2." Some researchers suggest the following default values: R2 = 0.5, ν = 0.01, and π = 0.5 (parameter of a prior Bernoulli distribution).

PerfKitBenchmarker

PerfKit Benchmarker is an open source benchmarking tool used to measure and compare cloud offerings. PerfKit Benchmarker is licensed under the Apache 2 license terms. PerfKit Benchmarker is a community effort involving over 500 participants including researchers, academic institutions and companies together with the originator, Google. == General == PerfKit Benchmarker (PKB) is a community effort to deliver a repeatable, consistent, and open way of measuring Cloud Performance. It supports a growing list of cloud providers including: Alibaba Cloud, Amazon Web Services, CloudStack, DigitalOcean, Google Cloud Platform, Kubernetes, Microsoft Azure, OpenStack, Rackspace, IBM Bluemix (Softlayer). In addition to Cloud Providers to supports container orchestration including Kubernetes [1] and Mesos [2] and local "static" workstations and clusters of computers [3]. The goal is to create an open source living benchmark [framework] that represents how Cloud developers are building applications, evaluating Cloud alternatives, learning how to architect applications for each cloud. Living because it will change and morph quickly as developers change. PerfKit Benchmarker measures the end to end time to provision resources in the cloud, in addition to reporting on the most standard metrics of peak performance, e.g.: latency, throughput, time-to-complete, IOPS. PerfKit Benchmarker reduces the complexity in running benchmarks on supported cloud providers by unified and simple commands. It's designed to operate via vendor provided command line tools. PerfKit Benchmarker contains a canonical set of public benchmarks. All benchmarks are running with default/initial state and configuration (Not tuned to in favor of any providers). This provides a way to benchmark across cloud platforms, while getting a transparent view of application throughput, latency, variance, and overhead. == History == PerfKit Benchmarker (PKB) was started by Anthony F. Voellm, Alain Hamel, and Eric Hankland at Google in 2014. Once an initial "alpha" was in place Anthony F. Voellm and Ivan Santa Maria Filho built a community including ARM, Broadcom, Canonical, CenturyLink, Cisco, CloudHarmony, CloudSpectator, EcoCloud@EPFL, Intel, Mellanox, Microsoft, Qualcomm Technologies, Inc., Rackspace, Red Hat, Tradeworx Inc., and Thesys Technologies LLC. This community worked together behind the scenes in a private GitHub project to create an open way to measure cloud performance. This community released the first public "beta" was released on February 11, 2015, and announced in a blog post at which point the GitHub project was open to everyone. After almost a year and with large adaption (600+ participants on GitHub) the V1.0.0 was released along with a detailed architectural design on December 10, 2015. == Benchmarks == A list of available benchmarks from PerfKitBenchmarker: (The latest set of benchmarks can be found at GitHub readme file.) == Industry participants == Since Google open sourced the PerfKitBenchmarker, it became a community effort from over 30 leading researchers, academic schools and industry companies. Those organizations include: ARM, Broadcom, Canonical, CenturyLink, Cisco, CloudHarmony, Cloud Spectator, EcoCloud@EPFL, Intel, Mellanox, Microsoft, Qualcomm Technologies, Rackspace, Red Hat, and Thesys Technologies. In addition, Stanford and MIT are leading quarterly discussions on default benchmarks and settings proposed by the community. EcoCloud@EPFL is integrating CloudSuite into PerfKit Benchmarker. == Example runs == On Google Cloud Platform On AWS On Azure On Rackspace On a local machine

