Explainable machine learning using SHAP: An application in Alzheimer’s disease diagnosis

Treballs Finals de Grau de Matemàtiques, Facultat de Matemàtiques, Universitat de Barcelona, Any: 2024, Director: Petia Radeva[en] Machine learning models are a powerful and increasingly ubiquitous tool in modern science, due to their ability to analyse massive amounts of data and extract valuable information. Nonetheless, the increasing complexity of such models usually impedes the interpretation of their decision-making processes. Shapley Additive Explanations (SHAP) is a recently developed explainability method that poses as a suitable candidate to solve this problem. Healthcare is a field where explainability emerges as a critical aspect for the deployment of machine learning techniques. Recently, some studies have started exploring the usage of SHAP on machine learning models for the diagnosis of Alzheimer’s disease (AD). The aim of this work is, firstly, to conduct a theoretical exploration of SHAP to assess its reliability, and then to apply it in a machine learning model for the diagnosis of AD. A theoretical description of SHAP has been done starting from its basis, which relies on results coming from cooperative game theory. A subsequent analysis has been done to study how factors such as feature correlation or feature interaction may affect the method. Numerical tests with synthetic data have been done to illustrate the previous theoretical discussions. Having theoretically presented and discussed the SHAP method, it has been applied in the context of AD diagnosis. Using publicly available data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset, a random forest algorithm has been implemented to classify AD patients and healthy controls, using features derived from structural magnetic resonance imaging and amyloid-beta positron emission tomography. This analysis has served as a proof of context of the clinical applicability of SHAP. Further work should be done in order to refine and fully adapt the method to the context of AD diagnosis

Exploring the INTEGRAL sources in search for new microquasars

Here we present a search for new microquasars among the sources detected with the INTEGRAL satellite (IGR sources). We focus on radio emitting IGR sources and report the discovery of two new probable extragalactic sources behind the galactic plane, as well as the detection at higher energies of the ASCA source AX J1639.0-4642, probably a new microquasar in the Galaxy and coincident with a high-energy gamma-ray emitting EGRET source.Fil: Ribó, Marc. CEA Saclay; FranciaFil: Combi, Jorge Ariel. Universidad de Jaén; España. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Argentino de Radioastronomía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Argentino de Radioastronomía; ArgentinaFil: Mirabel Miquele, Igor Felix. CEA Saclay; Franci

Optical photometric monitoring of gamma-ray binaries

Four gamma-ray binaries, namely PSR B1259-63, HESS J0632+057, HD 215227 and LS I +61 303, contain compact objects orbiting around massive Be stars. The nature of the compact object is only known in the case of PSR B1259-63, but the other systems could also contain young non-accreting pulsars with relativistic winds. Around periastron passage the compact objects should produce significant changes in the structure of the Be discs due to gravitational forces and eventually by ram pressure from the putative pulsar wind. Indeed, variability in the Halpha emission line has been detected in all these systems, and periodic variability in the optical photometry has been detected in two of them. However, there is lack of a systematic monitoring with accurate photometry, which could be used to constrain the shape of the disc during the periastron passage. This information is important to build accurate physical models to explain the broadband spectral energy distribution of these sources. Here we present an ongoing program to monitor the optical photometry of gamma-ray binaries and we show preliminary results for the case of HD 215227.Comment: 4 pages, 1 figure. Proceedings of the "5th International Symposium on High-Energy Gamma-Ray Astronomy", Heidelberg (Germany), 9-13 July 201

