The dynamics of networks enables the function of a variety of systems we rely on every day, from gene regulation and metabolism in the cell to the distribution of electric power and communication of information. Understanding, steering and predicting the function of interacting nonlinear dynamical systems, in particular if they are externally driven out of equilibrium, relies on obtaining and evaluating suitable models, posing at least two major challenges. First, how can we extract key structural system features of networks if only time series data provide information about the dynamics of (some) units? Second, how can we characterize nonlinear responses of nonlinear multi-dimensional systems externally driven by fluctuations, and consequently, predict tipping points at which normal operational states may be lost? Here we report recent progress on nonlinear response theory extended to predict tipping points and on model-free inference of network structural features from observed dynamics.
X-TREPAN: A MULTI CLASS REGRESSION AND ADAPTED EXTRACTION OF COMPREHENSIBLE D...cscpconf
In this work, the TREPAN algorithm is enhanced and extended for extracting decision trees from neural networks. We empirically evaluated the performance of the algorithm on a set of databases from real world events. This benchmark enhancement was achieved by adapting Single-test TREPAN and C4.5 decision tree induction algorithms to analyze the datasets. The models are then compared with X-TREPAN for comprehensibility and classification accuracy. Furthermore, we validate the experimentations by applying statistical methods. Finally, the modified algorithm is extended to work with multi-class regression problems and the ability to comprehend generalized feed forward networks is achieved.
X-TREPAN : A Multi Class Regression and Adapted Extraction of Comprehensible ...csandit
In this work, the TREPAN algorithm is enhanced and extended for extracting decision trees
from neural networks. We empirically evaluated the performance of the algorithm on a set of
databases from real world events. This benchmark enhancement was achieved by adapting
Single-test TREPAN and C4.5 decision tree induction algorithms to analyze the datasets. The
models are then compared with X-TREPAN for comprehensibility and classification accuracy.
Furthermore, we validate the experimentations by applying statistical methods. Finally, the
modified algorithm is extended to work with multi-class regression problems and the ability to
comprehend generalized feed forward networks is achieved.
X-TREPAN: A MULTI CLASS REGRESSION AND ADAPTED EXTRACTION OF COMPREHENSIBLE D...cscpconf
In this work, the TREPAN algorithm is enhanced and extended for extracting decision trees from neural networks. We empirically evaluated the performance of the algorithm on a set of databases from real world events. This benchmark enhancement was achieved by adapting Single-test TREPAN and C4.5 decision tree induction algorithms to analyze the datasets. The models are then compared with X-TREPAN for comprehensibility and classification accuracy. Furthermore, we validate the experimentations by applying statistical methods. Finally, the modified algorithm is extended to work with multi-class regression problems and the ability to comprehend generalized feed forward networks is achieved.
X-TREPAN : A Multi Class Regression and Adapted Extraction of Comprehensible ...csandit
In this work, the TREPAN algorithm is enhanced and extended for extracting decision trees
from neural networks. We empirically evaluated the performance of the algorithm on a set of
databases from real world events. This benchmark enhancement was achieved by adapting
Single-test TREPAN and C4.5 decision tree induction algorithms to analyze the datasets. The
models are then compared with X-TREPAN for comprehensibility and classification accuracy.
Furthermore, we validate the experimentations by applying statistical methods. Finally, the
modified algorithm is extended to work with multi-class regression problems and the ability to
comprehend generalized feed forward networks is achieved.
CHN and Swap Heuristic to Solve the Maximum Independent Set ProblemIJECEIAES
We describe a new approach to solve the problem to find the maximum independent set in a given Graph, known also as Max-Stable set problem (MSSP). In this paper, we show how Max-Stable problem can be reformulated into a linear problem under quadratic constraints, and then we resolve the QP result by a hybrid approach based Continuous Hopfeild Neural Network (CHN) and Local Search. In a manner that the solution given by the CHN will be the starting point of the local search. The new approach showed a good performance than the original one which executes a suite of CHN runs, at each execution a new leaner constraint is added into the resolved model. To prove the efficiency of our approach, we present some computational experiments of solving random generated problem and typical MSSP instances of real life problem.
