Pascal Pernot

French National Centre for Scientific Research | CNRS · Institut de Chimie (INC)

Nowadays, time-resolved spectroscopy data can be routinely and accurately collected in UV-Visible femtosecond transient absorption spectroscopy. However, the data analysis strategy and the postulation of a physically valid model for this kind of measurements may be tackled with many different approaches ranging from pure soft-modeling (model-free)...

Inference of physical parameters from reference data is a well studied problem with many intricacies (inconsistent sets of data due to experimental systematic errors, approximate physical models...). The complexity is further increased when the inferred parameters are used to make predictions (virtual measurements) because parameters uncertainty ha...

The comparison of benchmark error sets is an essential tool for the evaluation of theories in computational chemistry. The standard ranking of methods by their Mean Unsigned Error is unsatisfactory for several reasons linked to the non-normality of the error distributions and the presence of underlying trends. Complementary statistics have recently...

Molecular simulations are one of the most prominent discovery tools in science and engineering, widely adopted in applications ranging from drug discovery to materials design. The fidelity of the predictions of molecular simulations hinges on the reliability and accuracy of the chosen force fields. Thus, the quantification of uncertainties associat...

Validation of prediction uncertainty (PU) is becoming an essential task formodern computational chemistry. Designed to quantify the reliability ofpredictions in meteorology, the calibration-sharpness (CS) framework is nowwidely used to optimize and validate uncertainty-aware machine learning (ML)methods. However, its application is not limited to M...

Corneal transparency is essential to provide a clear view into and out of the eye, yet clinical means to assess such transparency are extremely limited and usually involve a subjective grading of visible opacities by means of slit-lamp biomicroscopy. Here, we describe an automated algorithm allowing extraction of quantitative corneal transparency p...

Post hoc recalibration of prediction uncertainties of machine learning regression problems by isotonic regression might present a problem for bin-based calibration error statistics (e.g. ENCE). Isotonic regression often produces stratified uncertainties, i.e. subsets of uncertainties with identical numerical values. Partitioning of the resulting da...

The Expected Normalized Calibration Error (ENCE) is a popular calibration statistic used in Machine Learning to assess the quality of prediction uncertainties for regression problems. Estimation of the ENCE is based on the binning of calibration data. In this short note, I illustrate an annoying property of the ENCE, i.e. its proportionality to the...

Light-induced charge accumulation is at the heart of biomimetic systems aiming at solar fuel production in the realm of artificial photosynthesis. Understanding the mechanisms upon which these processes operate is a necessary condition to drive down the rational catalyst design road. We have built a nanosecond pump-pump-probe resonance Raman setup...

The practice of uncertainty quantification (UQ) validation, notably in machine learning for the physico-chemical sciences, rests on several graphical methods (scattering plots, calibration curves, reliability diagrams and confidence curves) which explore complementary aspects of calibration, without covering all the desirable ones. For instance, no...

Metal halide perovskites (MHP, CsPbX3: X = Cl, Br, I) demonstrate high photogenerated charge-carrier production and mobility, which makes them promising candidates for photocatalysis. In this work, we investigated how...

In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchan...

Uncertainty propagation and sensitivity analysis have been applied to SMA-TB interatomic potentials that are often used in atomistic simulations to study metals and alloys. Usually, the parameters of potentials are estimated by a minimization method to best fit a set of experimental or ab initio computational data, such as bulk properties (e.g., co...

We review the alternative proposals introduced recently in the literature to update the standard formula to estimate the uncertainty on the mean of repeated measurements, and we compare their performances on synthetic examples with normal and non-normal error distributions.

In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchan...

Confidence curves are used in uncertainty validation to assess how large uncertainties ($u_{E}$) are associated with large errors ($E$). An oracle curve is usually used as reference, to give a measure of the quality of the tested datasets. The oracle is a perfect, deterministic, error predictor, such as $|E|=\pm u_{E}$, which corresponds to a very...

Context. The chemical building blocks of life contain a large proportion of nitrogen, an essential element. Titan, the largest moon of Saturn, with its dense atmosphere of molecular nitrogen and methane, offers an exceptional opportunity to explore how this element is incorporated into carbon chains through atmospheric chemistry in our Solar System...