The radio to TeV orbital variability of the microquasar LSI+61303

Context: .The microquasar LS I +61 303 has recently been detected at TeV energies by the Cherenkov telescope MAGIC, presenting variability on timescales similar to its orbital period. This system has been intensively observed at different wavelengths during the last three decades, showing a very complex behavior along the orbit.Aims: .We aim to explain, using a leptonic model in the accretion scenario, the observed orbital variability and spectrum from radio to TeV energies of LS I +61 303.Methods: .We apply a leptonic model based on accretion of matter from the slow inhomogeneous equatorial wind of the primary star, assuming particle injection proportional to the accretion rate. The relativistic electron energy distribution within the binary system is computed taking into account convective/adiabatic and radiative losses. The spectral energy distribution (SED) has been calculated accounting for synchrotron and (Thomson/Klein Nishina -KN-) inverse Compton (IC) processes and the photon-photon absorption in the ambient photon fields. The angle dependence of the photon-photon and IC cross sections has been considered in the calculations.Results: .We reproduce the main features of the observed light curves from LS I +61 303 at radio, X-rays, high-energy (HE), and very high-energy (VHE) gamma-rays, and the whole spectral energy distribution.Conclusions: .Our model is able to explain the radio to TeV orbital variability taking into account that radiation along the orbit is strongly affected by the variable accretion rate, the magnetic field strength, and by the ambient photon field via dominant IC losses and photon-photon absorption at periastron.Fil: Bosch Ramon, Valentí. Universidad de Barcelona; EspañaFil: Paredes, Josep Maria. Universidad de Barcelona; EspañaFil: Romero, Gustavo Esteban. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Argentino de Radioastronomía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Argentino de Radioastronomía; ArgentinaFil: Ribó, Marc. Universidad de Barcelona; Españ

REACT Aspiration Catheters: Clinical Experience and Technical Considerations

Catheter; Mechanical aspiration; StrokeCatéter; Aspiración mecánica; IctusCatèter; Aspiració mecànica; IctusAspiration catheters are widely used in mechanical thrombectomy procedures to treat acute ischemic stroke due to large vessel occlusion. The key performance requirements for aspiration catheters are ease of navigation and effective aspiration. In this work, we review the clinical experience and in vitro studies of REACT aspiration catheters (Medtronic, Minneapolis, MN, USA). In vitro experiments showed that REACT catheters exhibit solid performance in navigation and aspiration. Previous studies reported that the recanalization capacity of the aspiration catheters can be influenced by the devices’ inner diameter and tip distensibility, the catheter-to-vessel diameter ratio, the negative pressure delivered by the vacuum generator, the cyclical aspiration mode, the proximal flow arrest, and the angle of interaction between catheter and clot. REACT catheters can be navigated through the vasculature without any support from a microcatheter/ microwire in favorable anatomical configurations. In challenging situations, mostly encountered when crossing the ophthalmic segment of the internal carotid artery, the use of the stentriever anchoring technique or delivery assist catheter can facilitate the navigation. Three clinical studies reporting on 299 patients who underwent mechanical thrombectomy with REACT catheters were included in this review. Successful recanalization (modified treatment in cerebral ischemia score 2b–3) was achieved in 89–96% of cases, no procedural complications related to REACT catheters were reported, and functional independence (modified Rankin Scale 0–2) at 90-days was 24–36%. In vitro experimental evaluations and clinical studies support the safety and effectiveness of the REACT catheters

Response to letter: How much will a catheter tip expand in aspiration thrombectomy?

We thank Liu and Kallmes for their interest and valuable observations, which might help to improve the understanding of our study. Our findings show, in all catheters, an increased aspiration effective force as compared with the expected theoretical force corresponding to the labeled catheter diameter. This is an objective and evidenced finding