ABSTRACT: Once introduced the fundamental ideas of quantum computing, we will discuss the possibilities offered by quantum computers in machine learning.
BIO: Davide Pastorello obtained an M.Sc. in Physics (2011) and a Ph.D. in Mathematics (2014) from Trento University. After serving at the Dept. of Mathematics and DISI in Trento, he is currently an assistant professor at the Dept. of Mathematics, University of Bologna. His main research interests concern the mathematical aspects of quantum information theory, quantum computing, and quantum machine learning.
Awarded presentation of my research activity, PhD Day 2011, February 23th 2011, Cagliari, Italy.
This presentation has been awarded as the best one of the track on information engineering.
Want to know more?
see my publications at
http://prag.diee.unica.it/pra/ita/people/satta
A recent direction in Business Process Management studied methodologies to control the execution of Business Processes under several sources of uncertainty in order to always get to the end by satisfying all constraints. Current approaches encode business processes into temporal constraint networks or timed game automata in order to exploit their related strategy synthesis algorithms. However, the proposed encodings can only synthesize single-strategies and fail to handle loops. To overcome these limits I will discuss a recent approach based on supervisory control. The approach considers structured business processes with resources, parallel and mutually exclusive branches, loops, and uncertainty. I will discuss an encoding into finite state automata and prove that their concurrent behavior models exactly all possible executions of the process. After that, I will introduce tentative commitment constraints as a new class of constraints restricting the executions of a process. Finally, I will discuss a tree decomposition of the process that plays a central role in modular supervisory control.
In his ignite talk „The Digital Transformation of Education: A Hyper-Disruptive Era through Blockchain and Generative AI,“ Dr. Alexander Pfeiffer delves into the intricate challenges and potential benefits associated with integrating blockchain technologies and generative AI into the educational landscape. He scrutinizes consensus algorithms and explores sustainable methods of operating blockchain systems, while also examining how smart contracts and transactions can be tailored to meet the specific needs of the educational sector. Alexander underscores the importance of establishing secure digital identities and ensuring robust data protection, while simultaneously casting a critical eye on potential risks and vulnerabilities. The topic of digital identities, facilitated through tokenization, forms a bridge between storing data using blockchain-based databases and the increasingly urgent need for content verification of AI-generated material.
Alexander explores the profound alterations occurring in teaching methodologies, assignment creation, and evaluation processes, shedding light on the hyper-disruptive impact these changes are having on both research and practical applications in education. The production of textual content by educators and students is analyzed with a focus on ensuring clear traceability of content sources and editors, and its proper citation, a critical aspect in the responsible use of AI. In addition to generative text and graphics, AI plays a crucial role in future learning and assignment practices, particularly through adaptive game-based learning and assessment. Alexander will provide a brief glimpse into his game „Gallery-Defender,“ a prototype demonstrating how AI and blockchain can be effectively implemented in serious gaming scenarios.
Furthermore, he emphasizes the imperative for ongoing education and professional development for educational personnel, advocating for a proactive stance in addressing the (legal) challenges associated with AI-generated images and text. This ignite talk aims to provide a balanced and critically reflective perspective on hyper-disruptive technologies, setting the stage for further discourse and exploration in the subsequent discussion.
More Related Content
Similar to Nonequilibrium Network Dynamics_Inference, Fluctuation-Respones & Tipping Points.pdf
CHN and Swap Heuristic to Solve the Maximum Independent Set ProblemIJECEIAES
We describe a new approach to solve the problem to find the maximum independent set in a given Graph, known also as Max-Stable set problem (MSSP). In this paper, we show how Max-Stable problem can be reformulated into a linear problem under quadratic constraints, and then we resolve the QP result by a hybrid approach based Continuous Hopfeild Neural Network (CHN) and Local Search. In a manner that the solution given by the CHN will be the starting point of the local search. The new approach showed a good performance than the original one which executes a suite of CHN runs, at each execution a new leaner constraint is added into the resolved model. To prove the efficiency of our approach, we present some computational experiments of solving random generated problem and typical MSSP instances of real life problem.
