Slides of the course that I gave at the HBM 2012 connectome course on brain network modelling methods, with a focus on extracting connectivity graphs from correlation matrices and comparing them.
This presentation Neural Network will help you understand what is a neural network, how a neural network works, what can the neural network do, types of neural network and a use case implementation on how to classify between photos of dogs and cats. Deep Learning uses advanced computing power and special types of neural networks and applies them to large amounts of data to learn, understand, and identify complicated patterns. Automatic language translation and medical diagnoses are examples of deep learning. Most deep learning methods involve artificial neural networks, modeling how our brains work. Neural networks are built on Machine Learning algorithms to create an advanced computation model that works much like the human brain. This neural network tutorial is designed for beginners to provide them the basics of deep learning. Now, let us deep dive into these slides to understand how a neural network actually work.
Below topics are explained in this neural network presentation:
1. What is Neural Network?
2. What can Neural Network do?
3. How does Neural Network work?
4. Types of Neural Network
5. Use case - To classify between the photos of dogs and cats
Simplilearn’s Deep Learning course will transform you into an expert in deep learning techniques using TensorFlow, the open-source software library designed to conduct machine learning & deep neural network research. With our deep learning course, you'll master deep learning and TensorFlow concepts, learn to implement algorithms, build artificial neural networks and traverse layers of data abstraction to understand the power of data and prepare you for your new role as deep learning scientist.
Why Deep Learning?
It is one of the most popular software platforms used for deep learning and contains powerful tools to help you build and implement artificial neural networks.
Advancements in deep learning are being seen in smartphone applications, creating efficiencies in the power grid, driving advancements in healthcare, improving agricultural yields, and helping us find solutions to climate change. With this Tensorflow course, you’ll build expertise in deep learning models, learn to operate TensorFlow to manage neural networks and interpret the results.
You can gain in-depth knowledge of Deep Learning by taking our Deep Learning certification training course. With Simplilearn’s Deep Learning course, you will prepare for a career as a Deep Learning engineer as you master concepts and techniques including supervised and unsupervised learning, mathematical and heuristic aspects, and hands-on modeling to develop algorithms.
Learn more at: https://www.simplilearn.com
Hybrid neural networks for time series learning by Tian Guo, EPFL, SwitzerlandEuroIoTa
Time series is prevalent in the IoT environment and used for monitoring the evolving behavior of involved entities or objects over time. Analyzing and mining such time series data serve for revealing insightful long-term and instantaneous information behind the data, e.g., trend, event, correlation and causality and so on.
Inspired by the recent successes of neural networks, in this talk we present a novel end-to-end hybrid neural network for learning the local and global contextual features of time series. In particular, we explore the idea of hybrid neural networks in a specific time series learning problem, namely learning the local trend of time series. Local trends of time series characterize the intermediate upward and downward patterns of time series. Learning and forecasting the local trend in time series data play an important role in many real applications, ranging from investing in the stock market, resource allocation in data centers and load schedule in the smart grid. We propose TreNet, a hybrid neural network which leverages convolutional neural networks (CNNs) to extract salient features from local raw data of time series and a long-short term memory recurrent neural network (LSTM) to capture such dependency of local trends. Preliminary experimental results on real datasets demonstrate the superiority of TreNet over conventional CNN, LSTM, HMM method and various kernel based baselines.
This presentation Neural Network will help you understand what is a neural network, how a neural network works, what can the neural network do, types of neural network and a use case implementation on how to classify between photos of dogs and cats. Deep Learning uses advanced computing power and special types of neural networks and applies them to large amounts of data to learn, understand, and identify complicated patterns. Automatic language translation and medical diagnoses are examples of deep learning. Most deep learning methods involve artificial neural networks, modeling how our brains work. Neural networks are built on Machine Learning algorithms to create an advanced computation model that works much like the human brain. This neural network tutorial is designed for beginners to provide them the basics of deep learning. Now, let us deep dive into these slides to understand how a neural network actually work.
Below topics are explained in this neural network presentation:
1. What is Neural Network?
2. What can Neural Network do?
3. How does Neural Network work?
4. Types of Neural Network
5. Use case - To classify between the photos of dogs and cats
Simplilearn’s Deep Learning course will transform you into an expert in deep learning techniques using TensorFlow, the open-source software library designed to conduct machine learning & deep neural network research. With our deep learning course, you'll master deep learning and TensorFlow concepts, learn to implement algorithms, build artificial neural networks and traverse layers of data abstraction to understand the power of data and prepare you for your new role as deep learning scientist.
Why Deep Learning?
It is one of the most popular software platforms used for deep learning and contains powerful tools to help you build and implement artificial neural networks.
Advancements in deep learning are being seen in smartphone applications, creating efficiencies in the power grid, driving advancements in healthcare, improving agricultural yields, and helping us find solutions to climate change. With this Tensorflow course, you’ll build expertise in deep learning models, learn to operate TensorFlow to manage neural networks and interpret the results.
