* ML in HEP
* classification and regression
* knn classification and regression
* ROC curve
* optimal bayesian classifier
* Fisher's QDA
* intro to Logistic Regression
* Logistic regression, logistic loss (log loss)
* stochastic optimization
* adding new features, generalized linear model
* Kernel trick, intro to SVM
* Overfitting
* Decision trees for classification and regression
* Building trees greedily: Gini index, entropy
* Trees fighting with overfitting: pre-stopping and post-pruning
* Feature importances
Introduction to machine learning terminology.
Applications within High Energy Physics and outside HEP.
* Basic problems: classification and regression.
* Nearest neighbours approach and spacial indices
* Overfitting (intro)
* Curse of dimensionality
* ROC curve, ROC AUC
* Bayes optimal classifier
* Density estimation: KDE and histograms
* Parametric density estimation
* Mixtures for density estimation and EM algorithm
* Generative approach vs discriminative approach
* Linear decision rule, intro to logistic regression
* Linear regression
* Logistic regression, logistic loss (log loss)
* stochastic optimization
* adding new features, generalized linear model
* Kernel trick, intro to SVM
* Overfitting
* Decision trees for classification and regression
* Building trees greedily: Gini index, entropy
* Trees fighting with overfitting: pre-stopping and post-pruning
* Feature importances
Introduction to machine learning terminology.
Applications within High Energy Physics and outside HEP.
* Basic problems: classification and regression.
* Nearest neighbours approach and spacial indices
* Overfitting (intro)
* Curse of dimensionality
* ROC curve, ROC AUC
* Bayes optimal classifier
* Density estimation: KDE and histograms
* Parametric density estimation
* Mixtures for density estimation and EM algorithm
* Generative approach vs discriminative approach
* Linear decision rule, intro to logistic regression
* Linear regression
A review of one of the most popular methods of clustering, a part of what is know as unsupervised learning, K-Means. Here, we go from the basic heuristic used to solve the NP-Hard problem to an approximation algorithm K-Centers. Additionally, we look at variations coming from the Fuzzy Set ideas. In the future, we will add more about On-Line algorithms in the line of Stochastic Gradient Ideas...
In this talk we consider the question of how to use QMC with an empirical dataset, such as a set of points generated by MCMC. Using ideas from partitioning for parallel computing, we apply recursive bisection to reorder the points, and then interleave the bits of the QMC coordinates to select the appropriate point from the dataset. Numerical tests show that in the case of known distributions this is almost as effective as applying QMC directly to the original distribution. The same recursive bisection can also be used to thin the dataset, by recursively bisecting down to many small subsets of points, and then randomly selecting one point from each subset. This makes it possible to reduce the size of the dataset greatly without significantly increasing the overall error. Co-author: Fei Xie
One of the central tasks in computational mathematics and statistics is to accurately approximate unknown target functions. This is typically done with the help of data — samples of the unknown functions. The emergence of Big Data presents both opportunities and challenges. On one hand, big data introduces more information about the unknowns and, in principle, allows us to create more accurate models. On the other hand, data storage and processing become highly challenging. In this talk, we present a set of sequential algorithms for function approximation in high dimensions with large data sets. The algorithms are of iterative nature and involve only vector operations. They use one data sample at each step and can handle dynamic/stream data. We present both the numerical algorithms, which are easy to implement, as well as rigorous analysis for their theoretical foundation.
In this paper, we solve a semi-supervised regression
problem. Due to the luck of knowledge about the
data structure and the presence of random noise, the considered data model is uncertain. We propose a method which combines graph Laplacian regularization and cluster ensemble methodologies. The co-association matrix of the ensemble is calculated on both labeled and unlabeled data; this matrix is used as a similarity matrix in the regularization framework to derive the predicted outputs. We use the low-rank decomposition of the co-association matrix to significantly speedup calculations and reduce memory. Two clustering problem examples are presented.
Full version is here https://arxiv.org/abs/1901.03919
Robot의 Gait optimization, Gesture Recognition, Optimal Control, Hyper parameter optimization, 신약 신소재 개발을 위한 optimal data sampling strategy등과 같은 ML분야에서 약방의 감초 같은 존재인 GP이지만 이해가 쉽지 않은 GP의 기본적인 이론 및 matlab code 소개
https://telecombcn-dl.github.io/2017-dlai/
Deep learning technologies are at the core of the current revolution in artificial intelligence for multimedia data analysis. The convergence of large-scale annotated datasets and affordable GPU hardware has allowed the training of neural networks for data analysis tasks which were previously addressed with hand-crafted features. Architectures such as convolutional neural networks, recurrent neural networks or Q-nets for reinforcement learning have shaped a brand new scenario in signal processing. This course will cover the basic principles of deep learning from both an algorithmic and computational perspectives.