ABSTRACT: Once introduced the fundamental ideas of quantum computing, we will discuss the possibilities offered by quantum computers in machine learning.
BIO: Davide Pastorello obtained an M.Sc. in Physics (2011) and a Ph.D. in Mathematics (2014) from Trento University. After serving at the Dept. of Mathematics and DISI in Trento, he is currently an assistant professor at the Dept. of Mathematics, University of Bologna. His main research interests concern the mathematical aspects of quantum information theory, quantum computing, and quantum machine learning.
Awarded presentation of my research activity, PhD Day 2011, February 23th 2011, Cagliari, Italy.
This presentation has been awarded as the best one of the track on information engineering.
Want to know more?
see my publications at
http://prag.diee.unica.it/pra/ita/people/satta
Similar to Nonequilibrium Network Dynamics_Inference, Fluctuation-Respones & Tipping Points.pdf (20)
A recent direction in Business Process Management studied methodologies to control the execution of Business Processes under several sources of uncertainty in order to always get to the end by satisfying all constraints. Current approaches encode business processes into temporal constraint networks or timed game automata in order to exploit their related strategy synthesis algorithms. However, the proposed encodings can only synthesize single-strategies and fail to handle loops. To overcome these limits I will discuss a recent approach based on supervisory control. The approach considers structured business processes with resources, parallel and mutually exclusive branches, loops, and uncertainty. I will discuss an encoding into finite state automata and prove that their concurrent behavior models exactly all possible executions of the process. After that, I will introduce tentative commitment constraints as a new class of constraints restricting the executions of a process. Finally, I will discuss a tree decomposition of the process that plays a central role in modular supervisory control.
In his ignite talk „The Digital Transformation of Education: A Hyper-Disruptive Era through Blockchain and Generative AI,“ Dr. Alexander Pfeiffer delves into the intricate challenges and potential benefits associated with integrating blockchain technologies and generative AI into the educational landscape. He scrutinizes consensus algorithms and explores sustainable methods of operating blockchain systems, while also examining how smart contracts and transactions can be tailored to meet the specific needs of the educational sector. Alexander underscores the importance of establishing secure digital identities and ensuring robust data protection, while simultaneously casting a critical eye on potential risks and vulnerabilities. The topic of digital identities, facilitated through tokenization, forms a bridge between storing data using blockchain-based databases and the increasingly urgent need for content verification of AI-generated material.
Alexander explores the profound alterations occurring in teaching methodologies, assignment creation, and evaluation processes, shedding light on the hyper-disruptive impact these changes are having on both research and practical applications in education. The production of textual content by educators and students is analyzed with a focus on ensuring clear traceability of content sources and editors, and its proper citation, a critical aspect in the responsible use of AI. In addition to generative text and graphics, AI plays a crucial role in future learning and assignment practices, particularly through adaptive game-based learning and assessment. Alexander will provide a brief glimpse into his game „Gallery-Defender,“ a prototype demonstrating how AI and blockchain can be effectively implemented in serious gaming scenarios.
Furthermore, he emphasizes the imperative for ongoing education and professional development for educational personnel, advocating for a proactive stance in addressing the (legal) challenges associated with AI-generated images and text. This ignite talk aims to provide a balanced and critically reflective perspective on hyper-disruptive technologies, setting the stage for further discourse and exploration in the subsequent discussion.
