Archive for cognitive biases

Nature tidbits [23 October 2025]

Posted in Books, Kids, pictures, Running, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on November 27, 2025 by xi'an

In this October issue of nature, plenty of the “usual” topics, namely AI and Trump.2.0 wrecking balls, along with two cosmology entries that related to my trip to the early universe last week, and a pros-and-cons opposition about animal testing,

a discussion on the nature of the “little red dots” that have been recently observed and whose nature remains open, the most popular explanation (I was given during lunch) being black holes surrounded by gas (even though I cannot understand why the gas is not attracted by the black hole!) [and would have produced a more exciting cover!]

a review of the recent book Discordance: The Troubled History of the Hubble Constant by Jim Baggott, entitled Why we still don’t understand the Universe — even after a century of dispute! A review that regrets that more time is spent on the Hubble “constant” (which varies with time!) rather than more controversial issues like dark matter and dark energy (And strangely bemoans that the book is focussed on scientific developments, missing sociological ones. Duh?! (Bonus for a picture of suit-and-tie Edwin Hubble sitting at the centre of a telescope),

two entries on the well-being [or lack thereof] of PhD students, with nothing particularly surprising (eg, inclusivity and respect help!), and Brazil, Australia and Italy ranking top locations but in a comparative study that does not mention France (as often in international comparisons found in Nature) despite the place being in the top 10 countries delivering PhD degrees, not that I believe PhD students are particularly well-treated in French academia!, the (unexplained) surprise being Italy ranking so high given the close resemblance between the two countries (low stipends, shortage of postdoc and permanent positions, high teaching loads for the advisor, limited travel budgets),

a conference (purposedly) made of AI-written papers reviewed by AI referees, Agents4Science 2025, how universities are rushed into adapting to AI-fluent students, whose skills are changing, and the rise in fake authors produced by paper mills, with a limited range of acceptable solutions,

why Trump 2.0‘s blackmail on pharmaceutical companies is counter-productive and likely to slow down progress, and why his massive increase of highly qualified scientists is shooting (or nuking) USelf in the foot, given the huge proportion) of im/emigrated Nobel prize winners (for physics, chemistry, and medicine), along the (post-) Nobel prize in economics is a direct or indirect reply to this regression by awarding the Prize to economists who worked on the importance of creativity and science on growth (not very surprising at first look!)

Nature tidbits [30th October 2025]

Posted in Books, Kids, pictures, Running, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on November 22, 2025 by xi'an

In this October issue of nature, items of interest (to me) [already highlighted in an emailed News Highlight]:

Google claim a significant ‘quantum advantage’ by quantum-echoes algorithms that they say is 13,000 faster than classical algorithms, but it is unclear from the nature article where and when their algorithms can be used, apparently missing to apply to realistic scientific applications… (Along with a paper on an “atom-array architecture that enables continuous operation with reloading rates of up to 30,000 initialized qubits per second while preserving coherence across a rearranged large-scale qubit array”.)

On the Trump vs. Science scene, a predicted drop in PhD admissions as an adaptation to (uncertain) Trump’s cuts, bans, visa restrictions, and other attempts at arm-bending and blackmailing  (And the novelty of me receiving applications from the US, a first!) Some U.S. departments have simply cancelled PhD admissions… But some universities have so far resisted the Orange pressure. Namely, the MIT, Brown University, (good old) Penn, UCLA, the University of Virginia (albeit agreeing to a deal), Dartmouth College, and the University of Arizona in Tucson. Vanderbilt has given in. (UT Austin and Harvard seem to be continuing the discussion with the Trump administration.) Meanwhile, China is zooming past! The issue also contains articles on how fundamental science discoveries have had hugely practical consequences, in case one need argue with a sceptic.

As a less urgent issue, some researchers at Institut Pasteur in Paris identified new diseases that did not help Napoléon’s Grande Armée as it retreated from Moscow, from the DNA of 13 soldiers buried in Lithuania. (With nature failing to give credit to the painter Adolph Northen for his famous “Napoleon’s retreat from Moscow” illustrating the story, attributed to the researchers in the paper!)