You can gain in-depth knowledge of Deep Learning by taking our Deep Learning certification training course. With Simplilearn’s Deep Learning course, you will prepare for a career as a Deep Learning engineer as you master concepts and techniques including supervised and unsupervised learning, mathematical and heuristic aspects, and hands-on modeling to develop algorithms.
Learn more at: https://www.simplilearn.com
Hybrid neural networks for time series learning by Tian Guo, EPFL, SwitzerlandEuroIoTa
Time series is prevalent in the IoT environment and used for monitoring the evolving behavior of involved entities or objects over time. Analyzing and mining such time series data serve for revealing insightful long-term and instantaneous information behind the data, e.g., trend, event, correlation and causality and so on.
Inspired by the recent successes of neural networks, in this talk we present a novel end-to-end hybrid neural network for learning the local and global contextual features of time series. In particular, we explore the idea of hybrid neural networks in a specific time series learning problem, namely learning the local trend of time series. Local trends of time series characterize the intermediate upward and downward patterns of time series. Learning and forecasting the local trend in time series data play an important role in many real applications, ranging from investing in the stock market, resource allocation in data centers and load schedule in the smart grid. We propose TreNet, a hybrid neural network which leverages convolutional neural networks (CNNs) to extract salient features from local raw data of time series and a long-short term memory recurrent neural network (LSTM) to capture such dependency of local trends. Preliminary experimental results on real datasets demonstrate the superiority of TreNet over conventional CNN, LSTM, HMM method and various kernel based baselines.
Introduction to Graph Neural Networks: Basics and Applications - Katsuhiko Is...Preferred Networks
This presentation explains basic ideas of graph neural networks (GNNs) and their common applications. Primary target audiences are students, engineers and researchers who are new to GNNs but interested in using GNNs for their projects. This is a modified version of the course material for a special lecture on Data Science at Nara Institute of Science and Technology (NAIST), given by Preferred Networks researcher Katsuhiko Ishiguro, PhD.
Deep Learning with Audio Signals: Prepare, Process, Design, ExpectKeunwoo Choi
Is deep learning Alchemy? No! But it heavily relies on tips and tricks, a set of common wisdom that probably works for similar problems. In this talk, I’ll introduce what the audio/music research societies have discovered while playing with deep learning when it comes to audio classification and regression -- how to prepare the audio data and preprocess them, how to design the networks (or choose which one to steal from), and what we can expect as a result.
Jekaterina Novikova - Machine Learning Methods in Detecting Alzheimer’s Disea...MLconf
Machine Learning Methods in Detecting Alzheimer’s Disease from Speech and Language
Alzheimer's disease affects millions of people worldwide, and it is important to predict the disease as early and as accurate as possible. In this talk, I will discuss development of novel ML models that help classifying healthy people from those who develop Alzheimer's, using short samples of human speech. As an input to the model, features of different modalities are extracted from speech audio samples and transcriptions: (1) syntactic measures, such as e.g. production rules extracted from syntactic parse trees, (2) lexical measures, such as e.g. features of lexical richness and complexity and lexical norms, and (3) acoustic measures, such as e.g. standard Mel-frequency cepstral coefficients. I will present the ML model that detects cognitive impairment by reaching agreement among modalities. The resulting model is able to achieve state of the art performance in both supervised and semi-supervised manner, using manual transcripts of human speech. Additionally, I will discuss potential limitations of any fully-automated speech-based Alzheimer's disease detection model, focusing mostly on the analysis of the impact of a not-so-accurate automatic speech recognition (ASR) on the classification performance. To illustrate this, I will present the experiments with controlled amounts of artificially generated ASR errors and explain how the deletion errors affect Alzheimer's detection performance the most, due to their impact on the features of syntactic and lexical complexity.
The presentation focuses on one of the important aspects of Neurophysiology-- The sesnsorimotor integration for planning and execution of movement.
It highlights on the brain regions associated with motor functions, the crosstalk between association areas, hierarchical levels of movement execution and the diseases related to it.
Slides for a talk about Graph Neural Networks architectures, overview taken from very good paper by Zonghan Wu et al. (https://arxiv.org/pdf/1901.00596.pdf)
Intro to Complex Networks was a workshop for the master of students (M.Sc.) at the University of Zanjan. It was about Protein-Protein Interaction networks and some graph concepts.
Introduction to Graph Neural Networks: Basics and Applications - Katsuhiko Is...Preferred Networks
This presentation explains basic ideas of graph neural networks (GNNs) and their common applications. Primary target audiences are students, engineers and researchers who are new to GNNs but interested in using GNNs for their projects. This is a modified version of the course material for a special lecture on Data Science at Nara Institute of Science and Technology (NAIST), given by Preferred Networks researcher Katsuhiko Ishiguro, PhD.
Deep Learning with Audio Signals: Prepare, Process, Design, ExpectKeunwoo Choi
Is deep learning Alchemy? No! But it heavily relies on tips and tricks, a set of common wisdom that probably works for similar problems. In this talk, I’ll introduce what the audio/music research societies have discovered while playing with deep learning when it comes to audio classification and regression -- how to prepare the audio data and preprocess them, how to design the networks (or choose which one to steal from), and what we can expect as a result.
