This is a presentation I gave as a short overview of LSTMs. The slides are accompanied by two examples which apply LSTMs to Time Series data. Examples were implemented using Keras. See links in slide pack.
Recurrent Neural Networks have shown to be very powerful models as they can propagate context over several time steps. Due to this they can be applied effectively for addressing several problems in Natural Language Processing, such as Language Modelling, Tagging problems, Speech Recognition etc. In this presentation we introduce the basic RNN model and discuss the vanishing gradient problem. We describe LSTM (Long Short Term Memory) and Gated Recurrent Units (GRU). We also discuss Bidirectional RNN with an example. RNN architectures can be considered as deep learning systems where the number of time steps can be considered as the depth of the network. It is also possible to build the RNN with multiple hidden layers, each having recurrent connections from the previous time steps that represent the abstraction both in time and space.
This presentation on Recurrent Neural Network will help you understand what is a neural network, what are the popular neural networks, why we need recurrent neural network, what is a recurrent neural network, how does a RNN work, what is vanishing and exploding gradient problem, what is LSTM and you will also see a use case implementation of LSTM (Long short term memory). Neural networks used in Deep Learning consists of different layers connected to each other and work on the structure and functions of the human brain. It learns from huge volumes of data and used complex algorithms to train a neural net. The recurrent neural network works on the principle of saving the output of a layer and feeding this back to the input in order to predict the output of the layer. Now lets deep dive into this presentation and understand what is RNN and how does it actually work.
Below topics are explained in this recurrent neural networks tutorial:
1. What is a neural network?
2. Popular neural networks?
3. Why recurrent neural network?
4. What is a recurrent neural network?
5. How does an RNN work?
6. Vanishing and exploding gradient problem
7. Long short term memory (LSTM)
8. Use case implementation of LSTM
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.
And according to payscale.com, the median salary for engineers with deep learning skills tops $120,000 per year.
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. Those who complete the course will be able to:
Learn more at: https://www.simplilearn.com/
This is a presentation I gave as a short overview of LSTMs. The slides are accompanied by two examples which apply LSTMs to Time Series data. Examples were implemented using Keras. See links in slide pack.
Recurrent Neural Networks have shown to be very powerful models as they can propagate context over several time steps. Due to this they can be applied effectively for addressing several problems in Natural Language Processing, such as Language Modelling, Tagging problems, Speech Recognition etc. In this presentation we introduce the basic RNN model and discuss the vanishing gradient problem. We describe LSTM (Long Short Term Memory) and Gated Recurrent Units (GRU). We also discuss Bidirectional RNN with an example. RNN architectures can be considered as deep learning systems where the number of time steps can be considered as the depth of the network. It is also possible to build the RNN with multiple hidden layers, each having recurrent connections from the previous time steps that represent the abstraction both in time and space.
This presentation on Recurrent Neural Network will help you understand what is a neural network, what are the popular neural networks, why we need recurrent neural network, what is a recurrent neural network, how does a RNN work, what is vanishing and exploding gradient problem, what is LSTM and you will also see a use case implementation of LSTM (Long short term memory). Neural networks used in Deep Learning consists of different layers connected to each other and work on the structure and functions of the human brain. It learns from huge volumes of data and used complex algorithms to train a neural net. The recurrent neural network works on the principle of saving the output of a layer and feeding this back to the input in order to predict the output of the layer. Now lets deep dive into this presentation and understand what is RNN and how does it actually work.
Below topics are explained in this recurrent neural networks tutorial:
1. What is a neural network?
2. Popular neural networks?
3. Why recurrent neural network?
4. What is a recurrent neural network?
5. How does an RNN work?
6. Vanishing and exploding gradient problem
7. Long short term memory (LSTM)
8. Use case implementation of LSTM
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.
And according to payscale.com, the median salary for engineers with deep learning skills tops $120,000 per year.
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. Those who complete the course will be able to:
Learn more at: https://www.simplilearn.com/
This Edureka Recurrent Neural Networks tutorial will help you in understanding why we need Recurrent Neural Networks (RNN) and what exactly it is. It also explains few issues with training a Recurrent Neural Network and how to overcome those challenges using LSTMs. The last section includes a use-case of LSTM to predict the next word using a sample short story
Below are the topics covered in this tutorial:
1. Why Not Feedforward Networks?
2. What Are Recurrent Neural Networks?
3. Training A Recurrent Neural Network
4. Issues With Recurrent Neural Networks - Vanishing And Exploding Gradient
5. Long Short-Term Memory Networks (LSTMs)
6. LSTM Use-Case
Brief introduction on attention mechanism and its application in neural machine translation, especially in transformer, where attention was used to remove RNNs completely from NMT.
