An information-oriented paradigm in evaluating accuracy and agreement in radiology.

The goal of any radiological diagnostic process is to gain information about the patient's status. However, the mathematical notion of information is usually not adopted to measure the performance of a diagnostic test or the agreement among readers in providing a certain diagnosis. Indeed, commonly used metrics for assessing diagnostic accuracy (e.g., sensitivity and specificity) or inter-reader agreement (Cohen [Formula: see text] statistics) use confusion matrices containing the number of true- and false positives/negatives results of a test, or the number of concordant/discordant categorizations, respectively, thus lacking proper information content. We present a methodological paradigm, based on Shannon's information theory, aiming to measure both accuracy and agreement in diagnostic radiology. This approach models the information flow as a "diagnostic channel" connecting the state of the patient's disease and the radiologist or, in the case of agreement analysis, as an "agreement channel" linking two or more radiologists evaluating the same set of images. For both cases, we proposed some measures, derived from Shannon's mutual information, which can represent an alternative way to express diagnostic accuracy and agreement in radiology.Key points• Diagnostic processes can be modeled with information theory (IT).• IT metrics of diagnostic accuracy are independent from disease prevalence.• IT metrics of inter-reader agreements can overcome Cohen κ pitfalls.

Fifty years of Shannon information theory in assessing the accuracy and agreement of diagnostic tests.

Since 1948, Shannon theoretic methods for modeling information have found a wide range of applications in several areas where information plays a key role, which goes well beyond the original scopes for which they have been conceived, namely data compression and error correction over a noisy channel. Among other uses, these methods have been applied in the broad field of medical diagnostics since the 1970s, to quantify diagnostic information, to evaluate diagnostic test performance, but also to be used as technical tools in image processing and registration. This review illustrates the main contributions in assessing the accuracy of diagnostic tests and the agreement between raters, focusing on diagnostic test performance measurements and paired agreement evaluation. This work also presents a recent unified, coherent, and hopefully, final information-theoretical approach to deal with the flows of information involved among the patient, the diagnostic test performed to appraise the state of disease, and the raters who are checking the test results. The approach is assessed by considering two case studies: the first one is related to evaluating extra-prostatic cancers; the second concerns the quality of rapid tests for COVID-19 detection.

Pressure-flow breath representation eases asynchrony identification in mechanically ventilated patients.

Breathing asynchronies are mismatches between the requests of mechanically ventilated subjects and the support provided by mechanical ventilators. The most widespread technique in identifying these pathological conditions is the visual analysis of the intra-tracheal pressure and flow time-trends. This work considers a recently introduced pressure-flow representation technique and investigates whether it can help nurses in the early detection of anomalies that can represent asynchronies. Twenty subjects-ten Intensive Care Unit (ICU) nurses and ten persons inexperienced in medical practice-were asked to find asynchronies in 200 breaths pre-labeled by three experts. The new representation increases significantly the detection capability of the subjects-average sensitivity soared from 0.622 to 0.905-while decreasing the classification time-from 1107.0 to 567.1 s on average-at the price of a not statistically significant rise in the number of wrong identifications-specificity average descended from 0.589 to 0.52. Moreover, the differences in experience between the nurse group and the inexperienced group do not affect the sensitivity, specificity, or classification times. The pressure-flow diagram significantly increases sensitivity and decreases the response time of early asynchrony detection performed by nurses. Moreover, the data suggest that operator experience does not affect the identification results. This outcome leads us to believe that, in emergency contexts with a shortage of nurses, intensive care nurses can be supplemented, for the sole identification of possible respiratory asynchronies, by inexperienced staff.

An effective pressure-flow characterization of respiratory asynchronies in mechanical ventilation.

Ineffective effort during expiration (IEE) occurs when there is a mismatch between the demand of a mechanically ventilated patient and the support delivered by a Mechanical ventilator during the expiration. This work presents a pressure-flow characterization for respiratory asynchronies and validates a machine-learning method, based on the presented characterization, to identify IEEs. 1500 breaths produced by 8 mechanically-ventilated patients were considered: 500 of them were included into the training set and the remaining 1000 into the test set. Each of them was evaluated by 3 experts and classified as either normal, artefact, or containing inspiratory, expiratory, or cycling-off asynchronies. A software implementing the proposed method was trained by using the experts' evaluations of the training set and used to identify IEEs in the test set. The outcomes were compared with a consensus of three expert evaluations. The software classified IEEs with sensitivity 0.904, specificity 0.995, accuracy 0.983, positive and negative predictive value 0.963 and 0.986, respectively. The Cohen's kappa is 0.983 (with 95% confidence interval (CI): [0.884, 0.962]). The pressure-flow characterization of respiratory cycles and the monitoring technique proposed in this work automatically identified IEEs in real-time in close agreement with the experts.

Beyond kappa: an informational index for diagnostic agreement in dichotomous and multivalue ordered-categorical ratings.

Agreement measures are useful tools to both compare different evaluations of the same diagnostic outcomes and validate new rating systems or devices. Cohen's kappa (κ) certainly is the most popular agreement method between two raters, and proved its effectiveness in the last sixty years. In spite of that, this method suffers from some alleged issues, which have been highlighted since the 1970s; moreover, its value is strongly dependent on the prevalence of the disease in the considered sample. This work introduces a new agreement index, the informational agreement (IA), which seems to avoid some of Cohen's kappa's flaws, and separates the contribution of the prevalence from the nucleus of agreement. These goals are achieved by modelling the agreement-in both dichotomous and multivalue ordered-categorical cases-as the information shared between two raters through the virtual diagnostic channel connecting them: the more information exchanged between the raters, the higher their agreement. In order to test its fair behaviour and the effectiveness of the method, IA has been tested on some cases known to be problematic for κ, in the machine learning context and in a clinical scenario to compare ultrasound (US) and automated breast volume scanner (ABVS) in the setting of breast cancer imaging. Graphical Abstract To evaluate the agreement between the two raters [Formula: see text] and [Formula: see text] we create an agreement channel, based on Shannon Information Theory, that directly connects the random variables X and Y, that express the raters outcomes. They are the terminals of the chain X⇔ diagnostic test performed by [Formula: see text] ⇔ patient condition[Formula: see text] ⇔ diagnostic test performed by [Formula: see text] ⇔ Y.

Family fingerprints: a global approach to structural classification.

Protein domain classification is a useful tool to deduce functional properties of proteins. Many software to classify domains according to available databases have been proposed so far. This paper introduces the notion of "fingerprint" as an easy and readable digest of the similarities between a protein fragment and an entire set of sequences. This concept offers us a rationale for building an automatic SCOP classifier which assigns a query sequence to the most likely family. Fingerprint-based analysis has been implemented in a software tool and we report some experimental validations for it.

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.