Implementation of a Scaled-Down Power Substation for Traction Networks

El principal objectiu d’aquest projecte final de carrera ´es implementar dues fonts d’alimentaci´o de pot`encia a 162/3 Hz per a la tracci´o el`ectrica. La font d’alimentaci´o treballar`a com a subestaci o, proporcionant la pot`encia necess`aria i el voltatge sinuso¨ıdal a 162/3 Hz a una caten aria d’on es connectar`a una o m´es d’una locomotora. El sistema de tracci´o es composa de dues subestacions a cada extrem de la l´ınia, la caten`aria i la locomotora. Les subestacions s´on modelades com VSI m´es un filtre LC, la caten`aria com una imped`ancia variable i la locomotora com un VSI amb un filtre L en aquest cas. S’ha realitzat una revisi´o de la literatura per establir l’estat de l’art de les t`ecniques de control de la tensi´o i, seguidament, un estudi de la millor t`ecnica de control per inversors monof`asics. S’ha dissenyat, simulat, implementat en un DSPIC i validat experimentalment un control basat en controladors Proporcionals Resonants per regular la tensi´o de sortida de la subestaci´o en diferents escenaris. En primer lloc, el control de tensi´o ser`a avaluat provocant canvis bruscos de corrent amb una c`arrega resistiva, posteriorment amb una c`arrega resistiva-inductiva i, finalment, amb un convertidor de corrent (locomotora). Els objectius del projecte s’han superat satisfact`oriament i el model de subestaci´o d’alimentaci ´o per a la tracci´o el`ectrica est`a en servei. El control de tensi´o implementat ´es capa¸c de seguir la refer`encia amb error nul en estat estacionari i un temps de resposta de 10 ms. Aquest projecte final de carrera s’ha dut a terme a ”´Ecole Polytechnique F´ed´erale de Lausanne - Laboratoire d’´Electronique Industriel (EPFL-LEI)” situada a Lausanne, Suissa. ´Es una col laboraci´o entre el CITCEA-UPC i EPFL-LEI. Forma part d’una tesi doctoral que engloba aquest projecte final de carrera i un projecte de semestre. El principal objectiu de la tesi doctoral ´es validar experimentalment en una locomotora moderna FLIRT un m`etode de control per compensar la caiguda de tensi´o que existeix en les caten`aries injectant pot`encia reactiva capacitiva. Per aconseguir tal fi, abans el control s’ha de probar en un model del sistema ferroviari a escala redu¨ıda, amb la qual cosa es requeria un model de subestaci´o (aquest projecte final de carrera) i un model de locomotora (projecte de semestre)

Approaches to Endow Ribonucleases with Antitumor Activity: Lessons Learned from the Native Cytotoxic Ribonucleases

Typical antitumor drugs disrupt the flow of biochemical information from DNA to proteins with the aim of precluding uncontrolled cell proliferation and inducing cancer cell apoptosis. However, most of the currently used small antitumor drugs are genotoxic because they act over DNA. Pharmaceutical industry is now searching for a new line of cancer chemotherapeutics without genotoxic effects. Ribonucleases (RNases) are small basic proteins, present in all life forms, which belong to this kind of chemotherapeutics. Some of them present with remarkable selective antitumor activity linked to their ability to destroy RNA, a powerful way to control gene expression, leaving DNA unharmed. In the last two decades, the knowledge gained on the cytotoxic mechanism of these RNases has been used to engineer more powerful and selective variants to kill cancer cells. In this chapter, we describe the advances reached in endowing an RNase with antitumor abilities

Influencia de los inhibidores endógenos de la fibrinolisis sobre el tratamiento trombolítico del ictus con t-PA