Basics of RNNs and its applications with following papers:
- Generating Sequences With Recurrent Neural Networks, 2013
- Show and Tell: A Neural Image Caption Generator, 2014
- Show, Attend and Tell: Neural Image Caption Generation with Visual Attention, 2015
- DenseCap: Fully Convolutional Localization Networks for Dense Captioning, 2015
- Deep Tracking- Seeing Beyond Seeing Using Recurrent Neural Networks, 2016
- Robust Modeling and Prediction in Dynamic Environments Using Recurrent Flow Networks, 2016
- Social LSTM- Human Trajectory Prediction in Crowded Spaces, 2016
- DESIRE- Distant Future Prediction in Dynamic Scenes with Interacting Agents, 2017
- Predictive State Recurrent Neural Networks, 2017
Introduction For seq2seq(sequence to sequence) and RNNHye-min Ahn
This is my slides for introducing sequence to sequence model and Recurrent Neural Network(RNN) to my laboratory colleagues.
Hyemin Ahn, @CPSLAB, Seoul National University (SNU)
Recurrent Neural Network
ACRRL
Applied Control & Robotics Research Laboratory of Shiraz University
Department of Power and Control Engineering, Shiraz University, Fars, Iran.
Mohammad Sabouri
https://sites.google.com/view/acrrl/
An introductory but very precise slide on mathematics of RNN/LSTM algorithms. You would get a clearer understanding on RNN back/forward propagation with this.
*This slide is not finished yet. If you like it, please give me some feedback to motivate me.
I made this slide as an intern in DATANOMIQ Gmbh
URL: https://www.datanomiq.de/
Deep Learning: Recurrent Neural Network (Chapter 10) Larry Guo
This Material is an in_depth study report of Recurrent Neural Network (RNN)
Material mainly from Deep Learning Book Bible, http://www.deeplearningbook.org/
Topics: Briefing, Theory Proof, Variation, Gated RNNN Intuition. Real World Application
Application (CNN+RNN on SVHN)
Also a video (In Chinese)
https://www.youtube.com/watch?v=p6xzPqRd46w
Word Embeddings, Application of Sequence modelling, Recurrent neural network , drawback of recurrent neural networks, gated recurrent unit, long short term memory unit, Attention Mechanism
Transformer modality is an established architecture in natural language processing that utilizes a framework of self-attention with a deep learning approach.
This presentation was delivered under the mentorship of Mr. Mukunthan Tharmakulasingam (University of Surrey, UK), as a part of the ScholarX program from Sustainable Education Foundation.
This was a presentation done for the Techspace of IoT Asia 2017 oon 30th March 2017. This is an introductory session to introduce the concept of Long Short-Term Memory (LSTMs) for the prediction in Time Series. I also shared the Keras code to work out a simple Sin Wave example and a Household power consumption data to use for the predictions. The links for the code can be found in the presentation.
Long short-term memory (LSTM) network is a recurrent neural network (RNN), aimed to deal with the vanishing gradient problem present in traditional RNNs. Its relative insensitivity to gap length is its advantage over other RNNs, hidden Markov models and other sequence learning methods. It aims to provide a short-term memory for RNN that can last thousands of timesteps, thus "long short-term memory". It is applicable to classification, processing and predicting data based on time series, such as in handwriting, speech recognition, machine translation, speech activity detection, robot control, video games, and healthcare.
A common LSTM unit is composed of a cell, an input gate, an output gate and a forget gate. The cell remembers values over arbitrary time intervals and the three gates regulate the flow of information into and out of the cell. Forget gates decide what information to discard from a previous state by assigning a previous state, compared to a current input, a value between 0 and 1. A (rounded) value of 1 means to keep the information, and a value of 0 means to discard it. Input gates decide which pieces of new information to store in the current state, using the same system as forget gates. Output gates control which pieces of information in the current state to output by assigning a value from 0 to 1 to the information, considering the previous and current states. Selectively outputting relevant information from the current state allows the LSTM network to maintain useful, long-term dependencies to make predictions, both in current and future time-steps.