Jekaterina Novikova - Machine Learning Methods in Detecting Alzheimer’s Disea...MLconf
Machine Learning Methods in Detecting Alzheimer’s Disease from Speech and Language
Alzheimer's disease affects millions of people worldwide, and it is important to predict the disease as early and as accurate as possible. In this talk, I will discuss development of novel ML models that help classifying healthy people from those who develop Alzheimer's, using short samples of human speech. As an input to the model, features of different modalities are extracted from speech audio samples and transcriptions: (1) syntactic measures, such as e.g. production rules extracted from syntactic parse trees, (2) lexical measures, such as e.g. features of lexical richness and complexity and lexical norms, and (3) acoustic measures, such as e.g. standard Mel-frequency cepstral coefficients. I will present the ML model that detects cognitive impairment by reaching agreement among modalities. The resulting model is able to achieve state of the art performance in both supervised and semi-supervised manner, using manual transcripts of human speech. Additionally, I will discuss potential limitations of any fully-automated speech-based Alzheimer's disease detection model, focusing mostly on the analysis of the impact of a not-so-accurate automatic speech recognition (ASR) on the classification performance. To illustrate this, I will present the experiments with controlled amounts of artificially generated ASR errors and explain how the deletion errors affect Alzheimer's detection performance the most, due to their impact on the features of syntactic and lexical complexity.
The presentation focuses on one of the important aspects of Neurophysiology-- The sesnsorimotor integration for planning and execution of movement.
It highlights on the brain regions associated with motor functions, the crosstalk between association areas, hierarchical levels of movement execution and the diseases related to it.
Slides for a talk about Graph Neural Networks architectures, overview taken from very good paper by Zonghan Wu et al. (https://arxiv.org/pdf/1901.00596.pdf)
Intro to Complex Networks was a workshop for the master of students (M.Sc.) at the University of Zanjan. It was about Protein-Protein Interaction networks and some graph concepts.
The presentation that accompanied the paper submission to ITAB2010. The paper will become available from IEEE Xplore (http://ieeexplore.ieee.org/Xplore/dynhome.jsp)
Data science calls for rapid experimentation and building intuitions from the data. Yet, data science also underpins crucial decisions and operational logic. Writing production-ready and robust statistical analysis without cognitive overhead may seem a conundrum. I will explore simple, and less simple, practices for fast turn around and consolidation of data-science code. I will discuss how these considerations led to the design of scikit-learn, that enables easy machine learning yet is used in production. Finally, I will mention some scikit-learn gems, new or forgotten.
Lean Manga describing The Lean Brain.
For more information visit www.hoshinkanriforest.com or read the book The Hoshin Kanri Forest: Lean Strategic Organizational Design
Learning and comparing multi-subject models of brain functional connecitivityGael Varoquaux
High-level brain function arises through functional interactions. These can be mapped via co-fluctuations in activity observed in functional imaging.
First, I first how spatial maps characteristic of on-going activity in a population of subjects can be learned using multi-subject decomposition models extending the popular Independent Component Analysis. These methods single out spatial atoms of brain activity: functional networks or brain regions. With a probabilistic model of inter-subject variability, they open the door to building data-driven atlases of on-going activity.
Subsequently, I discuss graphical modeling of the interactions between brain regions. To learn highly-resolved large scale individual
graphical models models, we use sparsity-inducing penalizations introducing a population prior that mitigates the data scarcity at the subject-level. The corresponding graphs capture better the community structure of brain activity than single-subject models or group averages.
Finally, I address the detection of connectivity differences between subjects. Explicit group variability models of the covariance structure can be used to build optimal edge-level test statistics. On stroke patients resting-state data, these models detect patient-specific functional connectivity perturbations.
Connectomics: Parcellations and Network Analysis MethodsGael Varoquaux
Simple tutorial on methods for functional connectome analysis: learning regions, extracting functional signal, inferring the network structure, and comparing it across subjects.
Estimating Functional Connectomes: Sparsity’s Strength and LimitationsGael Varoquaux
Talk given at the OHBM 2017 education course.
I present the challenges and techniques to estimating meaningful brain functional connectomes from fMRI: why sparsity in inverse covariance leads to models that can interpreted as interactions between regions.
Then I discuss the limitations of sparse estimators and introduce shrinkage as an alternative. Finally, I discuss how to compare multiple functional connectomes.
Machine learning for functional connectomesGael Varoquaux
A tutorial on using machine-learning for functional-connectomes, for instance on resting-state fMRI. This is typically useful for population imaging: comparing traits or conditions across subjects.
Brain reading, compressive sensing, fMRI and statistical learning in PythonGael Varoquaux
Talk given at Gipsa-lab on using machine learning to learn from fMRI brain patterns and regions related to behavior. This talks focuses on the signal and inverse-problem aspects of the equation, as well as on the software.