The generation of Gaussian random fields over a physical domain is a challenging problem in computational mathematics, especially when the correlation length is short and the field is rough. The traditional approach is to make use of a truncated Karhunen-Loeve (KL) expansion, but the generation of even a single realisation of the field may then be effectively beyond reach (especially for 3-dimensional domains) if the need is to obtain an expected L2 error of say 5%, because of the potentially very slow convergence of the KL expansion. In this talk, based on joint work with Ivan Graham, Frances Kuo, Dirk Nuyens, and Rob Scheichl, a completely different approach is used, in which the field is initially generated at a regular grid on a 2- or 3-dimensional rectangle that contains the physical domain, and then possibly interpolated to obtain the field at other points. In that case there is no need for any truncation. Rather the main problem becomes the factorisation of a large dense matrix. For this we use circulant embedding and FFT ideas. Quasi-Monte Carlo integration is then used to evaluate the expected value of some functional of the finite-element solution of an elliptic PDE with a random field as input.
Markov chain Monte Carlo (MCMC) methods are popularly used in Bayesian computation. However, they need large number of samples for convergence which can become costly when the posterior distribution is expensive to evaluate. Deterministic sampling techniques such as Quasi-Monte Carlo (QMC) can be a useful alternative to MCMC, but the existing QMC methods are mainly developed only for sampling from unit hypercubes. Unfortunately, the posterior distributions can be highly correlated and nonlinear making them occupy very little space inside a hypercube. Thus, most of the samples from QMC can get wasted. The QMC samples can be saved if they can be pulled towards the high probability regions of the posterior distribution using inverse probability transforms. But this can be done only when the distribution function is known, which is rarely the case in Bayesian problems. In this talk, I will discuss a deterministic sampling technique, known as minimum energy designs, which can directly sample from the posterior distributions.
Information-theoretic clustering with applicationsFrank Nielsen
Information-theoretic clustering with applications
Abstract: Clustering is a fundamental and key primitive to discover structural groups of homogeneous data in data sets, called clusters. The most famous clustering technique is the celebrated k-means clustering that seeks to minimize the sum of intra-cluster variances. k-Means is NP-hard as soon as the dimension and the number of clusters are both greater than 1. In the first part of the talk, we first present a generic dynamic programming method to compute the optimal clustering of n scalar elements into k pairwise disjoint intervals. This case includes 1D Euclidean k-means but also other kinds of clustering algorithms like the k-medoids, the k-medians, the k-centers, etc.
We extend the method to incorporate cluster size constraints and show how to choose the appropriate number of clusters using model selection. We then illustrate and refine the method on two case studies: 1D Bregman clustering and univariate statistical mixture learning maximizing the complete likelihood. In the second part of the talk, we introduce a generalization of k-means to cluster sets of histograms that has become an important ingredient of modern information processing due to the success of the bag-of-word modelling paradigm.
Clustering histograms can be performed using the celebrated k-means centroid-based algorithm. We consider the Jeffreys divergence that symmetrizes the Kullback-Leibler divergence, and investigate the computation of Jeffreys centroids. We prove that the Jeffreys centroid can be expressed analytically using the Lambert W function for positive histograms. We then show how to obtain a fast guaranteed approximation when dealing with frequency histograms and conclude with some remarks on the k-means histogram clustering.
References: - Optimal interval clustering: Application to Bregman clustering and statistical mixture learning IEEE ISIT 2014 (recent result poster) http://arxiv.org/abs/1403.2485
- Jeffreys Centroids: A Closed-Form Expression for Positive Histograms and a Guaranteed Tight Approximation for Frequency Histograms.
IEEE Signal Process. Lett. 20(7): 657-660 (2013) http://arxiv.org/abs/1303.7286
http://www.i.kyoto-u.ac.jp/informatics-seminar/
A review of one of the most popular methods of clustering, a part of what is know as unsupervised learning, K-Means. Here, we go from the basic heuristic used to solve the NP-Hard problem to an approximation algorithm K-Centers. Additionally, we look at variations coming from the Fuzzy Set ideas. In the future, we will add more about On-Line algorithms in the line of Stochastic Gradient Ideas...