This Edureka Recurrent Neural Networks tutorial will help you in understanding why we need Recurrent Neural Networks (RNN) and what exactly it is. It also explains few issues with training a Recurrent Neural Network and how to overcome those challenges using LSTMs. The last section includes a use-case of LSTM to predict the next word using a sample short story
Below are the topics covered in this tutorial:
1. Why Not Feedforward Networks?
2. What Are Recurrent Neural Networks?
3. Training A Recurrent Neural Network
4. Issues With Recurrent Neural Networks - Vanishing And Exploding Gradient
5. Long Short-Term Memory Networks (LSTMs)
6. LSTM Use-Case
Brief introduction on attention mechanism and its application in neural machine translation, especially in transformer, where attention was used to remove RNNs completely from NMT.
Basics of RNNs and its applications with following papers:
- Generating Sequences With Recurrent Neural Networks, 2013
- Show and Tell: A Neural Image Caption Generator, 2014
- Show, Attend and Tell: Neural Image Caption Generation with Visual Attention, 2015
- DenseCap: Fully Convolutional Localization Networks for Dense Captioning, 2015
- Deep Tracking- Seeing Beyond Seeing Using Recurrent Neural Networks, 2016
- Robust Modeling and Prediction in Dynamic Environments Using Recurrent Flow Networks, 2016
- Social LSTM- Human Trajectory Prediction in Crowded Spaces, 2016
- DESIRE- Distant Future Prediction in Dynamic Scenes with Interacting Agents, 2017
- Predictive State Recurrent Neural Networks, 2017
Introduction For seq2seq(sequence to sequence) and RNNHye-min Ahn
This is my slides for introducing sequence to sequence model and Recurrent Neural Network(RNN) to my laboratory colleagues.
Hyemin Ahn, @CPSLAB, Seoul National University (SNU)
Recurrent Neural Network
ACRRL
Applied Control & Robotics Research Laboratory of Shiraz University
Department of Power and Control Engineering, Shiraz University, Fars, Iran.
Mohammad Sabouri
https://sites.google.com/view/acrrl/
An introductory but very precise slide on mathematics of RNN/LSTM algorithms. You would get a clearer understanding on RNN back/forward propagation with this.
*This slide is not finished yet. If you like it, please give me some feedback to motivate me.
I made this slide as an intern in DATANOMIQ Gmbh
URL: https://www.datanomiq.de/
Deep Learning: Recurrent Neural Network (Chapter 10) Larry Guo
This Material is an in_depth study report of Recurrent Neural Network (RNN)
Material mainly from Deep Learning Book Bible, http://www.deeplearningbook.org/
Topics: Briefing, Theory Proof, Variation, Gated RNNN Intuition. Real World Application
Application (CNN+RNN on SVHN)
Also a video (In Chinese)
https://www.youtube.com/watch?v=p6xzPqRd46w
Word Embeddings, Application of Sequence modelling, Recurrent neural network , drawback of recurrent neural networks, gated recurrent unit, long short term memory unit, Attention Mechanism
Transformer modality is an established architecture in natural language processing that utilizes a framework of self-attention with a deep learning approach.
This presentation was delivered under the mentorship of Mr. Mukunthan Tharmakulasingam (University of Surrey, UK), as a part of the ScholarX program from Sustainable Education Foundation.
This was a presentation done for the Techspace of IoT Asia 2017 oon 30th March 2017. This is an introductory session to introduce the concept of Long Short-Term Memory (LSTMs) for the prediction in Time Series. I also shared the Keras code to work out a simple Sin Wave example and a Household power consumption data to use for the predictions. The links for the code can be found in the presentation.
Long short-term memory (LSTM) network is a recurrent neural network (RNN), aimed to deal with the vanishing gradient problem present in traditional RNNs. Its relative insensitivity to gap length is its advantage over other RNNs, hidden Markov models and other sequence learning methods. It aims to provide a short-term memory for RNN that can last thousands of timesteps, thus "long short-term memory". It is applicable to classification, processing and predicting data based on time series, such as in handwriting, speech recognition, machine translation, speech activity detection, robot control, video games, and healthcare.
