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For independent affected sib pairs with IBD counts $n_0,n_1,n_2$, the likelihood function of the recombination fraction is proportional to $s^{2n_0+n_1}(1-s{)}^{2n_2+n_1}$, with $s=2\theta (1-\theta )$. At fixed sample size, the total shared-copy count $2n_2+n_1$ is a sufficient statistic by the Fisher-Neyman factorization theorem. Thus a one-sided likelihood-ratio test has the same ordering as a test for excess mean IBD sharing. This equivalence depends on the stated fully penetrant recessive model and does not extend to arbitrary disease models.

// Target: biology.bigb

A Bayes factor measures how data change the relative support for two specified statistical models. Write $m_j(D)=p(D\mid H_j)$ for their Bayesian model evidence and define the direction explicitly:For positive finite $m_0(D),m_1(D)$, a value above one favors $H_1$ over $H_0$; a value below one favors $H_0$ over $H_1$. Reversing the comparison gives $B_{01}={\mathrm{BF}}_{01}=1/{\mathrm{BF}}_{10}$, the opposite direction used in some formulas below.

For mutually exclusive, exhaustive $H_0,H_1$ with positive prior probabilities, divide their two Bayes' theorem formulas. Their common data normalizer cancels, leavingThe Bayes factor therefore multiplies prior odds into posterior odds. It is evidence conditional on the specified statistical models and their within-model prior distributions; it is not $\mathbb{P}(H_1\mid D)$. Model prior probabilities supply a separate input.^[ref]

For an original stipulated example, consider ten independent and identically distributed Bernoulli trials, with heads as success. Compare $H_0:p=0.4$ with $H_1:p=0.7$, both fixed before seeing the data. Take $D$ to be one particular ordered sequence containing eight heads and two tails. The likelihood function under either point model is $p^8(1-p{)}^2$, soIf $\mathbb{P}(H_1)=0.1$, the prior odds for $H_1$ against $H_0$ are $1/9$. Hence the posterior odds are $21.9909706/9\approx 2.4434412$, andEqual model prior probabilities would instead give ${\mathrm{BF}}_{10}/(1+{\mathrm{BF}}_{10})\approx 0.956505$. The same Bayes factor can thus accompany different posterior probabilities. These statements condition on the two-model comparison; they do not establish that either statistical model describes a real coin.

Using the heads count $K=8$ instead of the ordered sequence changes the sample space. The binomial distribution assigns it mass $\left(\genfrac{}{}{0ex}{}{10}{8}\right)p^8(1-p{)}^2$. The same binomial coefficient multiplies both models' Bayesian model evidence and cancels in their Bayes factor. Mixing an ordered-sequence numerator with a count denominator would introduce an erroneous factor of $45$.

Fix the candidate statistical models, their parameter prior distributions, and model prior probabilities before using the current data for this update. The Bayes factor is useful because it separates evidence from model prior odds, but it still depends on the parameter prior distributions. An improper prior has an arbitrary multiplicative normalization: multiplying its kernel by $c$ multiplies its formal marginal likelihood by $c$, even if the within-model posterior distribution is normalizable. Without a separately justified convention, the ordinary Bayes factor is then undefined up to arbitrary constants.^[ref]

The Bayesian model evidence is the prior predictive distribution evaluated at the data $D$. For a statistical model $H_j$ with a normalized prior density ${\pi }_j$, its marginal likelihood isThis is an expected value of the likelihood function under the prior distribution; for discrete statistical parameters, replace the integral by a sum. For continuous observations, $m_j(D)$ is a probability density function value with respect to a specified data reference measure, rather than a probability of one exact observation. Comparisons must use the same data and reference measure. The same $m_j(D)$ normalizes the within-model Bayesian posterior and supplies the between-model comparison in a Bayes factor.^[ref]

A normalized prior distribution makes the Bayesian model evidence an average, so it cannot exceed the largest likelihood function value on its support. A broad prior distribution can assign little mass to values that predict the data well, even when one value gives an excellent fit. The worked uniform-alternative binomial Bayes factor below makes the difference between averaging and maximum likelihood estimation explicit.