In this talk we consider the question of how to use QMC with an empirical dataset, such as a set of points generated by MCMC. Using ideas from partitioning for parallel computing, we apply recursive bisection to reorder the points, and then interleave the bits of the QMC coordinates to select the appropriate point from the dataset. Numerical tests show that in the case of known distributions this is almost as effective as applying QMC directly to the original distribution. The same recursive bisection can also be used to thin the dataset, by recursively bisecting down to many small subsets of points, and then randomly selecting one point from each subset. This makes it possible to reduce the size of the dataset greatly without significantly increasing the overall error. Co-author: Fei Xie
One of the central tasks in computational mathematics and statistics is to accurately approximate unknown target functions. This is typically done with the help of data — samples of the unknown functions. The emergence of Big Data presents both opportunities and challenges. On one hand, big data introduces more information about the unknowns and, in principle, allows us to create more accurate models. On the other hand, data storage and processing become highly challenging. In this talk, we present a set of sequential algorithms for function approximation in high dimensions with large data sets. The algorithms are of iterative nature and involve only vector operations. They use one data sample at each step and can handle dynamic/stream data. We present both the numerical algorithms, which are easy to implement, as well as rigorous analysis for their theoretical foundation.
In this paper, we solve a semi-supervised regression
problem. Due to the luck of knowledge about the
data structure and the presence of random noise, the considered data model is uncertain. We propose a method which combines graph Laplacian regularization and cluster ensemble methodologies. The co-association matrix of the ensemble is calculated on both labeled and unlabeled data; this matrix is used as a similarity matrix in the regularization framework to derive the predicted outputs. We use the low-rank decomposition of the co-association matrix to significantly speedup calculations and reduce memory. Two clustering problem examples are presented.
Full version is here https://arxiv.org/abs/1901.03919
Robot의 Gait optimization, Gesture Recognition, Optimal Control, Hyper parameter optimization, 신약 신소재 개발을 위한 optimal data sampling strategy등과 같은 ML분야에서 약방의 감초 같은 존재인 GP이지만 이해가 쉽지 않은 GP의 기본적인 이론 및 matlab code 소개
https://telecombcn-dl.github.io/2017-dlai/
Deep learning technologies are at the core of the current revolution in artificial intelligence for multimedia data analysis. The convergence of large-scale annotated datasets and affordable GPU hardware has allowed the training of neural networks for data analysis tasks which were previously addressed with hand-crafted features. Architectures such as convolutional neural networks, recurrent neural networks or Q-nets for reinforcement learning have shaped a brand new scenario in signal processing. This course will cover the basic principles of deep learning from both an algorithmic and computational perspectives.
The generation of Gaussian random fields over a physical domain is a challenging problem in computational mathematics, especially when the correlation length is short and the field is rough. The traditional approach is to make use of a truncated Karhunen-Loeve (KL) expansion, but the generation of even a single realisation of the field may then be effectively beyond reach (especially for 3-dimensional domains) if the need is to obtain an expected L2 error of say 5%, because of the potentially very slow convergence of the KL expansion. In this talk, based on joint work with Ivan Graham, Frances Kuo, Dirk Nuyens, and Rob Scheichl, a completely different approach is used, in which the field is initially generated at a regular grid on a 2- or 3-dimensional rectangle that contains the physical domain, and then possibly interpolated to obtain the field at other points. In that case there is no need for any truncation. Rather the main problem becomes the factorisation of a large dense matrix. For this we use circulant embedding and FFT ideas. Quasi-Monte Carlo integration is then used to evaluate the expected value of some functional of the finite-element solution of an elliptic PDE with a random field as input.
Markov chain Monte Carlo (MCMC) methods are popularly used in Bayesian computation. However, they need large number of samples for convergence which can become costly when the posterior distribution is expensive to evaluate. Deterministic sampling techniques such as Quasi-Monte Carlo (QMC) can be a useful alternative to MCMC, but the existing QMC methods are mainly developed only for sampling from unit hypercubes. Unfortunately, the posterior distributions can be highly correlated and nonlinear making them occupy very little space inside a hypercube. Thus, most of the samples from QMC can get wasted. The QMC samples can be saved if they can be pulled towards the high probability regions of the posterior distribution using inverse probability transforms. But this can be done only when the distribution function is known, which is rarely the case in Bayesian problems. In this talk, I will discuss a deterministic sampling technique, known as minimum energy designs, which can directly sample from the posterior distributions.