Consultable des del TDXTítol obtingut de la portada digitalitzadaIntroducción Los inhibidores endógenos de la fibrinolisis juegan un papel esencial en el balance coagulación/fibrinolisis pudiendo estar involucrados en la respuesta al tratamiento trombolítico del ictus. Mientras que por una parte pueden inducir resistencia al t-PA limitando los beneficios de la trombólisis, por otra, pueden favorecer los procesos de sangrado en las transformaciones hemorrágicas. Objetivos El objetivo de este estudio es determinar el impacto de los niveles pre-tratamiento de inhibidores de la fibrinolisis (Inhibidor del Activador del Plasminógeno (PAI-1), lipoproteína(a), Inhibidor de la Fibrinolisis Activado por Trombina (TAFI) y homocisteína) sobre recanalización arterial, transformación hemorrágica sintomática (SICH) y evolución clínica. Métodos Estudiamos pacientes consecutivos con un ictus por oclusión de la arteria cerebral media tratados con t-PA. Se obtuvieron muestras de sangre justo antes de la administración de t-PA para la determinación de las moléculas inhibidoras de la fibrinolisis. Se determinó la recanalización arterial mediante monitorización continua por Doppler Transcraneal. Una tomografía computarizada craneal a las 24 horas o inmediatamente después de observar un empeoramiento clínico permitió descartar la presencia de una transformación hemorrágica sintomática. El estado neurológico se determinó mediante la escala NIHSS y la discapacidad a largo plazo mediante la escala modificada de Rankin (mRS) al tercer mes. Resultados Estudiamos 77 pacientes (40% mujeres, edad media 75 años). Al ingreso la mediana en la escala NIHSS fue de 17 (rango, 7 a 22) y el tiempo medio de tratamiento desde el inicio de los síntomas fue de 160 minutos. En aquellos pacientes que presentaron una recanalización arterial después de la infusión de t-PA se observaron niveles basales de PAI-1 inferiores que en los que peristió la oclusión (27.8 ng/ml Vs 38.8 ng/ml; p=0.047). Igualmente, aquellos pacientes que presentaron una mejoría clínica espectacular (decremento > 10 puntos en la escala NIHSS) a las 12 horas mostraron niveles significativamente más bajos de PAI-1 (24.6 ng/ml Vs 36.1 ng/ml; p=0.012) así como aquellos con una independencia funcional (mRS≤2) al tercer mes (24.4 ng/ml Vs 34.3 ng/ml; p=0.03). Se observó además una tendencia a presentar niveles más bajos de lipoproteina(a) en aquellos pacientes que recanalizaron tras una hora, mientras que no se observó ninguna relación entre TAFI o Homocisteína y recanalización. El modelo de regresión logística mostró que el único predictor independiente de resistencia a la trombólisis era presentar niveles basales de PAI-1>34 ng/ml (OR 12.8; 95%CI 1.7-97.2; p=0.014) Seis pacientes (7.9%) presentaron una SICH. Los análisis de las variables clínicas y radiológicas no mostraron relación con el desarrollo de SICH. Al analizar los datos de laboratorio se observó que los pacientes con SICH presentaron niveles basales de PAI-1 más bajos (21.7+/-3.5 ng/mL versus 31.8+/-12.1 ng/mL; p180% (OR, 12.9; CI, 1.41 to 118.8; P=0.02) y PAI-1 180% al ingreso era capaz de predecir SICH con una sensibilidad de 75% , una especificidad de 97.6% (P 10 points in NIHSS) at 12 hours exhibited significantly lower PAI-1 levels (24.6 ng/ml Vs 36.1 ng/ml; p=0.012) as did those functionally independent (mRS≤2) at third month (24.4 ng/ml Vs 34.3 ng/ml; p=0.03). We observed a trend towards lower lipoprotein(a) in patients who achieved recanalization at 1 hour, whereas no relation was found between TAFI or homocysteine levels and recanalization. After a regression model was applied the only independent predictor of thrombolysis resistance was baseline PAI-1>34 ng/ml (OR 12.8; 95%CI 1.7-97.2; p=0.014) Six patients (7.9%) presented with a SICH. In analyses based on clinical and radiological variables, no relation could be found with SICH. When laboratory data were analyzed, patients who experienced SICH showed lower baseline PAI-1 (21.7+/-3.5 ng/mL versus 31.8+/-12.1 ng/mL; P180% (OR, 12.9; CI, 1.41 to 118.8; P=0.02) and PAI-1 180% had a sensibility of 75% and a specificity of 97.6% (P<0.01) predicting SICH, with a positive predictive value of 75% and negative predictive value of 97.6%. Conclusion High PAI-1 levels interfere with tPA-induced recanalization in stroke, predicting a higher susceptibility towards clot-lysis resistance and poor outcome. On the other hand, very low PAI-1 and high TAFI levels predict SICH after tPA therapy. In the future, rapid determination of these biomarkers could be used to improve thrombolysis safety and efficacy