For observations $\mathcal{D}$ and graph $G$, Bayes' theorem gives $p(G\mid \mathcal{D})\propto \pi (G)\int p(\mathcal{D}\mid {\theta }_G,G)\pi ({\theta }_G\mid G)d{\theta }_G$. Here $\pi (G)$ is the graph prior distribution and ${\theta }_G$ the local distribution statistical parameters. The integral is Bayesian model evidence; it averages over nuisance parameters with a proper statistical parameter prior distribution. For independent complete observations, the node-factorized likelihood function and independence of local statistical parameter prior distributions make the evidence factor over nodes; suitable conjugate priors can make the local integrals analytic. With missing node observations, integrating out unobserved values can couple the local parameters, so independence of local prior distributions alone does not guarantee this factorization. Proper priors and coherent hyperparameters matter for comparing different graphs.

Inference of a posterior distribution over phylogenetic trees and model parameters by combining a sequence likelihood function with a prior distribution. Integrating nuisance parameters is distinct from maximizing the likelihood.

The Bayesian posterior is the conditional probability distribution of an unknown statistical parameter after observing data. Suppose a continuous prior distribution has prior density $\pi (\theta )$ relative to Lebesgue measure $d\theta$, and $p(d\mid \theta )$ is the sampling probability mass function or probability density function of the observed data $d$ in the statistical model. Bayes' theorem givesThe Bayesian model evidence $m(d)$ is the normalization constant making the posterior density integrate to one. The strict positive, finite condition is essential: a zero or infinite normalizer does not define this posterior distribution, even if the unnormalized expression can be written down. Other reference measures give the corresponding density formula; discrete parameter values replace the integral by a sum. The posterior propriety article gives examples where normalization fails.

With $d$ fixed, $L(\theta ;d)=p(d\mid \theta )$ is a likelihood function of $\theta$. Its normalization as a sampling distribution is over possible data, not over parameter values. In particular, a likelihood function is not a probability density function for $\Theta$ and need not integrate to one over $\theta$. The prior density supplies the probability weighting, and the Bayesian model evidence normalizes their product. This distinction prevents a tempting mistake: reversing the conditioning merely by exchanging the words “data” and “parameter”.

For eight heads among ten conditionally independent Bernoulli trials, take the observed data to be the heads count $D=8$. Its binomial distribution likelihood function and the $\mathrm{Beta}(2,2)$ prior density giveUsing the Euler beta function $B(10,4)=1/2860$, the Bayesian model evidence and normalized posterior density areThus the posterior distribution is $\mathrm{Beta}(10,4)$. If the data are instead one particular ordered sequence with eight heads and two tails, its likelihood function omits the factor 45 and its Bayesian model evidence becomes $3/1430$. The factor cancels in Bayes' theorem, leaving the same posterior distribution; these two data descriptions have different sampling probabilities but identical information about $\theta$ here.

The prior density and posterior density use the left axis and each integrate to one. The dashed likelihood function uses the right axis and is divided by its maximum solely to compare its shape; it is not a parameter probability density function. The likelihood function peaks at $8/10$, while the posterior mode is $9/12=3/4$ and the posterior mean is $5/7$. Multiplying by the prior density shifts the preferred values toward one half while preserving a range of possibilities.

The resulting posterior variance is $10\cdot 4/(14^2\cdot 15)=2/147\approx 0.0136054$, compared with prior variance $1/20$. In this example the update reduces uncertainty. The posterior predictive probability of heads on the next conditionally independent toss is $\mathbb{E}[\Theta \mid D=8]=5/7$, and the credible interval above reports a 95% range. These are summaries of the same posterior distribution, rather than competing estimates of one density peak.

Bayesian statistics expresses uncertainty about an unknown statistical parameter through a probability distribution, then uses Bayes' theorem to update it after observing data. The prior distribution describes uncertainty before the current observations; the likelihood function describes how the statistical model generates those observations at each parameter value; the posterior distribution describes uncertainty conditional on the observations and that model. A physical parameter can have one fixed value while its value remains uncertain to us. Assigning it a probability distribution represents that uncertainty under the chosen model, rather than requiring the physical parameter to change randomly between measurements.