Information-theoretic clustering with applicationsFrank Nielsen
Information-theoretic clustering with applications
Abstract: Clustering is a fundamental and key primitive to discover structural groups of homogeneous data in data sets, called clusters. The most famous clustering technique is the celebrated k-means clustering that seeks to minimize the sum of intra-cluster variances. k-Means is NP-hard as soon as the dimension and the number of clusters are both greater than 1. In the first part of the talk, we first present a generic dynamic programming method to compute the optimal clustering of n scalar elements into k pairwise disjoint intervals. This case includes 1D Euclidean k-means but also other kinds of clustering algorithms like the k-medoids, the k-medians, the k-centers, etc.
We extend the method to incorporate cluster size constraints and show how to choose the appropriate number of clusters using model selection. We then illustrate and refine the method on two case studies: 1D Bregman clustering and univariate statistical mixture learning maximizing the complete likelihood. In the second part of the talk, we introduce a generalization of k-means to cluster sets of histograms that has become an important ingredient of modern information processing due to the success of the bag-of-word modelling paradigm.
Clustering histograms can be performed using the celebrated k-means centroid-based algorithm. We consider the Jeffreys divergence that symmetrizes the Kullback-Leibler divergence, and investigate the computation of Jeffreys centroids. We prove that the Jeffreys centroid can be expressed analytically using the Lambert W function for positive histograms. We then show how to obtain a fast guaranteed approximation when dealing with frequency histograms and conclude with some remarks on the k-means histogram clustering.
References: - Optimal interval clustering: Application to Bregman clustering and statistical mixture learning IEEE ISIT 2014 (recent result poster) http://arxiv.org/abs/1403.2485
- Jeffreys Centroids: A Closed-Form Expression for Positive Histograms and a Guaranteed Tight Approximation for Frequency Histograms.
IEEE Signal Process. Lett. 20(7): 657-660 (2013) http://arxiv.org/abs/1303.7286
http://www.i.kyoto-u.ac.jp/informatics-seminar/
The amount of digital data in the new era has grown exponentially in recent years and with the development of new technologies, is growing more rapidly than ever before.
Nevertheless, simply knowing that all these data are out there is easily understandable, utilizing these data to turn a profit is not trivial.
The need of data mining techniques able to extract profitable insight information is the next frontier of innovation, competition and profit.
A data analytic services provider, in order to well-scale and exponentially grow its profit, has to deal with scalability, multi-tenancy and self-adaptability.
In big data applications, machine learning is a very powerful instrument but a bad choice regarding the algorithm and its configuration parameters can easily lead to poor results. The key problem is automating the tuning process without a priori knowledge of the data and without human intervention.
In this research project we implemented and analysed TunUp: A Distributed Cloud-based Genetic Evolutionary Tuning for Data Clustering.
The proposed solution automatically evaluates and tunes data clustering algorithms, so that big data services can self-adapt and scale in a cost-efficient manner.
For our experiments, we considered k-means as clustering algorithm, that is a simple but popular algorithm, widely used in many data mining applications.
Clustering outputs are evaluated using four internal techniques: AIC, Dunn, Davies-Bouldin and Silhouette and an external evaluation: AdjustedRand.
We then performed a correlation t-test in order to validate and benchmark our internal techniques against AdjustedRand.
Defined the best evaluation criteria, the main challenge of k-means is setting the right value of k, that represents the number of clusters, and the distance measure used to compute distances of each pair of points in the data space.
To address this problem we propose an implementation of the Genetic Evolutionary Algorithm that heuristically finds out an optimal configuration of our clustering algorithm.
In order to improve performances, we implemented a parallel version of genetic algorithm developing a REST API and deploying several instances in the Amazon Cloud Computing (EC2) infrastructure.
In conclusion, with this research we contributed building and analysing TunUp, an open solution for evaluation, validation and tuning of data clustering algorithms, with a particularly focused on cloud services.
Our experiments show the quality and efficiency of tuning k-means on a set of public datasets.
The research also provides a Roadmap that gives indications of how the current system should be extended and utilized for future clustering applications, such as: Tuning of existing clustering algorithms, Supporting new algorithms design, Evaluation and comparison of different algorithms.