Talk giving at PRNI 2016 for the paper https://arxiv.org/pdf/1606.06439v1.pdf
Abstract — Spatially-sparse predictors are good models for
brain decoding: they give accurate predictions and their weight
maps are interpretable as they focus on a small number of
regions. However, the state of the art, based on total variation or
graph-net, is computationally costly. Here we introduce sparsity
in the local neighborhood of each voxel with social-sparsity, a
structured shrinkage operator. We find that, on brain imaging
classification problems, social-sparsity performs almost as well as
total-variation models and better than graph-net, for a fraction
of the computational cost. It also very clearly outlines predictive
regions. We give details of the model and the algorithm
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.
Integrability and weak diffraction in a two-particle Bose-Hubbard model jiang-min zhang
We report a bound state, which is embedded in the continuum spectrum, of the one-dimensional two-particle (Bose or Fermion) Hubbard model with an impurity potential. The state has the Bethe-ansatz form, although this model is nonintegrable. Moreover, for a wide region in parameter space, its energy is located in the continuum band. A remarkable advantage of this state with respect to similar states in other systems is the simple analytical form of the wave function and eigenvalue. This state can be tuned in and out of the continuum continuously.
Representation of of Stochastic Processes in Stochastic Processes in Real and Spectral Domains Real and Spectral Domains and and Monte Monte-Carlo sampling
Network and risk spillovers: a multivariate GARCH perspectiveSYRTO Project
M. Billio, M. Caporin, L. Frattarolo, L. Pelizzon: “Network and risk spillovers: a multivariate GARCH perspective”.
Final SYRTO Conference - Université Paris1 Panthéon-Sorbonne
February 19, 2016
Evaluating machine learning models and their diagnostic valueGael Varoquaux
Model evaluation is, in my opinion, the most overlooked step of the machine-learning pipeline. Reliably estimating a model's performance for a given purpose is crucial and difficult. In this talk, I first discuss choosing metric informative for the application, stressing the importance of the class prevalence in classification settings. I will then discussing procedures to estimate the generalization performance, drawing a distinction between evaluating a learning procedure or a prediction rule, and discussing how to give confidence intervals to the performance estimates.
Measuring mental health with machine learning and brain imagingGael Varoquaux
The study of mental health relies vastly on behavior testing and questionnaires. I discuss how
machine learning on large brain-imaging cohorts can open new alleys for markers of mental health. My
claims are that challenges are the amount of diagnosed conditions rather than heterogeneity of the
conditions and that we should turn to proxy labels. I discuss another fundamental challenge to this
agenda: the external and construct validity of brain-imaging based markers.
A tutorial on machine learning to build prediction models with missing values.
The slides cover both theoretical results (statistical learning) and practical advice, with a focus on implementation in Python with scikit-learn
Dirty data science machine learning on non-curated dataGael Varoquaux
These slides are a one-hour course on machine learning with non-curated data.
According to industry surveys, the number one hassle of data scientists is cleaning the data to analyze it. Here, I survey what "dirtyness" forces time-consuming cleaning. We will then cover two specific aspects of dirty data: non-normalized entries and missing values. I show how, for these two problems, machine-learning practice can be adapted to work directly on a data table without curation. The normalization problem can be tackled by adapting methods from natural language processing. The missing-values problem will lead us to revisit classic statistical results in the setting of supervised learning.
Representation learning in limited-data settingsGael Varoquaux
A 4-hour long didactic course on simple notions of representations and how to use them in limited-data settings:
- A supervised learning point of view, giving intuitions and math on what are representations are why they matter
- Building simple unsupervised learning models to extract representation: from matrix decomposition for signals to embeddings of entities
- Evaluating models in limited-data settings, often a bottleneck
This slide-deck was given as a course at the 2021 DeepLearn summer school.
Better neuroimaging data processing: driven by evidence, open communities, an...Gael Varoquaux
My current thoughts about methods validity and design in brain imaging.
Data processing is a significant part of a neuroimaging study. The choice of corresponding methods and tools is crucial. I will give an opinionated view how on a path to building better data processing for neuroimaging. I will take examples on endeavors that I contributed to: defining standards for functional-connectivity analysis, the nilearn neuroimaging tool, the scikit-learn machine-learning toolbox -an industry standard with a million regular users. I will cover not only the technical process -statistics, signal processing, software engineering- but also the epistemology of methods development. Methods govern our results, they are more than a technical detail.
Functional-connectome biomarkers to meet clinical needs?Gael Varoquaux
Extracting Functional-Connectome Biomarkers with Machine Learning: a talk in the symposium on how do current predictive connectivity models meet clinician’s needs?
This talk is a bit provocative and first sets visions, before bringing a few technical suggestions
Atlases of cognition with large-scale human brain mappingGael Varoquaux
Cognitive neuroscience uses neuroimaging to identify brain systems engaged in specific cognitive tasks. However, linking unequivocally brain systems with cognitive functions is difficult: each task probes only a small number of facets of cognition, while brain systems are often engaged in many tasks. We develop a new approach to generate a functional atlas of cognition, demonstrating brain systems selectively associated with specific cognitive functions. This approach relies upon an ontology that defines specific cognitive functions and the relations between them, along with an analysis scheme tailored to this ontology. Using a database of thirty neuroimaging studies, we show that this approach provides a highly-specific atlas of mental functions, and that it can decode the mental processes engaged in new tasks.