For example, suppose ten Bernoulli trials are independent conditional on an unknown heads probability $\theta$, with a beta distribution prior $\mathrm{Beta}(2,2)$. Eight heads and two tails give the posterior distribution $\mathrm{Beta}(10,4)$ by Beta-binomial conjugacy. Its posterior mean is $10/14=5/7\approx 0.714286$, between the prior mean $1/2$ and observed binomial proportion $8/10$. The Bayesian posterior below computes the whole update, and the credible interval below summarizes its remaining uncertainty. The conjugate update is explained in MIT 18.05, Reading 15: beta and normal conjugate priors.

The useful feature is that one posterior distribution supports several questions: a posterior mean estimates a value, a credible interval reports a range, and a posterior predictive distribution predicts a future observation while averaging over parameter uncertainty. With conditionally independent new data, today's posterior distribution can become tomorrow's prior distribution. These conclusions remain conditional on the statistical model and prior distribution; a precise update does not establish that either assumption fits the experiment.

A historical starting point is Thomas Bayes's essay in the 1763 volume of the Royal Society's Philosophical Transactions, communicated after his death by Richard Price. Its opening problem asks for uncertainty about an unknown event probability given observed successes and failures: the same direction of reasoning illustrated by the coin example. See Bayes and Price, An Essay towards solving a Problem in the Doctrine of Chances, opening letter and problem.

For independent geometric random variables with success probability $p$, observing $d$ terminal events and $F$ preceding failed Bernoulli trials gives likelihood function proportional to $p^d(1-p{)}^F$. Multiplication by a beta distribution prior $\mathrm{Beta}(a,b)$ gives the posterior distribution $\mathrm{Beta}(a+d,b+F)$. With complete waiting times $x_1,\dots ,x_n$, take $d=n$ and $F={\sum }_i(x_i-1)$.

A waiting time that is right-censored after $c$ failed trials contributes $(1-p{)}^c$: increase $F$ by $c$ without increasing $d$. This requires the censoring mechanism to be ignorable, as with an externally fixed observation horizon. Counting a censored waiting time as an observed event changes the likelihood function and biases the update.

A capture-recapture model is a statistical model for repeated observations of identifiable individuals, including those missed on some occasions. A closed-population capture-recapture model estimates a fixed population cardinality; models allowing individuals to enter or leave can instead describe survival and recruitment. The sampling assumptions determine which likelihood function is appropriate.

For the two-sample closed-population capture-recapture model, condition on the sample sizes $M$ and $C$. If the second sample selects $C$ distinct individuals from $N$ by simple random sampling, then the overlap $R$ has the hypergeometric distribution:Here $r$ is an integer and the probability mass function is zero outside these bounds. The binomial coefficients count choices of $r$ marked and $C-r$ unmarked individuals, divided by all equally likely size-$C$ subsets. The hypergeometric distribution has expected valueEquating the observed overlap with this expected value gives the Lincoln-Petersen estimator. The underlying sampling without replacement, probability mass function, and expected value are developed in Raymond P. Guiteras, MIT 14.30 hypergeometric distribution handout, §§1–4 and 8.

For the toy counts $M=20$, $C=25$, and $R=5$, hold the observations fixed and vary the unknown integer $N$. The likelihood function isValues below forty cannot contain the observed set union. Exact comparison of consecutive likelihoods gives two tied maximum-likelihood estimates, $N=99$ and $N=100$. The Lincoln-Petersen estimator returns $100$; the Chapman estimator returns $90$ and is a different rule for estimation.

The vertical scale is $L(N)/{\max }_{n\ge 40}L(n)$. This relative likelihood compares how well candidate statistical parameters explain the same observations; it is not a posterior probability. The displayed range $40\le N\le 300$ is only a plotting window. The likelihood function remains positive for every integer $N\ge 40$ and tends to zero as $N$ increases, so the curve has a continuing right tail. The data do not justify truncating statistical inference at three hundred. The conditional hypergeometric distribution formulation also appears in Louis-Paul Rivest and Mamadou Yauck, Small Sample Estimators for Two-way Capture Recapture Experiments, §3, equation (5).