A common LSTM unit is composed of a cell, an input gate, an output gate and a forget gate. The cell remembers values over arbitrary time intervals and the three gates regulate the flow of information into and out of the cell. Forget gates decide what information to discard from a previous state by assigning a previous state, compared to a current input, a value between 0 and 1. A (rounded) value of 1 means to keep the information, and a value of 0 means to discard it. Input gates decide which pieces of new information to store in the current state, using the same system as forget gates. Output gates control which pieces of information in the current state to output by assigning a value from 0 to 1 to the information, considering the previous and current states. Selectively outputting relevant information from the current state allows the LSTM network to maintain useful, long-term dependencies to make predictions, both in current and future time-steps.
Foundation of Generative AI: Study Materials Connecting the Dots by Delving i...Fordham University
In recent years, the field of artificial intelligence (AI) has witnessed remarkable advancements, particularly in the domain of Generative models. Generative AI, a subset of machine learning, focuses on developing systems that can create novel and realistic content, ranging from text, speech, images to the multimodal content. This burgeoning field has demonstrated unprecedented potential to revolutionize various industries, making it imperative to introduce dedicated study materials on the foundation of Generative AI. With the increasing integration of Generative AI in various industries, professionals with expertise in this field are in high demand, and thus we believe that the publication of the slides are extremely important to meet the current need. The proposed outline aims to equip students with the knowledge and skills required to harness the creative power of AI and navigate the ethical implications associated with Generative technologies. * Materials used in this PPT were collected from Wikipedia, Google Image, and OpenAI GPT. No copyright is claimed by the author.
Deep learning (also known as deep structured learning or hierarchical learning) is the application of artificial neural networks (ANNs) to learning tasks that contain more than one hidden layer. Deep learning is part of a broader family of machine learning methods based on learning data representations, as opposed to task-specific algorithms. Learning can be supervised, partially supervised or unsupervised.
The slides for the equation deviation of recurrent neural network (RNN), back-propagation through time and Sequence-to-sequence (Seq2Seq) models in image/video captioning tasks. Used in group paper reading in University of Sydney.
The slides includes an introduction to Long Short-term Memory (LSTM ) >> A novel approach in dealing with vanishing gradients in deep neural networks. Made for students, and anyone out there who'd love to learn about recurrent artificial neural networks, specifically of the LSTMs architecture.
Reference material has been attached to further your reading.
https://telecombcn-dl.github.io/2017-dlcv/
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 and Q-nets for reinforcement learning have shaped a brand new scenario in signal processing. This course will cover the basic principles and applications of deep learning to computer vision problems, such as image classification, object detection or image captioning.
This lecture provides an introduction to recurrent neural networks, which include a layer whose hidden state is aware of its values in a previous time-step.
These slides were used in the Master in Computer Vision Barcelona 2019/2020, in the Module 6 dedicated to Video Analysis.
http://pagines.uab.cat/mcv/
Machine Learning - Introduction to Recurrent Neural NetworksAndrew Ferlitsch
Abstract: This PDSG workshop introduces basic concepts of recurrent neural networks. Concepts covered are feed forward vs. recurrent, time progression, memory cells, short term memory predictions and long term memory predictions.
Level: Fundamental
Requirements: No prior programming or statistics knowledge required.
Multiple Resonant Multiconductor Transmission line Resonator Design using Cir...Sasidhar Tadanki
In this thesis, a new design procedure to determine resonant conditions for a multiconductor transmission line (MTL) resonator is proposed. The MTL is represented as a multiport network using its port admittance matrix. Closed form solutions for different port resonant modes are calculated by solving the eigenvalue problem of the admittance matrix using the block matrix algebra. A port admittance matrix can be formulated to take one of the following forms depending on the type of MTL structure: i) a circulant matrix, ii) a circulant block matrix (CB), or iii) a block circulant circulant block matrix (BCCB). A circulant matrix can be diagonalized by a simple Fourier matrix, and a BCCB matrix can be diagonalized by using matrices formed from Kronecker products of Fourier matrices. For a CB matrix, instead of diagonalizing to compute the eigenvalues, a powerful technique called “reduced dimension method” can be used. Application of block matrix algebra helps reduce the computational complexity and also simplifies the formulation of the analytical solutions.