Zeuthen strategy

The Zeuthen strategy in cognitive science is a negotiation strategy used by some artificial agents. Its purpose is to measure the willingness to risk conflict. An agent will be more willing to risk conflict if it does not have much to lose in case that the negotiation fails. In contrast, an agent is less willing to risk conflict when it has more to lose. The value of a deal is expressed in its utility. An agent has much to lose when the difference between the utility of its current proposal and the conflict deal is high. When both agents use the monotonic concession protocol, the Zeuthen strategy leads them to agree upon a deal in the negotiation set. This set consists of all conflict free deals, which are individually rational and Pareto optimal, and the conflict deal, which maximizes the Nash product. The strategy was introduced in 1930 by the Danish economist Frederik Zeuthen. == Three key questions == The Zeuthen strategy answers three open questions that arise when using the monotonic concession protocol, namely: Which deal should be proposed at first? On any given round, who should concede? In case of a concession, how much should the agent concede? The answer to the first question is that any agent should start with its most preferred deal, because that deal has the highest utility for that agent. The second answer is that the agent with the smallest value of Risk(i,t) concedes, because the agent with the lowest utility for the conflict deal profits most from avoiding conflict. To the third question, the Zeuthen strategy suggests that the conceding agent should concede just enough raise its value of Risk(i,t) just above that of the other agent. This prevents the conceding agent to have to concede again in the next round. == Risk == Risk ( i , t ) = { 1 U i ( δ ( i , t ) ) = 0 U i ( δ ( i , t ) ) − U i ( δ ( j , t ) ) U i ( δ ( i , t ) ) otherwise {\displaystyle {\text{Risk}}(i,t)={\begin{cases}1&U_{i}(\delta (i,t))=0\\{\frac {U_{i}(\delta (i,t))-U_{i}(\delta (j,t))}{U_{i}(\delta (i,t))}}&{\text{otherwise}}\end{cases}}} Risk(i,t) is a measurement of agent i's willingness to risk conflict. The risk function formalizes the notion that an agent's willingness to risk conflict is the ratio of the utility that agent would lose by accepting the other agent's proposal to the utility that agent would lose by causing a conflict. Agent i is said to be using a rational negotiation strategy if at any step t + 1 that agent i sticks to his last proposal, Risk(i,t) > Risk(j,t). == Sufficient concession == If agent i makes a sufficient concession in the next step, then, assuming that agent j is using a rational negotiation strategy, if agent j does not concede in the next step, he must do so in the step after that. The set of all sufficient concessions of agent i at step t is denoted SC(i, t). == Minimal sufficient concession == δ ′ = arg ⁡ max δ ∈ S C ( A , t ) { U A ( δ ) } {\displaystyle \delta '=\arg \max _{\delta \in {SC(A,t)}}\{U_{A}(\delta )\}} is the minimal sufficient concession of agent A in step t. Agent A begins the negotiation by proposing δ ( A , 0 ) = arg ⁡ max δ ∈ N S U A ( δ ) {\displaystyle \delta (A,0)=\arg \max _{\delta \in {NS}}U_{A}(\delta )} and will make the minimal sufficient concession in step t + 1 if and only if Risk(A,t) ≤ Risk(B,t). Theorem If both agents are using Zeuthen strategies, then they will agree on δ = arg ⁡ max δ ′ ∈ N S { π ( δ ′ ) } , {\displaystyle \delta =\arg \max _{\delta '\in {NS}}\{\pi (\delta ')\},} that is, the deal which maximizes the Nash product. Proof Let δA = δ(A,t). Let δB = δ(B,t). According to the Zeuthen strategy, agent A will concede at step t {\displaystyle t} if and only if R i s k ( A , t ) ≤ R i s k ( B , t ) . {\displaystyle Risk(A,t)\leq Risk(B,t).} That is, if and only if U A ( δ A ) − U A ( δ B ) U A ( δ A ) ≤ U B ( δ B ) − U B ( δ A ) U B ( δ B ) {\displaystyle {\frac {U_{A}(\delta _{A})-U_{A}(\delta _{B})}{U_{A}(\delta _{A})}}\leq {\frac {U_{B}(\delta _{B})-U_{B}(\delta _{A})}{U_{B}(\delta _{B})}}} U B ( δ B ) ( U A ( δ A ) − U A ( δ B ) ) ≤ U A ( δ A ) ( U B ( δ B ) − U B ( δ A ) ) {\displaystyle U_{B}(\delta _{B})(U_{A}(\delta _{A})-U_{A}(\delta _{B}))\leq U_{A}(\delta _{A})(U_{B}(\delta _{B})-U_{B}(\delta _{A}))} U A ( δ A ) U B ( δ B ) − U A ( δ B ) U B ( δ B ) ≤ U A ( δ A ) U B ( δ B ) − U A ( δ A ) U B ( δ A ) {\displaystyle U_{A}(\delta _{A})U_{B}(\delta _{B})-U_{A}(\delta _{B})U_{B}(\delta _{B})\leq U_{A}(\delta _{A})U_{B}(\delta _{B})-U_{A}(\delta _{A})U_{B}(\delta _{A})} − U A ( δ B ) U B ( δ B ) ≤ − U A ( δ A ) U B ( δ A ) {\displaystyle -U_{A}(\delta _{B})U_{B}(\delta _{B})\leq -U_{A}(\delta _{A})U_{B}(\delta _{A})} U A ( δ A ) U B ( δ A ) ≤ U A ( δ B ) U B ( δ B ) {\displaystyle U_{A}(\delta _{A})U_{B}(\delta _{A})\leq U_{A}(\delta _{B})U_{B}(\delta _{B})} π ( δ A ) ≤ π ( δ B ) {\displaystyle \pi (\delta _{A})\leq \pi (\delta _{B})} Thus, Agent A will concede if and only if δ A {\displaystyle \delta _{A}} does not yield the larger product of utilities. Therefore, the Zeuthen strategy guarantees a final agreement that maximizes the Nash Product.