In this period of ERC announcements of their grantees, an analysis of the two-digit rise in applications. Unsurprising, given the international context. Along with a decrease in funding due to a lack of adjustment against inflation since 2007. (Incidentally, I found out this week that Torsten Elßin—at the Max Planck Institute for Astrophysics—I visited once had been selected for a Synergy grant on a 3D Milky Way Atlas. Along another cosmology Synergy grant at MPA on the Epoch of Reionization.)

A runner’s must-read that starts with the statement “the human body has a ‘metabolic ceiling’ that even the most extreme athletes cannot surpass”. Which would be 2.4 times the basal metabolic rate (BMR) for extended periods—by which the authors mean 30 weeks and over!, not a half-marathon. Not so exciting a paper in the end.

As predicted by the cover, a Royal Society meeting acknowledging the AI language models killed Turing’ test and questioning the next one. Since assessing the capacities and limitations of novel AIs and AGIs sounds more relevant and societally important. To wit, “;the Turing test of the future should question whether an AI is safe, reliable and provides meaningful benefit, he said, and should also ask who bears the cost of that benefit”. (As discussed in the book review of The Means of Prediction: How AI Really Works (and Who Benefits) by Maximilian Kasy, in the same volume. And yet another paper on AI biases.)

Nature tidbits

Posted in Books, Kids, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on June 10, 2024 by xi'an

I was quite glad to have taken this 28 March issue of Nature for the train ride to Marseille earlier this month, as it proved full of great entries. Starting with a tribune from a PhD candidate from Ghana unable to speak at a tropical ecology conference in Lisbon for being denied a Schengen visa by the Dutch embassy in Accra, despite providing a serious amount of supporting material. This is a general issue related to international conferences that I plan to include in my presentation in a round table about the future of conference at the ISBA 2024 conference next month. Researchers and students from low-income countries are regularly victims of arbitrary rejections by consular and embassy officers, with little leeway from inviting universities and academic societies for counteracting such arbitrariness. An example came last year when, as part of our Data Science for Social Good program at Warwick, one computer student from Pakistan got denied a visa, while another one with an almost identical profile did receive her visa.

In News in focus, the development of a revolutionary (CAR-T) cancer therapy by  a Munbai company at 1/10 the cost of similar products in the US, with several impressive innovations (and a clinical trial over 33 people). The coverage of Michel Talagrand’s 2024 Abel prize, the deteriorating state of scientific research in Russia, a review on how the Big Bang got its name (hint: it was on BBC 3), and remembering India’s Chipko tree-hugging women of Western Himalayas of 50 years ago. The development of signs for scientific terms to add to the Indian and American sign languages.

There is also an almost sleuthing story on the debates in the ecology community about the theory of “Mother Tree”, introduced by Suzanne Simard, about trees communicating among themselves by underground fungal networks, and thus creating a “wood wide web“.  With mature trees favouring their own kin, a theory that critics in the field deem incompatible with evolutionary theory and more crucially missing supporting evidence. (Arguments from Simard that “the European male society hates the mother tree” concept do not help towards a rational denate. The Guardian now has a podcast about this debate.)

And another story on the (racial and gender) bias of AI image generators. With the conclusion that removing such biases goes through open sourcing. And regulation like the EU’s AI Act. that requires technical documentation on the training datasets. Plus a retrospective on the theory of bird-flight origins, with John Ostrom proposing in 1974 that the evolution to flight was ground-up rather than tree-down.

A cover-paper on IBM error correcting code for quantum computing that only requires each qubit to connect with six others (just like birds in murmuration only keep track of seven neighbours) for an error threshold less than 1%. (With the property that 12 logical qubits can be preserved for 10⁶ cyclces using 288 qubits in total.)

prior elicitation

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , , , , , , on January 13, 2022 by xi'an

“We believe that an elicitation method should support elicitation both in the parameter and observable space, should be model-agnostic, and should be sample-efficient since human effort is costly.”

Petrus Mikkola et al. arXived a long paper on prior elicitation addressing the (most relevant) question: Why are we not widely use prior elicitation? With a massive bibliography that could be (partly) commented (and corrected as some references are incomplete, as eg my book chapter on priors!). I think the paper would make a terrific discussion paper.