To demonstrate the effectiveness of the proposed methods (2n port model and reduced dimension method), a two-step approach was adopted. First, a standard published Radio Frequency (RF) coil is analyzed using the proposed models. The obtained resonant conditions are then compared with the published values and are verified by full-wave numerical simulations. Second, two new dual-tuned RF coils for magnetic resonance (MR) imaging, a surface coil design using the 2n port model and a volume coil design using the reduced dimensions method, are proposed, constructed, and bench tested. Their validation is carried out by employing 3D EM simulations as well as undertaking MR imaging in clinical scanners. Imaging experiments were conducted on phantoms, and the investigations indicate that these RF coils achieve good performance characteristics and a high signal-to-noise ratio in the regions of interest.
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 .
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...!
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.
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.
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.
1. Long short-term memory
Hochreiter, Sepp, and Jürgen Schmidhuber. "Long short-term
memory." Neural computation 9.8 (1997): 1735-1780.
01
Long Short-Term Memory (LSTM)
Olivia Ni
2. • Recurrent Neural Networks (RNN)
• The Problem of Long-Term Dependencies
• LSTM Networks
• The Core Idea Behind LSTMs
• Step-by-Step LSTM Walk Through
• Variants on LSTMs
• Conclusions & References
• Appendix (BPTT Gradient Exploding/ Vanishing)
02
Outline
3. • Idea:
• condition the neural network on all previous information and tie the weights
at each time step
• Assumption: temporal information matters (i.e. time series data)
03
Recurrent Neural Networks (RNN)
RNN RNNRNN
𝐼𝑛𝑝𝑢𝑡 𝑡
𝑂𝑢𝑡𝑝𝑢𝑡 𝑡
𝑆𝑇𝑀 𝑡−1 𝑆𝑇𝑀 𝑡
𝐼𝑛𝑝𝑢𝑡 𝑡−1
𝑂𝑢𝑡𝑝𝑢𝑡 𝑡−1
𝐼𝑛𝑝𝑢𝑡 𝑡+1
𝑂𝑢𝑡𝑝𝑢𝑡 𝑡+1
𝑆𝑇𝑀 𝑡−2 𝑆𝑇𝑀 𝑡+1
• STM = Short-term memory
4. • RNN Definition:
• Model Training:
• All model parameters 𝜃 = 𝑈, 𝑉, 𝑊 can be updated by gradient descent
04
Recurrent Neural Networks (RNN)
𝑆𝑡 = 𝜎 𝑈𝑥𝑡 + 𝑊𝑠𝑡−1
𝑂𝑡 = 𝑠𝑜𝑓𝑡𝑚𝑎𝑥 𝑉𝑠𝑡
𝜃 𝑖+1
← 𝜃 𝑖
− 𝜂𝛻𝜃 𝐶 𝜃 𝑖
5. • Example: (Consider trying to predict the last word in the text)
• Issue: in theory, RNNs can handle such “long-term dependencies,” but
they cannot in practice!!
“The clouds are in the sky.”
“I grew up in France… I speak fluent French.”
05
The Problem of Long-Term Dependencies
6. • RNN Training Issue:
(1) The gradient is a product of Jacobian matrices, each associated with a step
in the forward computation
(2) Multiply the same matrix at each time step during BPTT
• The gradient becomes very small or very large quickly
• Vanishing or Exploding gradient
• The error surface is either very flat or very steep
06
The Problem of Long-Term Dependencies
7. • Possible Solutions:
• Gradient Exploding:
• Clipping (https://arxiv.org/abs/1211.5063?context=cs)
• Gradient Vanishing:
• Better Initialization (https://arxiv.org/abs/1504.00941)
• Gating Mechanism (LSTM, GRU, …, etc.)
• Attention Mechanism (https://arxiv.org/pdf/1706.03762.pdf)
07
The Problem of Long-Term Dependencies
9. 09
LSTM Networks – The Core Idea Behind LSTMs
• STM = Short-term memory
• LSTM = Long Short-term memory
𝐿𝑆𝑇𝑀
𝑆𝑇𝑀
𝑆𝑇𝑀
10. 10
LSTM Networks – Step-by-Step LSTM Walk Through (0/4)
• The cell state runs straight down
the entire chain, with only some
minor linear interactions.
Easy for information to flow
along it unchanged
• The LSTM does have the ability
to remove or add information to
the cell state, carefully regulated
by structures called gates.