Similarity encoding for learning on dirty categorical variablesGael Varoquaux
For statistical learning, categorical variables in a table are usually considered as discrete entities and encoded separately to feature vectors, e.g., with one-hot encoding. "Dirty" non-curated data gives rise to categorical variables with a very high cardinality but redundancy: several categories reflect the same entity. In databases, this issue is typically solved with a deduplication step. We show that a simple approach that exposes the redundancy to the learning algorithm brings significant gains. We study a generalization of one-hot encoding, similarity encoding, that builds feature vectors from similarities across categories. We perform a thorough empirical validation on non-curated tables, a problem seldom studied in machine learning. Results on seven real-world datasets show that similarity encoding brings significant gains in prediction in comparison with known encoding methods for categories or strings, notably one-hot encoding and bag of character n-grams. We draw practical recommendations for encoding dirty categories: 3-gram similarity appears to be a good choice to capture morphological resemblance. For very high-cardinality, dimensionality reduction significantly reduces the computational cost with little loss in performance: random projections or choosing a subset of prototype categories still outperforms classic encoding approaches.
Towards psychoinformatics with machine learning and brain imagingGael Varoquaux
Informatics in the psychological sciences brings fascinating challenges as mental processes or pathologies have fuzzy definition and are hard to quantify. Brain imaging brings rich data on the neural substrate of these concepts, yet it is a non trivial link.
The goal of this presentation is to put forward basic ideas of "psychoinformatics", using advanced processing on brain images to quantify better the elements of psychology.
It discusses how machine learning can bridge brain images to behavior: to describe better mental processes involved in brain activity, or to extract biomarkers of pathologies, individual traits, or cognition.
Simple representations for learning: factorizations and similarities Gael Varoquaux
Real-life data seldom comes in the ideal form for statistical learning.
This talk focuses on high-dimensional problems for signals and
discrete entities: when dealing with many, correlated, signals or
entities, it is useful to extract representations that capture these
correlations.
Matrix factorization models provide simple but powerful representations. They are used for recommender systems across discrete entities such as users and products, or to learn good dictionaries to represent images. However they entail large computing costs on very high-dimensional data, databases with many products or high-resolution images. I will present an
algorithm to factorize huge matrices based on stochastic subsampling that gives up to 10-fold speed-ups [1].
With discrete entities, the explosion of dimensionality may be due to variations in how a smaller number of categories are represented. Such a problem of "dirty categories" is typical of uncurated data sources. I will discuss how encoding this data based on similarities recovers a useful category structure with no preprocessing. I will show how it interpolates between one-hot encoding and techniques used in character-level natural language processing.
[1] Stochastic subsampling for factorizing huge matrices, A Mensch, J Mairal, B Thirion, G Varoquaux, IEEE Transactions on Signal Processing 66 (1), 113-128
[2] Similarity encoding for learning with dirty categorical variables. P Cerda, G Varoquaux, B Kégl Machine Learning (2018): 1-18
A tutorial on Machine Learning, with illustrations for MR imagingGael Varoquaux
Machine learning builds predictive models from the data. It is massive used on medical images these days, for a variety of applications ranging from segmentation to diagnosis.
This is an introductory tutorial to machine learning from giving intuitions on the statistical point of view. It introduce the methodology, the concepts behind the central models, the validation framework and some caveats to look for.
It also discusses some applications to drawing conclusions from brain imaging, and use these applications to highlight various technical aspects to running machine learning models on high-dimensional data such as medical imaging.
Scikit-learn and nilearn: Democratisation of machine learning for brain imagingGael Varoquaux
This talk describe our efforts to bring easily usable machine learning to brain mapping. It covers both questions that machine learning can answer as well as two softwares developed to facilitate machine learning and it's application to neuroimaging.
Computational practices for reproducible scienceGael Varoquaux
Reconciling bleeding-edge scientific results and reproducible research may seem a conundrum in our fast-paced high-pressure academic world. I discuss the practices that I found useful in computational work. At a high level, it is important to navigate the space between rapid experimentation and industrial-grade software development. I advocate adopting more and more software-engineering best practices as a project matures. I will also discuss how to turn the computational work into libraries, and to ensure the quality of the resulting libraries. And I conclude on how those libraries need to fit in the larger picture of the exercise of research to give better science.
Slides for my keynote at Scipy 2017
https://youtu.be/eVDDL6tgsv8
Computing has been driving forward a revolution in how science and technology can solve new problems. Python has grown to be a central player in this game, from computational physics to data science. I would like to explore some lessons learned doing science with Python as well as doing Python libraries for science. What are the ingredients that the scientists need? What technical and project-management choices drove the success of projects I've been involved with? How do these demands and offers shape our ecosystem?
In this talk, I'd like to share a few thoughts on how we code for science and innovation, with the modest goal of changing the world.
Scientist meets web dev: how Python became the language of dataGael Varoquaux
Python started as a scripting language, but now it is the new trend everywhere and in particular for data science, the latest rage of computing. It didn’t get there by chance: tools and concepts built by nerdy scientists and geek sysadmins provide foundations for what is said to be the sexiest job: data scientist.