The simulation of melee combat is central to many contemporary and traditional strategic games and simulations. In order to elevate this element of play from mere exercises of stats-comparison and dice rolling to a meaningful experience of play, strategy games rely on a rich plethora of cultural motives as deciding factors of their mechanic design. On the example of Samurai-themed skirmishing games, my talk elaborates on the impact that (popular) culture and other inspirations have on gaming experiences. It provides concrete examples from Japanese history, its traditional cinema, and postmodern Western reflections of Japanese cultural practices. Based on these insights, it compares four tabletop strategy games, muses on which phenomena they have adapted in their mechanics, and asks why or why not they may succeed in capturing a cultural essence via their rules.
Ultimately, this comparative approach shall serve to decipher the interplay of dice mechanics and aesthetic properties as the longing for a dramatic ideal in tabletop gaming and encourage participants to reflect on the idea in a subsequent, shared gaming experience.
How does a development team expand on an already existing game?
We will look at the two community driven and committee led expansions to the abandoned Tabletop game 'GuildBall' and explore the stages of development that the game went through. The art and lore driven approach employed will show us how rough sketches and concept ideas become a fully fledged ruleset and ultimately miniatures that can be put on the table. We will also explore pitfalls in rules design like over complicating abilities, the lack of streamlining across the game or simply creating expansions who break the game instead of the mold.
Exploring the development and production pipelines for miniatures in the tabletop wargaming industry. Including a look at the career route taken by the speaker, a case study on developing anatomical archetypes for consistent design outcomes, and a brief look at the various production methods available to the industry.
In recent years, we have experienced an exponential growth in the amount of data generated by IoT devices. Data have to be processed strict low latency constraints, that cannot be addressed by conventional computing paradigm and architectures. On top of this, if we consider that we recently hit the limit codified by the Moore’s law, satisfying low-latency requirements of modern applications will become even more challenging in the future. In this talk, we discuss challenges and possibilities of heterogeneous distributed systems in the Post-Moore era.
In the modern world, we are permanently using, leveraging, interacting with, and relying upon systems of ever higher sophistication, ranging from our cars, recommender systems in eCommerce, and networks when we go online, to integrated circuits when using our PCs and smartphones, security-critical software when accessing our bank accounts, and spreadsheets for financial planning and decision making. The complexity of these systems coupled with our high dependency on them implies both a non-negligible likelihood of system failures, and a high potential that such failures have significant negative effects on our everyday life. For that reason, it is a vital requirement to keep the harm of emerging failures to a minimum, which means minimizing the system downtime as well as the cost of system repair. This is where model-based diagnosis comes into play.
Model-based diagnosis is a principled, domain-independent approach that can be generally applied to troubleshoot systems of a wide variety of types, including all the ones mentioned above. It exploits and orchestrates techniques for knowledge representation, automated reasoning, heuristic problem solving, intelligent search, learning, stochastics, statistics, decision making under uncertainty, as well as combinatorics and set theory to detect, localize, and fix faults in abnormally behaving systems.
In this talk, we will give an introduction to the topic of model-based diagnosis, point out the major challenges in the field, and discuss a selection of approaches from our research addressing these challenges. For instance, we will present methods for the optimization of the time and memory performance of diagnosis systems, show efficient techniques for a semi-automatic debugging by interacting with a user or expert, and demonstrate how our algorithms can be effectively leveraged in important application domains such as scheduling or the Semantic Web.
Function-as-a-Service (FaaS) is the latest paradigm of cloud computing in which developers deploy their codes as serverless functions, while the entire underlying platform and infrastructure is completely managed by cloud providers. Each cloud provider offers a huge set of cloud services and many libraries to simplify development and deployment, but only inside their clouds, often in a single cloud region. With such „help“ of cloud providers, users are locked to use resources and services of the selected cloud provider, which are often limited. Moreover, such heterogeneous and distributed environment of multiple cloud regions and providers challenge scientists to engineer cloud applications, often in a form of serverless workflows. In this talk, I will present our design principle „code once, run everywhere, with everything“. In particular, I will present challenges and our approaches and techniques how to program, model, orchestrate, and run distributed serverless workflow applications in federated FaaS.