Anomaly detection using deep one class classifier홍배 김
- Anomaly detection의 다양한 방법을 소개하고
- Support Vector Data Description (SVDD)를 이용하여
cluster의 모델링을 쉽게 하도록 cluster의 형상을 단순화하고
boundary근방의 애매한 point를 처리하는 방법 소개
MVPA with SpaceNet: sparse structured priorsElvis DOHMATOB
The GraphNet (aka S-Lasso), as well as other “sparsity + structure” priors like TV (Total-Variation), TV-L1, etc., are not easily applicable to brain data because of technical problems
relating to the selection of the regularization parameters. Also, in
their own right, such models lead to challenging high-dimensional optimization problems. In this manuscript, we present some heuristics for speeding up the overall optimization process: (a) Early-stopping, whereby one halts the optimization process when the test score (performance on leftout data) for the internal cross-validation for model-selection stops improving, and (b) univariate feature-screening, whereby irrelevant (non-predictive) voxels are detected and eliminated before the optimization problem is entered, thus reducing the size of the problem. Empirical results with GraphNet on real MRI (Magnetic Resonance Imaging) datasets indicate that these heuristics are a win-win strategy, as they add speed without sacrificing the quality of the predictions. We expect the proposed heuristics to work on other models like TV-L1, etc.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
2. INTRO NOTES
4 days
two lectures, two practice seminars every day
this is introductory track to machine learning
kaggle competition!
3. WHAT IS ML ABOUT?
Inference of statistical dependencies which give us ability to
predict
Data is cheap, knowledge is precious
4. WHERE ML IS CURRENTLY USED?
Search engines, spam detection
Security: virus detection, DDOS defense
Computer vision and speech recognition
Market basket analysis, Customer relationship management
(CRM)
Credit scoring, fraud detection
Health monitoring
Churn prediction
... and hundreds more
5. ML IN HIGH ENERGY PHYSICS
High-level triggers (LHCb trigger system: )
Particle identification
Tagging
Stripping line
Analysis
40MHz → 5kHz
Different data is used on different stages
6. GENERAL NOTION
In supervised learning the training data is represented as set
of pairs
,xi yi
is index of event
is vector of features available for event
is target — the value we need to predict
i
xi
yi
7. CLASSIFICATION EXAMPLE
, if finite set
on the plot: ,
Examples:
defining type of particle (or decay
channel)
— binary classification, 1
is signal, 0 is bck
∈ Yyi Y
∈xi ℝ2
∈ {0, 1, 2}yi
Y = {0, 1}
8. REGRESSION
y ∈ ℝ
Examples:
predicting price of house by it's positions
predicting number of customers / money income
reconstructing real momentum of particle
Why need automatic classification/regression?
in applications up to thousands of features
higher quality
much faster adaptation to new problems
9. CLASSIFICATION BASED ON
NEAREST NEIGHBOURS
Given training set of objects and their labels we
predict the label for new observation.
{ , }xi yi
= , j = arg ρ(x, )ŷ yj min
i
xi
13. OVERFITTING
what is the quality of classification on training dataset when
?
answer: it is ideal (closest neighbor is event itself)
quality is lower when
this doesn't mean is the best,
it means we cannot use training events to estimate quality
when classifier's decision rule is too complex and captures
details from training data that are not relevant to
distribution, we call this overfitting (more details tomorrow)
k = 1
k > 1
k = 1
17. COMPUTATIONAL COMPLEXITY
Given that dimensionality of space is and there are
training samples:
d n
training time ~ O(save a link to data)
prediction time: for each samplen × d
19. BALL TREE
training time ~
prediction time ~ for each sample
O(d × n log(n))
log(n) × d
Other option exist: KD-tree.
20. OVERVIEW OF KNN
1. Awesomely simple classifier and regressor
2. Have too optimistic quality on training data
3. Quite slow, though optimizations exist
4. Hard times with data of high dimensions
5. Too sensitive to scale of features
21. SENSITIVITY TO SCALE OF FEATURES
Euclidean distance:
ρ(x, y = ( − + ( − + ⋯ + ( −)
2
x1 y1 )
2
x2 y2 )
2
xd yd )
2
Change scale fo first feature:
ρ(x, y = (10 − 10 + ( − + ⋯ + ( −)
2
x1 y1 )
2
x2 y2 )
2
xd yd )
2
ρ(x, y ∼ 100( −)
2
x1 y1 )
2
Scaling of features frequently increases quality.
22. DISTANCE FUNCTION MATTERS
Minkowski distance
Canberra
Cosine metric
(x, y) = ( −ρp
∑i
xi yi )
p
ρ(x, y) = ∑i
| − |xi yi
| | + | |xi yi
ρ(x, y) =
< x, y >
|x| |y|
25. MEASURING QUALITY OF BINARY
CLASSIFICATION
The classifier's output in binary classification is real variable
Which classifier is better?