The absence of a general procedure for prior elicitation is indeed hindering the adoption of Bayesian methods outside our core community and is thus eventually detrimental to their wider development. It also carries the dangers of misled or misleading prior choices. The authors put forward the absence of “software that integrates well with the current probabilistic programming tools used for other parts of the modelling workflow.” This requires setting principles that avoid “just-press-key” solutions. (Aside: This reminds me of my very first prospective PhD student, who was then working in a startup [although the name was not yet in use in the early 1990’s!] and had build such a software in a discretised, low dimension, conjugate prior, environment by returning a form of decision-theoretic impact of the chosen hyperparameters. He alas aborted his PhD attempt due to the short-term pressing matters in the under-staffed company…)

“We inspect prior elicitation from the perspectives of (1) properties of the prior distribution itself, (2) the model family and the prior elicitation method’s dependence on it, (3) the underlying elicitation space, (4) how the method interprets the information provided by the expert, (5) computation, (6) the form and quantity of interaction with the expert(s), and (7) the assumed capability of the expert (…)”

Prior elicitation is indeed a delicate balance between incorporating expert opinion(s) and avoiding over-standardisation. In my limited experience, experts tend to be over-confident about their own opinion and unwilling to attach uncertainty to their assessments. Even when being inconsistent. When several experts are involved (as, very briefly, in Section 3.6), building a common prior quickly becomes a challenge, esp. if their interests (or utility functions) diverge. As illustrated in the case of the whaling commission analysed by Adrian Raftery in the late 1990’s. (The above quote involves a single expert.) Actually, I dislike the term expert altogether, as it comes without any grading of the reliability of the person.To hit (!) at an early statement in the paper (p.5), should the prior elicitation always depend on the (sampling) model, as experts may ignore or misapprehend the model? The posterior already accounts for the likelihood and the parameter may pre-exist wrt the model, as eg cosmological constants or vaccine efficiency… In a sense, the model should be involved as little as possible in the elicitation as the expert could confuse her beliefs about the parameter with those about the accuracy of the model. (I realise this is not necessarily a mainstream position as illustrated by this paper by Andrew and friends!)

And isn’t the first stumbling block the inability of most to represent one’s prior knowledge in probabilistic terms? Innumeracy is a shared shortcoming in the general population (and since everyone’s an expert!), as repeatedly demonstrated since the start of the Covid-19 pandemic. (See also the above point about inconsistency. Accounting for such inconsistencies in a Bayesian way is a natural answer, albeit requiring the degree of expertise and reliability to be tested.)

Is prior elicitation feasible beyond a few dimensions? Even when using the constrictive tool of copulas one hits a wall after a few dimensions, assuming the expert is willing to set a prior correlation matrix.  Most of the methods described in Section 3.1 only apply to textbook examples. In their third dimension (!), the authors mention neural network parameters but later fail to cover this type of issue. (This was the example I had in mind indeed.) And they move from parameter space to observable space. Distinguishing predictive elicitation from observational elicitation, the former being what I would have suggested from scratch. Obviously, the curse of dimensionality strikes again unless one considers summary statistics (like in ABC).

While I am glad conjugate priors do not get the lion’s share, using as in Section 3.3.. non-parametric or machine learning solutions to construct the prior sounds unrealistic. (And including maximum entropy priors into that category seems wrong since they are definitely parametric.)

The proposed Bayesian treatment of the expert’s “data” (Section 4.1) is rational but requires an additional model construct to link the expert’s data with the parameter to reach a Bayes formula like (4.1). Plus a primary prior (which could then be one of the reference priors.) Reducing the expert’s input to imaginary observations may prove too narrow, though. The notion of an iterative elicitation is most appealing and its sequential aspect may not be particularly problematic in opposition to posteriors relying on using the data twice or more. I am much less buying the hierarchical construct of Section 4.3 because they imply a return to conjugate priors and hyperpriors, are not necessarily correctly understood by experts, do not always cater to observational elicitation, and are not an answer to high-dimension challenges.

Given the state of the art, it sounds like we are still far from seeing prior elicitation as a natural part of Bayesian software and probabilistic programming. Even when using a modular, model-agnostic strategy. But this is most certainly a worthy prospect!