Zero recaptures require care. With $R=0$ and positive $M,C$, the Lincoln-Petersen estimator has no finite ratio, but the capture-recapture model still gives a valid likelihood function:This likelihood function increases toward one as $N$ grows, so there is no finite maximum-likelihood estimate. For the same sample sizes twenty and twenty-five with zero overlap, forty-five distinct individuals would be observed. Lack of overlap supplies a lower bound but very weak information about large population cardinalities.

In more elaborate capture-recapture models, a first-recapture array $m_{ij}$ counts individuals released at occasion $i$ and next observed at $j$. A probability of survival ${\varphi }_j$ and a probability of detection $P_{j+1}$ contribute a no-observation continuation factor ${\varphi }_j(1-P_{j+1})$. The resulting likelihood function depends on both survival and detection; these probabilities need not be separately identifiable at the last observation interval. Missing-count EM for capture-recapture describes one way to fit such a model, and identifiability remains a separate issue from computing an estimator output.

A conditional likelihood function conditions on an initial observation or another specified statistic. In an autoregressive model, conditioning on the first observed state avoids modeling its initial density. For Gaussian transitions, maximizing this likelihood is a regression problem; treating an autoregressive coefficient as known changes the exact distribution of an estimated mean.

Assume independent individual event times with positive time-constant hazard multipliers and a common baseline hazard whose cumulative hazard tends to infinity. Transforming each event time by that cumulative hazard then gives independent exponential event times with corresponding rates, so all event orders exist. Their complete-order probabilities select each next label proportionally to its remaining multiplier. Marginalizing over the position of a deleted label leaves the order law of the other exponential times, hence the same sequential formula without that label. This proves the deletion identity used when unobserved ranks are summed out. It does not supply a likelihood function for censoring times; ignoring censoring in observed survival analysis still needs independent censoring.

For one uniformly sampled integer $Y\in \{1,\dots ,N\}$, the likelihood function for the unknown endpoint is $N^{-1}{1}_{N\ge y}$. A flat improper prior on positive integers gives an improper posterior distribution, since the harmonic series diverges. A reciprocal prior instead gives a proper posterior proportional to $N^{-2}$ for $N\ge y$, with approximate survival probability $y/n$ and finite quantiles, but infinite posterior mean. A uniform prior cut off at $M$ gives posterior mean $(M-y+1)/(H_M-H_{y-1})\sim M/\log M$, demonstrating sensitivity to that arbitrary cutoff.

For $Q(\theta \mid {\theta }_0)={\mathbb{E}}_{{\theta }_0}[\log p_{\theta }(Y,Z)\mid Y]$, the Jensen inequality givesThus any expectation-maximization algorithm M-step that increases $Q$ cannot decrease the observed-data likelihood function.^[ref]

For a short proof, assume common support and finite expressions, and keep the E-step conditional distribution $q_t(z)=p_{{\theta }^{(t)}}(z\mid y)$ fixed. The concavity of the logarithm and Jensen's inequality giveThis evidence lower bound equals $Q(\theta \mid {\theta }^{(t)})-{\mathbb{E}}_{q_t}\log q_t(Z)$. At $\theta ={\theta }^{(t)}$, the ratio inside the expectation is the constant $p_{{\theta }^{(t)}}(y)$, so equality holds. During the M-step, the second term is constant; increasing $Q$ raises a lower bound that touches the current log-likelihood. HenceIncreasing likelihood values alone do not establish convergence of the statistical parameters or attainment of a global maximum. In a differentiable finite mixture model, the gradient of $\ell$ equals the candidate-parameter gradient of $Q$ evaluated at the current fit. Thus an interior fixed point of an exact M-step is a stationary point, which need not be a local maximum; the Identical-mean EM trap is an explicit counterexample. Small changes in log-likelihood can also occur before the means have settled, so inspecting both is useful.