All of them are identical
28. ROC CURVE
Contains important information:
all possible combinations of signal and background
efficiencies you may achieve by setting threshold
Particular values of thresholds (and initial pdfs) don't
matter, ROC curve doesn't contain this information
ROC curve = information about order of events:
Comparison of algorithms should be based on information
from ROC curve
s s b s b ... b b s b b
32. STATISTICAL MACHINE LEARNING
Machine learning we use in practice is based on statistics
1. Main assumption: the data is generated from probabilistic
distribution:
2. Does there really exist the distribution of people / pages?
3. In HEP these distributions do exist
p(x, y)
33. OPTIMAL CLASSIFICATION. OPTIMAL
BAYESIAN CLASSIFIER
Assuming that we know real distributions we
reconstruct using Bayes' rule
p(x, y)
p(y|x) = =
p(x, y)
p(x)
p(y)p(x|y)
p(x)
=
p(y = 1 | x)
p(y = 0 | x)
p(y = 1) p(x | y = 1)
p(y = 0) p(x | y = 0)
LEMMA (NEYMAN–PEARSON):
p(y = 1 | x)
34. The best classification quality is provided by
(optimal bayesian classifier)
p(y = 0 | x)
OPTIMAL BINARY CLASSIFICATION
Optimal bayesian classifier has highest possible ROC curve.
Since the classification quality depends only on order,
gives optimal classification quality too!p(y = 1 | x)
=
p(y = 1 | x)
p(y = 0 | x)
p(y = 1) p(x | y = 1)
p(y = 0) p(x | y = 0)
35. FISHER'S QDA (QUADRATIC DISCRIMINANT
ANALYSIS)
Reconstructing probabilities from
data, assuming those are multidimensional normal
distributions:
p(x | y = 1), p(x | y = 0)
p(x | y = 0) ∼ ( , )μ0 Σ
0
p(x | y = 1) ∼ ( , )μ1 Σ
1
36.
37. QDA COMPLEXITY
samples, dimensionsn d
training takes
computing covariation matrix
inverting covariation matrix
prediction takes for each sample
O(n + )d
2
d
3
O(n )d
2
O( )d
3
O( )d
2
f (x) = exp
(
− (x − μ (x − μ)
)
1
(2π |Σ)
k/2
|
1/2
1
2
)
T
Σ
−1
38. QDA
simple decision rule
fast prediction
many parameters to reconstruct in high dimensions
data almost never has gaussian distribution
39. WHAT ARE THE PROBLEMS WITH
GENERATIVE APPROACH?
Generative approach: trying to reconstruct , then use
it to predict.
p(x, y)
Real life distributions hardly can be reconstructed
Especially in high-dimensional spaces
So, we switch to discriminative approach: guessing p(y|x)
40. This is (finding parameters ).
LINEAR DECISION RULE
Decision function is linear:
d(x) =< w, x > +w0
{
d(x) > 0,
d(x) < 0,
class + 1
class − 1
parametric model w, w0
41. FINDING OPTIMAL PARAMETERS
A good initial guess: get such , that error of
classification is minimal ([true] = 1, [false] = 0):
Discontinuous optimization (arrrrgh!)
Let's make decision rule smooth
w, w0
= [ ≠ sgn(d( ))]
∑
i∈events
yi xi
(x)p+1
(x)p−1
= f (d(x))
= 1 − (x)p+1
⎧
⎩
⎨
⎪
⎪
f (0) = 0.5
f (x) > 0.5
f (x) < 0.5
if x > 0
if x < 0
42. LOGISTIC FUNCTION
a smooth step rule.
σ(x) = =
e
x
1 + e
x
1
1 + e
−x
PROPERTIES
1. monotonic,
2.
3.
4.
σ(x) ∈ (0, 1)
σ(x) + σ(−x) = 1
(x) = σ(x)(1 − σ(x))σ′
2 σ(x) = 1 + tanh(x/2)
44. Optimizing log-likelihood (with probabilities obtained with
logistic function)
LOGISTIC REGRESSION
d(x)
(x)p+1
(x)p−1
=
=
=
< w, x > +w0
σ(d(x))
σ(−d(x))
= − ln( ( )) = L( , ) → min
1
N ∑
i∈events
pyi
xi
1
N ∑
i
xi yi
45. Exercise: find expression and build plot for L( , )xi yi
DATA SCIENTIST PIPELINE
1. Experiments in appropriate high-level language or
environment
2. After experiments are over — implement final algorithm in
low-level language (C++, CUDA, FPGA)
Second point is not always needed.