Uncertainty quantification (UQ) in computational chemistry (CC) is still in its infancy. Very few CC methods are designed to provide a confidence level on their predictions, and most users still rely improperly on the mean absolute error as an accuracy metric. The development of reliable uncertainty quantification methods is essential, notably for...

Confirming the result of a calculation by a calculation with a different method is often seen as a validity check. However, when the methods considered are all subject to the same (systematic) errors, this practice fails. Using a statistical approach, we define measures for reliability and similarity, and we explore the extent to which the similari...

PURPOSE: To develop an automated algorithm allowing extraction of quantitative corneal transparency parameters from clinical spectral-domain OCT images. To establish a representative dataset of normative transparency values from healthy corneas. METHODS: SD-OCT images of 83 normal corneas (ages 22-50 years) from a standard clinical device (RTVue-XR...

Afin de préparer une inter comparaison entre des installations IBA travaillant avec des faisceaux extraits sur des objets du patrimoniaux, nous avons réaliser ce travail de comparer différentes méthodes de calcul L’inter comparaison entre laboratoire a pour objectif : La détermination d’une valeur de consensus X ass et son incertitudes u x _ass La...

Context. Characterizing temperate (200–1000 K) super-Earth atmospheres is one of the future challenges in exoplanetary science. One of the major difficulties comes from the ubiquity of aerosols in these objects, which complicates the spectroscopic analyses. The knowledge gained on the Solar System is then crucial to better understand the chemical p...

We present an automated data analysis procedure for clinical spectral-domain OCT, capable of correcting instrument-related hyperreflective artifacts, and its application to normal corneas. Quantitative parameters related to corneal transparency are extracted from 85 eyes.

We present an automated data analysis procedure for clinical SD-OCT images, capable of correcting hyperreflective artifacts due to the instrument. Quantitative parameters related to corneal transparency are extracted from n=85 normal corneas. ECBO 2021, paper EW1C.5.

The distribution of errors is a central object in the assessment and benchmarking of computational chemistry methods. The popular and often blind use of the mean unsigned error as a benchmarking statistic leads to ignore distributions features that impact the reliability of the tested methods. We explore how the Gini coefficient offers a global rep...

The distribution of errors is a central object in the assesment and benchmarking of computational chemistry methods. The popular and often blind use of the mean unsigned error as a benchmarking statistic leads to ignore distributions features that impact the reliability of the tested methods. We explore how the Gini coefficient offers a global repr...

Quantum machine learning models have been gaining significant traction within atomistic simulation communities. Conventionally, relative model performances are being assessed and compared using learning curves (prediction error vs. training set size). This article illustrates the limitations of using the Mean Absolute Error (MAE) for benchmarking,...

Invited for the cover of this issue are the groups of Roman Dembinski, Mehran Mostafavi, and Amitava Adhikary at the Polish Academy of Sciences, Université Paris‐Saclay, and Oakland University. The image depicts a doughnut as a way of illustrating the hole transfer process. Read the full text of the article at 10.1002/chem.202000247. “Direction of...

The direction of hole transfer (unpaired spin) in the DNA‐component, occurring between base and modified phosphate, is depicted in the cover artwork. This process critically determines the DNA‐backbone damage. In one‐electron oxidized phosphorodithioate nucleotide, the hole is initially localized on guanine base as a cation radical (Gua.+). Next, v...

With the upcoming launch of space telescopes dedicated to the study of exoplanets, the Atmospheric Remote-Sensing Infrared Exoplanet Large-survey (ARIEL) and the James Webb Space Telescope (JWST), a new era is opening in the exoplanetary atmospheric explorations. However, especially in relatively cold planets around later-type stars, photochemical...

In Paper I [P. Pernot and A. Savin, J. Chem. Phys. 152, 164108 (2020)], we introduced the systematic improvement probability as a tool to assess the level of improvement on absolute errors to be expected when switching between two computational chemistry methods. We also developed two indicators based on robust statistics to address the uncertainty...

