Human probability judgments are systematically biased, in apparent tension with Bayesian models of cognition. But perhaps the brain does not represent probabilities explicitly, but approximates probabilistic calculations through a process of sampling, as used in computational probabilistic models in statistics. Naïve probability estimates can be obtained by calculating the relative frequency of an event within a sample, but these estimates tend to be extreme when the sample size is small. We propose instead that people use a generic prior to improve the accuracy of their probability estimates based on samples, and we call this model the Bayesian sampler. The Bayesian sampler trades off the coherence of probabilistic judgments for improved accuracy, and provides a single framework for explaining phenomena associated with diverse biases and heuristics such as conservatism and the conjunction fallacy. The approach turns out to provide a rational reinterpretation of "noise" in an important recent model of probability judgment, the probability theory plus noise model (Costello & Watts, 2014, 2016a, 2019Costello, Watts, & Fisher, 2018), making equivalent average predictions for simple events, conjunctions, and disjunctions. The Bayesian sampler does, however, make distinct predictions for conditional probabilities, and we show in a new experiment that this model better captures these judgments both qualitatively and quantitatively.

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.

Human probability judgments are systematically biased, in apparent tension with Bayesian models of cognition. But perhaps the brain does not represent probabilities explicitly, but approximates probabilistic calculations through a process of sampling, as used in computational probabilistic models in statistics. Naïve probability estimates can be obtained by calculating the relative frequency of an event within a sample, but these estimates tend to be extreme when the sample size is small. We propose instead that people use a generic prior to improve the accuracy of their probability estimates based on samples, and we call this model the Bayesian sampler. The Bayesian sampler trades off the coherence of probabilistic judgments for improved accuracy, and provides a single framework for explaining phenomena associated with diverse biases and heuristics such as conservatism and the conjunction fallacy. The approach turns out to provide a rational reinterpretation of “noise” in an important recent model of probability judgment, the probability theory plus noise model (Costello & Watts, 2014, 2016a, 2017, 2019; Costello, Watts, & Fisher, 2018), making equivalent average predictions for simple events, conjunctions, and disjunctions. The Bayesian sampler does, however, make distinct predictions for conditional probabilities, and we show in a new experiment that this model better captures these judgments both qualitatively and quantitatively.

In Bayesian cognitive science, the mind is seen as a spectacular probabilistic-inference machine. But judgment and decision-making (JDM) researchers have spent half a century uncovering how dramatically and systematically people depart from rational norms. In this article, we outline recent research that opens up the possibility of an unexpected reconciliation. The key hypothesis is that the brain neither represents nor calculates with probabilities but approximates probabilistic calculations by drawing samples from memory or mental simulation. Sampling models diverge from perfect probabilistic calculations in ways that capture many classic JDM findings, which offers the hope of an integrated explanation of classic heuristics and biases, including availability, representativeness, and anchoring and adjustment.