Tutorial @Ubicomp 2015: Bridging the Gap -- Machine Learning for Ubiquitous Computing (study design and deployment session).
A tutorial on promises and pitfalls of Machine Learning for Ubicomp (and Human Computer Interaction). From Practitioners for Practitioners.
Presenter: Mayank Goel <india.mayank@gmail.com>
video recording of talks as they wer held at Ubicomp:
https://youtu.be/LgnnlqOIXJc?list=PLh96aGaacSgXw0MyktFqmgijLHN-aQvdq
Practical Data Science with R, Second Edition takes a practice-oriented approach to explaining basic principles in the ever-expanding field of data science. You’ll jump right to real-world use cases as you apply the R programming language and statistical analysis techniques to carefully explained examples based in marketing, business intelligence, and decision support.
Take 42% off the entire book. Just enter slzumel3 into the discount code box at checkout at manning.com.
Slides for my talk at the Quantified Self Dublin meetup (https://www.meetup.com/Quantified-Self-Dublin/). Overview of my findings from a descriptive analysis of personal Fitbit sleep data.
Learn how to create and parametrized Ensembles and how to interpret them using the Partial Dependence Plot (PDP) or the Field Importance Report provided by BigML.
Top 10 Data Science Practitioner PitfallsSri Ambati
Top 10 Data Science Practitioner Pitfalls Meetup with Erin LeDell and Mark Landry on 09.09.15
- Powered by the open source machine learning software H2O.ai. Contributors welcome at: https://github.com/h2oai
- To view videos on H2O open source machine learning software, go to: https://www.youtube.com/user/0xdata
Get detail about what is machine learning is about, its applications from computational biology, web search, finance, e-commerce, social media and much more.
Practical Data Science with R, Second Edition takes a practice-oriented approach to explaining basic principles in the ever-expanding field of data science. You’ll jump right to real-world use cases as you apply the R programming language and statistical analysis techniques to carefully explained examples based in marketing, business intelligence, and decision support.
Take 42% off the entire book. Just enter slzumel3 into the discount code box at checkout at manning.com.
Slides for my talk at the Quantified Self Dublin meetup (https://www.meetup.com/Quantified-Self-Dublin/). Overview of my findings from a descriptive analysis of personal Fitbit sleep data.
Learn how to create and parametrized Ensembles and how to interpret them using the Partial Dependence Plot (PDP) or the Field Importance Report provided by BigML.
Top 10 Data Science Practitioner PitfallsSri Ambati
Top 10 Data Science Practitioner Pitfalls Meetup with Erin LeDell and Mark Landry on 09.09.15
- Powered by the open source machine learning software H2O.ai. Contributors welcome at: https://github.com/h2oai
- To view videos on H2O open source machine learning software, go to: https://www.youtube.com/user/0xdata
Get detail about what is machine learning is about, its applications from computational biology, web search, finance, e-commerce, social media and much more.
Lecture 2: Data, pre-processing and post-processing
Chapters 2,3 from the book “Introduction to Data Mining” by Tan, Steinbach, Kumar.
Chapter 1 from the book Mining Massive Datasets by Anand Rajaraman and Jeff Ullman
This is a general interest talk on how we can use artificial intelligence (specifically machine learning) to screen literature in support of systematic reviews for chemical risk assessment.
In this talk I go over some of the challenges in using machine learning to screen the literature, how we tend to approach this type of challenge (using term frequency-inverse document frequency) and several caveats. Also included is a brief introduction to undersampling, oversampling, and bagging to try to prevent challenges posed by imbalanced data.
My slides for my talk regarding machine learning and data science. Includes working examples with accompanying repo with reproducible code and data sets available.
The Simulacrum, a Synthetic Cancer DatasetCongChen35
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The Simulacrum imitates some of the data held securely by the Public Health England’s National Cancer Registration and Analysis Service.
The data in the Simulacrum is entirely artificial. It does not contain data about real patients, so users can never identify a real person. It is free to use and allows anyone who wants to use record-level cancer data to do so, safe in the knowledge that while the data feels like the real thing, there is no danger of breaching patient confidentiality.
Module 1 introduction to machine learningSara Hooker
We believe in building technical capacity all over the world.
We are building and teaching an accessible introduction to machine learning for students passionate about the power of data to do good.
Welcome to the course! These modules will teach you the fundamental building blocks and the theory necessary to be a responsible machine learning practitioner in your own community. Each module focuses on accessible examples designed to teach you about good practices and the powerful (yet surprisingly simple) algorithms we use to model data.
To learn more about our work, visit www.deltanalytics.org
Building High Available and Scalable Machine Learning ApplicationsYalçın Yenigün
The slide contains some high level information about some machine learning algorithms, cross validation and feature extraction techniques. It also contains high level techniques about high available and scalable ML products.
This talk addresses product managers and discusses basics of statistics and analytics and ways to use them effectively in their products.
Video: https://youtu.be/Rsrp040DYKg (orientation is fixed after a few minutes)
April 22, 2017 - Product Folks! Meetup Amman, Jordan
From Labelling Open data images to building a private recommender systemPierre Gutierrez
Recommender systems are paramount for e-business companies. There is an increasing need to take into account all the user information to tailor the best product proposition. One of them is the content that the user actually sees: the visual of the product.
When it comes to hostels, some people can be more attracted by pictures of the room, the building or even the nearby beach.
In this talk, we will describe how we improved an e-business vacation retailer recommender system using the content of images. We’ll explain how to leverage open dataset and pre-trained deep learning models to derive user taste information. This transfer learning approach enables companies to use state of the art machine learning methods without having deep learning expertise.
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.
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This is a general interest talk on how we can use artificial intelligence (specifically machine learning) to screen literature in support of systematic reviews for chemical risk assessment.
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Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
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Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
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 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.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
6. What do you need to be careful about?
• Study environment/situation
• Participants
• Quantity of data
• Data annotation
• Data collection procedure
• Basically everything!
20. Statistics and Visualizations
.8 0.9 1
e (Liters/s)
0.7 0.8 0.9 1
−30
−20
−10
0
10
20
30
Flow−rate (Liters/s)
PercentageDifference
30
Estimated Value
• Bland Altman Plots
21. Statistics and Visualizations
• Power Analysis
• t-test
• chi-square test
• ANOVA
• etc.
You either need prior data or an intuition of your problem
to run these analyses
22. Data Collection Sessions
• Sometimes you need to collect same data multiple
times, in different sessions.
• Example:
4Appliances
1Minute
20Instances
26. In summary
• No secret sauce
• Depends on the problem & the phenomenon sensed
• Run a pilot study
• Be prepared to iterate and collect more data
• Try to make a real time system and test it out