The comparison of benchmark error sets is an essential tool for the evaluation of theories in computational chemistry. The standard ranking of methods by their mean unsigned error is unsatisfactory for several reasons linked to the non-normality of the error distributions and the presence of underlying trends. Complementary statistics have recently...

With the upcoming launch of space telescopes dedicated to the study of exoplanets, the \textit{Atmospheric Remote-Sensing Infrared Exoplanet Large-survey} (ARIEL) and the \textit{James Webb Space Telescope} (JWST), a new era is opening in the exoplanetary atmospheric explorations. However, especially in relatively cold planets around later-type sta...

Quantum machine learning models have been gaining significant traction within atomistic simulation communities. Conventionally, relative model performances are being assessed and compared using learning curves (prediction error vs. training set size). This article illustrates the limitations of using the Mean Absolute Error (MAE) for benchmarking,...

Computational chemistry has become an important complement to experimental measurements. In order to choose among the multitude of the existing approximations, it is common to use benchmark data sets, and to issue recommendations based on numbers such as mean absolute errors. We argue, using as an example band gaps calculated with density functiona...

Computational chemistry has become an important complement to experimental measurements. In order to choose among the multitude of the existing approximations, it is common to use benchmark data sets, and to issue recommendations based on numbers such as mean absolute errors. We argue, using as an example band gaps calculated with density functiona...

In the first part of this study (Paper I), we introduced the systematic improvement probability (SIP) as a tool to assess the level of improvement on absolute errors to be expected when switching between two computational chemistry methods. We developed also two indicators based on robust statistics to address the uncertainty of ranking in computat...

The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S- )=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G.+ -P(S- )=S. The ionization potential of G-P(S-...

Thanks to the \textit{Cassini} spacecraft onboard instruments, it has been known that Titan's ionospheric chemistry is complex and the molecular growth is initiated through the photolysis of the most abundant species directly in the upper atmosphere. Among the pool of chemical compounds formed by the photolysis, N-bearing species are involved in th...

Thanks to the Cassini spacecraft onboard instruments, it has been known that Titan's ionospheric chemistry is complex and the molecular growth is initiated through the photolysis of the most abundant species directly in the upper atmosphere. Among the pool of chemical compounds formed by the photolysis, N-bearing species are involved in the haze fo...

Loss of corneal transparency, as occurs with various pathologies, infections, immune reactions, trauma, aging, and surgery, is a major cause of visual handicap worldwide. However, current means to assess corneal transparency are extremely limited and clinical and eye-bank practice usually involve a subjective and qualitative observation of opacitie...

We demonstrate the feasibility of deriving quantitative measures of corneal transparency from objective analysis of stromal light backscattering with full-field optical coherence tomography (FF-OCT), addressing an unmet need in ophthalmology.

The Cassini Mission has greatly improved our understanding of the dynamics and chemical processes occurring in Titan's atmosphere. It has also provided us with more insight into the formation of the aerosols in the upper atmospheric layers. However, the chemical composition and mechanisms leading to their formation were out of reach for the instrum...

The Cassini Mission has greatly improved our understanding of the dynamics and chemical processes occurring in Titan's atmosphere. It has also provided us with more insight into the formation of the aerosols in the upper atmospheric layers. However, the chemical composition and mechanisms leading to their formation were out of reach for the instrum...

The ultrafast radiolytic behavior of Tributyl Phosphate, TBP, has been investigated using 7 ps electron pulses with 7 MeV kinetic energy, from which two key species have been observed and characterized: the TBP solvated electron ( ), and the TBP triplet excited state TBP* (3a) or its fragmentation products. The TBP solvated electron exhibits a broa...

In irradiated DNA, by base-to-base and backbone-to-base hole transfer processes, the hole (i.e., the unpaired spin) localizes on the most electropositive base, guanine. Phosphate radicals formed via ionization events in DNA-backbone must play an important role in the backbone-to-base hole transfer process. However, earlier works on irradiated hydra...

Benchmarking studies in computational chemistry use reference datasets to assess the accuracy of a method through error statistics. The commonly used error statistics, such as the mean signed and mean unsigned errors, do not inform end-users on the expected amplitude of prediction errors attached to these methods. We show that, the distributions of...