In this talk I give a personal perspective on the progress of the scientific Python ecosystem, from numerical physics to data mining. What made Python suitable for science; Why the cultural gap between scientific Python and the broader Python community turned out to be a gold mine; And where this richness might lead us.
The talk will discuss low-level and high-level technical aspects, such as how the Python world makes it easy to move large chunks of number across code. It will touch upon current technical details that make scikit-learn and joblib stand.
Machine learning and cognitive neuroimaging: new tools can answer new questionsGael Varoquaux
Machine learning is geared towards prediction. However, aside diagnosis or prognosis in the clinics, cognitive neuroimaging strives for uncovering insights from the data, rather than minimizing prediction error. I review various inferences on brain function that have been drawn using pattern recognition techniques, focusing on decoding. In particular, I discuss using generalization as a test for information, multivariate analysis to interpret overlapping activation patterns, and decoding for principled reverse inference. I give each time a statistical view and a cognitive imaging view.
Personal point of view on scikit-learn: past, present, and future.
This talks gives a bit of history, mentions exciting development, and a personal vision on the future.
Inter-site autism biomarkers from resting state fMRIGael Varoquaux
We present an automated pipeline to learn predictive biomarkers from resting-state fMRI. We apply it to classifying autism on unseen sites, demonstrating the feasibility of biomarkers on weakly standardized functional imaging data.
We study the steps of the pipeline that are important to predict and can show that 1) the choice of atlas is the most important choice. Ideally the atlas should be made of functional regions learned from the data. 2) "tangent space" parametrization of the connectivity is the best performer.
We conclude on general recommendations for predictive biomarkers from resting-state fMRI
Brain maps from machine learning? Spatial regularizationsGael Varoquaux
Pattern Recognition for NeuroImaging (PR4NI)
We will show empirically how the pattern recognition techniques-commonly used, such as SVMs, provide low-quality brain maps, eventhough they give very good prediction accuracy. We will give an overview of recently developed techniques to impose priors on patterns particularly well suited to neuroimaging: selecting a small number of spatially-structured predictive brain regions. These tools reconcile machine learning with
brain mapping by giving maps more useful to draw neuroscientific conclusions. In addition, they are more robust to cross-individuals spatial variability and thus generalize well across subjects.
Essentials of Automations: The Art of Triggers and Actions in FMESafe Software
In this second installment of our Essentials of Automations webinar series, we’ll explore the landscape of triggers and actions, guiding you through the nuances of authoring and adapting workspaces for seamless automations. Gain an understanding of the full spectrum of triggers and actions available in FME, empowering you to enhance your workspaces for efficient automation.
We’ll kick things off by showcasing the most commonly used event-based triggers, introducing you to various automation workflows like manual triggers, schedules, directory watchers, and more. Plus, see how these elements play out in real scenarios.
Whether you’re tweaking your current setup or building from the ground up, this session will arm you with the tools and insights needed to transform your FME usage into a powerhouse of productivity. Join us to discover effective strategies that simplify complex processes, enhancing your productivity and transforming your data management practices with FME. Let’s turn complexity into clarity and make your workspaces work wonders!
GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs.
1. Unifying Large Language Models and Knowledge Graphs: A Roadmap.
https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
In his public lecture, Christian Timmerer provides insights into the fascinating history of video streaming, starting from its humble beginnings before YouTube to the groundbreaking technologies that now dominate platforms like Netflix and ORF ON. Timmerer also presents provocative contributions of his own that have significantly influenced the industry. He concludes by looking at future challenges and invites the audience to join in a discussion.
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
Generative AI Deep Dive: Advancing from Proof of Concept to ProductionAggregage
Join Maher Hanafi, VP of Engineering at Betterworks, in this new session where he'll share a practical framework to transform Gen AI prototypes into impactful products! He'll delve into the complexities of data collection and management, model selection and optimization, and ensuring security, scalability, and responsible use.
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
Climate Impact of Software Testing at Nordic Testing DaysKari Kakkonen
My slides at Nordic Testing Days 6.6.2024
Climate impact / sustainability of software testing discussed on the talk. ICT and testing must carry their part of global responsibility to help with the climat warming. We can minimize the carbon footprint but we can also have a carbon handprint, a positive impact on the climate. Quality characteristics can be added with sustainability, and then measured continuously. Test environments can be used less, and in smaller scale and on demand. Test techniques can be used in optimizing or minimizing number of tests. Test automation can be used to speed up testing.
PHP Frameworks: I want to break free (IPC Berlin 2024)Ralf Eggert
In this presentation, we examine the challenges and limitations of relying too heavily on PHP frameworks in web development. We discuss the history of PHP and its frameworks to understand how this dependence has evolved. The focus will be on providing concrete tips and strategies to reduce reliance on these frameworks, based on real-world examples and practical considerations. The goal is to equip developers with the skills and knowledge to create more flexible and future-proof web applications. We'll explore the importance of maintaining autonomy in a rapidly changing tech landscape and how to make informed decisions in PHP development.
This talk is aimed at encouraging a more independent approach to using PHP frameworks, moving towards a more flexible and future-proof approach to PHP development.