If a model configuration leaves a parameter absent from its likelihood function, giving that parameter an independent flat improper prior makes the posterior distribution normalization infinite whenever the configuration has positive prior distribution mass. Integrate first over that parameter: a positive constant likelihood function factor is repeated over all of $\mathbb{R}$. This occurs for the second segment mean of a Gaussian change-point detection model when the proposed split is after the final observation. There is no posterior distribution or valid Gibbs sampler for that joint kernel. A proper prior distribution on the unused parameter is necessary if the no-change configuration is retained.

For density $r(x-\theta {)}^{r-1}$ on $[\theta ,\theta +1]$, $0<r<1$, the interior likelihood function increases without bound as $\theta$ approaches the sample minimum. The extended-likelihood estimator is that minimum. An arbitrary finite reassignment of the density at the endpoint can eliminate an attained finite maximum, so the endpoint convention must be stated.

The expectation-maximization algorithm fits a latent-variable model by alternating a conditional expectation over the latent variables with a maximization over the statistical parameters. Its target is the observed-data likelihood function, although its updates use the simpler complete-data log-likelihood.^[ref]

Write $y$ for the observations, $z$ for the latent variables, and $p_{\theta }(y,z)$ for their joint probability density function or probability mass function. The observed-data log-likelihood iswhere the integral becomes a sum for discrete $z$. Directly maximizing a logarithm of this sum can be awkward. The E-step instead computes a conditional distribution at the current statistical parameters ${\theta }^{(t)}$; the M-step uses it to construct a new fit. The attractive idea is to retain uncertainty about the hidden labels while recovering simple weighted means and other complete-data updates. The Known-variance Gaussian mixture EM example shows the mechanism without estimating a variance or mixture weight.

Arthur Pentland Dempster, Nan M. Laird, and Donald B. Rubin gave the general framework its name in their 1977 paper, which also discusses earlier special-case algorithms.^[ref]

The Felsenstein pruning algorithm computes a site likelihood function by sum-product belief propagation from leaves to root. For a finite-state Markov kernel $K$, the subtree likelihood function obeys $L_v(a)={\prod }_{w\text{ child of }v}{\sum }_{b}K(a,b)L_w(b)$, with observed-state indicators at leaves. Summing against the root probability distribution gives the site likelihood function. An outward pass gives edge posterior probabilities and expected transition counts for the expectation-maximization algorithm.

In a parametric statistical model, the likelihood function compares parameter values, while sampling distributions calibrate tests and confidence intervals. A sufficient statistic retains the parameter information. Conditioning on an observed ancillary statistic restricts that calibration to experiments with the same ancillary configuration, instead of averaging over configurations whose distribution is unrelated to the parameter. Since the ancillary's marginal law is parameter-free, conditional and unconditional likelihoods have the same parameter-dependent factor. With a nuisance parameter, a conditional law or pivotal quantity must remove it before inference for the parameter of interest can use a nuisance-free reference law.

For independent observations $y_s\sim N(\beta +d_s,V_s)$, put $a_s=V_s^{-1}$, $S={\sum }_s{a}_s$, $r_s=y_s-d_s$, $\bar{r}=S^{-1}{\sum }_s{a}_s{r}_s$ and $Q={\sum }_s{a}_s(r_s-\bar{r}{)}^2$. Integrating the likelihood function against a flat improper prior on $\beta$ gives, up to the arbitrary prior constant,Indeed ${\sum }_s{a}_s(r_s-\beta {)}^2=Q+S(\beta -\bar{r}{)}^2$, and the remaining one-dimensional Gaussian integral is $\sqrt{2\pi /S}$. The conditional Bayesian posterior of $\beta$ is $N(\bar{r},S^{-1})$.

For inverse-gamma distribution observations of known shape $k$ and scale $\Theta$, their likelihood function in $\Theta$ is proportional to ${\Theta }^{nk}\exp (-\Theta {\sum }_i{x}_i^{-1})$. A shape-$\alpha$, rate-$\lambda$ gamma distribution conjugate prior therefore gives the displayed Bayesian posterior. The Bayes estimator under squared error loss of the conditional claim expected value $\Theta /(k-1)$ is $(\alpha +nk)/[(k-1)(\lambda +{\sum }_i{x}_i^{-1})]$. It depends on reciprocals, rather than the sample mean of the claims.