11. 11
LSTM Networks – Step-by-Step LSTM Walk Through (1/4)
• Forget gate (sigmoid + pointwise
multiplication operation):
decides what information we’re
going to throw away from the
cell state
• 1: ‘’Complete keep this”
• 0: “Complete get rid of this”
12. 12
LSTM Networks – Step-by-Step LSTM Walk Through (2/4)
• Input gate (sigmoid + pointwise
multiplication operation):
decides what new information
we’re going to store in the cell
state
Vanilla RNN
13. 13
LSTM Networks – Step-by-Step LSTM Walk Through (3/4)
• Cell state update: forgets the
things we decided to forget
earlier and add the new
candidate values, scaled by how
much we decided to update
• 𝑓𝑡: decide which to forget
• 𝑖 𝑡: decide which to update
⟹ 𝐶𝑡 has been updated at timestamp 𝑡, which change slowly!
14. 14
LSTM Networks – Step-by-Step LSTM Walk Through (4/4)
• Output gate (sigmoid + pointwise
multiplication operation):
decides what new information
we’re going to output
⟹ ℎ 𝑡 has been updated at timestamp 𝑡, which change faster!
15. 15
LSTM Networks – Variants on LSTMs (1/3)
• LSTM with Peephole Connections
• Idea: allow gate layers to look at
the cell state
16. 16
LSTM Networks – Variants on LSTMs (2/3)
• LSTM with Coupled Forget/ Input
Gate
• Idea: we only forget when we’re
going to input something in its
place, and vice versa.
17. 17
LSTM Networks – Variants on LSTMs (3/3)
• Gated Recurrent Unit (GRU)
• Idea:
• combine the forget and input gates
into a single “update gate”
• merge the cell state and hidden state
Update gate:
Reset gate:
State Candidate:
Current State:
18. Explain by
- Backpropagation
Through Time (BPTT)
RNN Training Issue:
- Gradient Vanishing
- Gradient Exploding
Review
- Backpropagation (BP)
18
Appendix – The Problem of Long-Term Dependencies
19. 𝜕 𝐶 𝜃
𝜕 𝑤𝑖𝑗
𝑙
𝜕 𝐶 𝜃
𝜕 𝑤𝑖𝑗
𝑙
• Gradient Descent for Neural Networks
• Computing the gradient includes millions of parameters.
• To compute it efficiently, we use backpropagation.
• Compute the gradient based on two pre-computed terms from forward and backward pass.
19
Appendix – The Problem of Long-Term Dependencies
𝜕 𝐶 𝜃
𝜕 𝑤𝑖𝑗
𝑙
BPTT
BP
20. 𝜕 𝐶 𝜃
𝜕 𝑤𝑖𝑗
𝑙
=
𝜕 𝐶 𝜃
𝜕 𝑧𝑖
𝑙
𝜕 𝑧𝑖
𝑙
𝜕 𝑤𝑖𝑗
𝑙
• WLOG, we use 𝑤𝑖𝑗
𝑙
to demonstrate
• Forward pass:
20
Appendix – The Problem of Long-Term Dependencies
𝜕 𝑧𝑖
𝑙
𝜕 𝑤𝑖𝑗
𝑙
= ൝
𝑥𝑗 , 𝑖𝑓 𝑙 = 1
𝑎𝑗
𝑙−1
, 𝑖𝑓 𝑙 > 1
(𝑙 = 1) (𝑙 > 1)
BPTT
BP
28. • Understand the difficulty of training recurrent neural networks
• Gradient Exploding
• Gradient Vanishing
• One possible solution for solving the gradient vanishing problem is
“Gating mechanism”, which is the key concept of LSTM
• LSTM can be “deep” if we stack multiple LSTM cells
• Extensions:
• Uni-directional v.s. Bi-directional
• One-to-one, One-to-many, Many-to-one, Many-to-Many (w/ or w/o Encoder-Decoder)
28
Conclusions
29. • Understanding LSTM Networks
http://colah.github.io/posts/2015-08-Understanding-LSTMs/
• Prof. Hung-yi Lee Courses
https://www.youtube.com/watch?v=xCGidAeyS4M
https://www.youtube.com/watch?v=rTqmWlnwz_0
• On the difficulty of training recurrent neural networks
https://arxiv.org/abs/1211.5063
• UDACITY Courses: Intro to Deep Learning with PyTorch
https://classroom.udacity.com/courses/ud188
29
References