Dr. Sean Tan, Head of Data Science, Changi Airport Group
Discover how Changi Airport Group (CAG) leverages graph technologies and generative AI to revolutionize their search capabilities. This session delves into the unique search needs of CAG’s diverse passengers and customers, showcasing how graph data structures enhance the accuracy and relevance of AI-generated search results, mitigating the risk of “hallucinations” and improving the overall customer journey.
Encryption in Microsoft 365 - ExpertsLive Netherlands 2024Albert Hoitingh
In this session I delve into the encryption technology used in Microsoft 365 and Microsoft Purview. Including the concepts of Customer Key and Double Key Encryption.
UiPath Test Automation using UiPath Test Suite series, part 5DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 5. In this session, we will cover CI/CD with devops.
Topics covered:
CI/CD with in UiPath
End-to-end overview of CI/CD pipeline with Azure devops
Speaker:
Lyndsey Byblow, Test Suite Sales Engineer @ UiPath, Inc.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
SAP Sapphire 2024 - ASUG301 building better apps with SAP Fiori.pdfPeter Spielvogel
Building better applications for business users with SAP Fiori.
• What is SAP Fiori and why it matters to you
• How a better user experience drives measurable business benefits
• How to get started with SAP Fiori today
• How SAP Fiori elements accelerates application development
• How SAP Build Code includes SAP Fiori tools and other generative artificial intelligence capabilities
• How SAP Fiori paves the way for using AI in SAP apps
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdf
Brain network modelling: connectivity metrics and group analysis
1. Advanced network modelling II:
connectivity measures, group analysis
Ga¨l Varoquaux
e INRIA, Parietal
Neurospin
Learning objectives
Extraction of the
network structure from
the observations
Statistics for comparing
correlations structures
Interpret network
structures
2. Problem setting and vocabulary
Given regions,
infer and compare
connections
Graph: set of nodes and connections
Weighted or not.
Directed or not.
Can be represented by an
adjacency matrix.
G Varoquaux 2
3. Functional network analysis: an outline
1 Signal extraction
2 Connectivity graphs
3 Comparing connections
4 Network-level summary
G Varoquaux 3
5. 1 Choice of regions
Too many regions gives
harder statistical problem:
⇒ ∼ 30 ROIs for
group-difference analysis
Nearly-overlapping regions
will mix signals
Avoid too small regions ⇒ ∼ 10mm radius
Capture different functional networks
G Varoquaux 5
6. 1 Time-series extraction
Extract ROI-average signal:
weighted-mean with weights
given by white-matter probability
Low-pass filter fMRI data
(≈ .1 Hz – .3 Hz)
Regress out confounds:
- movement parameters
- CSF and white matter signals
- Compcorr: data-driven noise identification
[Behzadi 2007]
G Varoquaux 6
7. 2 Connectivity graphs
From correlations to connections
Functional connectivity:
correlation-based statistics
G Varoquaux 7
8. 2 Correlation, covariance
For x and y centered:
1
covariance: cov(x, y) = xi yi
n i
cov(x, y)
correlation: cor(x, y) =
std(x) std(y)
Correlation is normalized: cor(x, y) ∈ [−1, 1]
Quantify linear dependence between x and y
Correlation matrix
1
functional connectivity graphs
[Bullmore1996,..., Eguiluz2005, Achard2006...]
G Varoquaux 8
9. 2 Partial correlation
Remove the effect of z by regressing it out
x/z = residuals of regression of x on z
In a set of p signals,
partial correlation: cor(xi/Z , xj/Z ), Z = {xk , k = i, j}
partial variance: var(xi/Z ), Z = {xk , k = i}
Partial correlation matrix
[Marrelec2006, Fransson2008, ...]
G Varoquaux 9
10. 2 Inverse covariance
K = Matrix inverse of the covariance matrix
On the diagonal: partial variance
Off diagonal: scaled partial correlation
Ki,j = −cor(xi/Z , xj/Z ) std(xi/Z ) std(xj/Z )
Inverse covariance matrix
[Smith 2010, Varoquaux NIPS 2010, ...]
G Varoquaux 10
11. 2 Summary: observations and indirect effects
Observations Direct connections
Correlation Partial correlation
1 1
2 2
0 0
3 3
4 4
+ Variance: + Partial variance
amount of observed signal innovation term
G Varoquaux 11
12. 2 Summary: observations and indirect effects
Observations Direct connections
Correlation Partial correlation
[Fransson 2008]: partial correlations highlight the
backbone of the default mode
G Varoquaux 11
13. 2 Inverse covariance and graphical model
Gaussian graphical models
Zeros in inverse covariance give
conditional independence
xi , xj independent
Σ−1 = 0 ⇔
i,j
conditionally on {xk , k = i, j}
Robust to the Gaussian assumption
G Varoquaux 12
14. 2 Inverse covariance matrix estimation
p nodes, n observations (e.g. fMRI volumes)
0 1
If not n p 2 , 2
ambiguities:
0 1
?
0
?