The reactivity of a series of commonly used halogenated compounds (trihalomethanes, chlorofluorocarbon, hydrochlorofluorocarbon, fluorocarbons and hydrofluoroolefin) with hydroxide and oxygen anion is studied in a compact FT-ICR. O- is formed by dissociative electron attachment to N2 O and HO- by a further ion-molecule reaction with ammonia. Kineti...

Statistical estimation of the prediction uncertainty of physical models is typically hindered by the inadequacy of these models due to various approximations they are built upon. The prediction errors due to model inadequacy can be handled either by correcting the model's results, or by adapting the model's parameters uncertainty to generate predic...

It is generally considered that the pre-solvated electron and the solvated electron reacting with a solute yield the same product. Silver cyanide complex, Ag(CN)2-, is used as a simple probe to demonstrate unambiguously the existence of a different reduction mechanism for pre-hydrated electrons. Using systematic multichannel transient absorption me...

In its introductory sections, the title article seems to assert that there is a failure of the method of propagation of uncertainties (PoU), when applied to a linearized Arrhenius model. In consequence, the PoU formula is replaced by an expression of the confidence limits that can be easily implemented in Excel. This letter explicits that the obser...

NMR measurements show that diethyl carbonate (DEC, a solvent with a low dielectric constant) solutions of LiClO4 contain (LiClO4)n oligomers. The reduction of these species by solvated electrons and pre-solvated electrons is followed by picosecond pulse radiolysis measurements. The data analysis shows that several anions absorbing in the NIR and vi...

Requiring that several properties are well reproduced is a severe test on density functional approximations. This can be assessed through the estimation of joint and conditional success probabilities. An example is provided for a small set of molecules, for properties characterizing the transition states (geometries and energies).

The chemical composition of Titan organic haze is poorly known. To address this issue, laboratory analogs named tholins are synthesized, and analyzed by methods requiring often an extraction process in a carrier solvent. These methods exclude the analysis of the insoluble tholins fraction and assume a hypothetical chemical equivalence between solub...

Benchmark calculations provide a large amount of information that can be very useful in assessing the performance of density functional approximations, and for choosing the one to use. In order to condense the information some indicators are provided. However, these indicators might be insufficient and a more careful analysis is needed, as shown by...

Cryptochromes and photolyases are flavoproteins that undergo cascades of electron/hole transfers after excitation of the flavin cofactor. It was recently discovered that animal (6-4) photolyases, as well as animal cryptochromes, feature a chain of four tryptophan residues while other members of the family contain merely a tryptophan triad. Transien...

The Cassini-Huygens space mission revealed that the chemistry initiating Titan's aerosols formation starts in the upper layers of the atmosphere (~1000 km). The grains then sediment until deposition at the surface. Despite all the data collected, the photochemical evolution of the aerosols between 1000 and 600 km is still unknown, especially regard...

Pour certains modèles, réduire la variance d'une ou plusieurs variables d'entrée provoque une augmentation de la variance de la sortie du modèle. Ce phénomène n'est pas concevable dans le cadre des modèles linéaires décrits par le GUM, mais peut être, en revanche, observable par propagation des distributions sur des modèles non-linéaires. Dans tous...

experiment, the proportion of matter going into each channel, called the branching ratio, is determined. Therefore two dierent problems have to be adressed: a pdf for the global rate constant and correlated pdfs for the branching ratios must be separately elicited. Whereas standard loguniform or lognormal elicitation are relevant for the global rat...

Titan is the largest satellite of Saturn. Its upper atmosphere is well-known for the production of a phochemical organic smog. We simulate this ionospheric chemistry with a RF plasma setup. We present here the study of the gas phase composition, neutral and positively charged species, correlated with aerosol production efficiency. Titan is the larg...

Pulse radiolysis was used to study the mechanism of HO.-induced polymerization of poly(3,4-ethylenedioxythiophene), PEDOT, in aqueous solution. A step-by-step mechanism has been found which involves a recurrent oxidation process by HO. hydroxyl radicals produced by water radiolysis. Besides, the cation radical, EDOT.+, has been proposed as the prom...