1 0 1
2 2 2
Thresholding partial correlations does not
recover ground truth independence structure
G Varoquaux 13
15. 2 Inverse covariance matrix estimation
Sparse Inverse Covariance estimators:
Joint estimation of
connections and values
Sparsity amount set by cross-validation,
to maximize likelihood of left-out data
Group-sparse inverse covariance: learn
simultaneously different values with same
connections
[Varoquaux, NIPS 2010]
G Varoquaux 14
17. 3 Comparing connections
Detecting and localizing differences
Learning sculpts the spontaneous activity of the resting
human brain [Lewis 2009]
Cor ...learn... cor differences
G Varoquaux 15
18. 3 Pair-wise tests on correlations
Correlations ∈ [−1, 1]
⇒ cannot apply Gaussian
statistics, e.g. T tests
Z-transform:
1 1 + cor
Z = arctanh cor = ln
2 1 − cor
Z (cor) is normaly-distributed:
1
For n observations, Z (cor) = N Z (cor), √
n
G Varoquaux 16
19. 3 Indirect effects: to partial or not to partial?
0 0 0 0
5 Correlation matrices 5 5 5
10 10 10 10
15 15 15 15
20 20 20 20
25 Control 25 Control 25 Control Large lesion
25
0 5 10 15 20 25 0 5 10 15 20 25 0 5 10 15 20 25 0 5 10 15 20 25
0 0 0 0
5 Partial correlation matrices
5 5 5
10 10 10 10
15 15 15 15
20 20 20 20
25 Control 25 Control 25 Control Large lesion
25
0 5 10 15 20 25 0 5 10 15 20 25 0 5 10 15 20 25 0 5 10 15 20 25
Spread-out variability in correlation matrices
Noise in partial-correlations
Strong dependence between coefficients
[Varoquaux MICCAI 2010]
G Varoquaux 17
21. 3 Graph-theoretical analysis
Summarize a graph by a few key metrics, expressing
its transport properties [Bullmore & Sporns 2009]
[Eguiluz 2005]
Permutation testing for null distribution
Use a good graph (sparse inverse covariance)
[Varoquaux NIPS 2010]
G Varoquaux 19
23. 4 Network-wide activity: generalized variance
Quantify amount of signal in Σ?
Determinant: |Σ|
= generalized variance
= volume of ellipse
G Varoquaux 21
24. 4 Integration across networks
Networks-level sub-matrices ΣA
Network integration: = log |ΣA |
Cross-talk between network A
and B: mutual information =
log |ΣAB | − log |ΣA | − log |ΣB |
Information-theoretical interpretation: entropy and
cross-entropy
[Tononi 1994, Marrelec 2008, Varoquaux NIPS 2010]
G Varoquaux 22
25. Wrapping up: pitfalls
Missing nodes
Very-correlated nodes:
e.g. nearly-overlapping regions
Hub nodes give more noisy partial
correlations
G Varoquaux 23
26. Wrapping up: take home messages
Regress confounds out from signals
Inverse covariance to capture
only direct effects
0 0
Correlations cofluctuate 5
10
5
10
⇒ localization of differences 15
20
15
20
is difficult 25
0 5 10 15 20 25
25
0 5 10 15 20 25
Networks are interesting units for
comparison
http://gael-varoquaux.info
G Varoquaux 24
27. References (not exhaustive)
[Achard 2006] A resilient, low-frequency, small-world human brain
functional network with highly connected association cortical hubs, J
Neurosci
[Behzadi 2007] A component based noise correction method (CompCor)
for BOLD and perfusion based fMRI, NeuroImage
[Bullmore 2009] Complex brain networks: graph theoretical analysis of
structural and functional systems, Nat Rev Neurosci
[Eguiluz 2005] Scale-free brain functional networks, Phys Rev E
[Frasson 2008] The precuneus/posterior cingulate cortex plays a pivotal
role in the default mode network: Evidence from a partial correlation
network analysis, NeuroImage
[Fox 2005] The human brain is intrinsically organized into dynamic,
anticorrelated functional networks, PNAS
[Lewis 2009] Learning sculpts the spontaneous activity of the resting
human brain, PNAS
[Marrelec 2006] Partial correlation for functional brain interactivity
investigation in functional MRI, NeuroImage
28. References (not exhaustive)
[Marrelec 2007] Using partial correlation to enhance structural equation
modeling of functional MRI data, Magn Res Im
[Marrelec 2008] Regions, systems, and the brain: hierarchical measures
of functional integration in fMRI, Med Im Analys
[Smith 2010] Network Modelling Methods for fMRI, NeuroImage
[Tononi 1994] A measure for brain complexity: relating functional
segregation and integration in the nervous system, PNAS
[Varoquaux MICCAI 2010] Detection of brain functional-connectivity
difference in post-stroke patients using group-level covariance modeling,
Med Imag Proc Comp Aided Intervention
[Varoquaux NIPS 2010] Brain covariance selection: better individual
functional connectivity models using population prior, Neural Inf Proc Sys
[Varoquaux 2012] Markov models for fMRI correlation structure: is
brain functional connectivity small world, or decomposable into
networks?, J Physio Paris