As the network softwarization trend started by SDN and NFV keeps evolving, the hardware/software continuum becomes more relevant than ever, offering new offloading/acceleration opportunities at node and network-wide scales. This talk will review evolving transformations behind network softwarization with a special focus on network refactoring and offloading trends leading to “fluid networks planes”, characterized by multiple candidate options for the specific HW/SW embodiment and the location of chained network functions, from the edge to core, from one administrative provider to another, from programmable silicon to portable lightweight virtualized containers. The talk will overview concrete examples from the literature with a special focus on the role of Machine Learning to assist key (automated) decision-making steps. Lastly, the talk will conclude with a glimpse on ongoing ML work applied to Youtube video QoE prediction in live 5G networks.
When it comes to integrating digital technologies into the classroom in higher education, many teachers face similar challenges. Nevertheless, it is difficult for teachers to share experiences because it is usually not possible to transfer successful teaching scenarios directly from one area to another, as subject-specific characteristics make it difficult to reuse them. To address this problem, instructional scenarios can be described as patterns that have been used previously in educational contexts. Patterns can capture proven teaching strategies and describe instructional scenarios in a consistent structure that can be reused. Because priorities for content, methods, and tools are different in each domain, a consensus-tested taxonomy was first developed with the goal of modeling a domain-independent database to collect digital instructional practices. In addition, this presentation will present preliminary insights into a data-driven approach to identifying effective instructional practices from interdisciplinary data as patterns. A web-based application will be developed for this that can both collect teaching/learning scenarios and individually extract scenarios from patterns for a learning platform.
The advent of fog and edge computing has prompted predictions that they will take over the traditional cloud for information processing and knowledge extraction in Internet of Things (IoT) systems. Notwithstanding the fact that fog and edge computing have undoubtedly large potential, these predictions are probably oversimplified and wrongly portray the relations between cloud, fog and edge computing.
Concretely, fog and edge computing have been introduced as an extension of the cloud services towards the data sources, thus forming the computing continuum. The computing continuum enables the creation of a new type of services, spanning across distributed infrastructures, supporting various IoT applications. These applications have a large spectrum of requirements, burdensome to meet with "distant'' cloud data centers. However, the introduction of the computing continuum raises multiple challenges for management, deployment and orchestration of complex distributed applications, such as: increased network heterogeneity, limited resource capacity of edge devices, fragmented storage management, high mobility of edge devices and limited support of native monolithic applications. These challenges primarily concern the complexity and the large diversity of the devices, managed by different entities (cloud providers, universities, private institutions), which range from single-board computers such as Raspberry Pis to powerful multi-processor servers.
Therefore, in this talk, we will discuss novel algorithms for low latency, scalable, and sustainable computing over heterogeneous resources for information processing and reasoning, thus enabling transparent integration of IoT applications. We will tackle the heterogeneity challenge of dynamically changing topologies of the computing infrastructure and present a novel concept for sustainable processing at scale.
East-west oriented photovoltaic power system is a new trend in orienting photovoltaic system. This lecture presents an evaluation of east–west oriented photovoltaic power system. A comparison between east–west oriented photovoltaic system and south oriented photovoltaic system in terms of cost of energy and technical requirement is conducted is presented in this lecture. In addition to that, the benefits of using east–west oriented photovoltaic system are discussed in this paper.
Randomized Signature or random feature selection are two instances of machine learning, where randomly chosen structures appear to be highly expressive. We analyze several aspects of the theory behind it, show that these structures have several theoretically attractive properties and introduce two classes of examples from finance (joint works with Christa Cuchiero, Lukas Gonon, Lyudmila Grigoryeva, Martin Larsson, and Juan-Pablo Ortega).
We live in a “digital” world, the separation between physical and virtual makes (almost) no sense anymore. Here, the Corona pandemic has also acted as an accelerator/magnifier demonstrating that the future of our digital society is here with all its possibilities, but also shortcomings.
In his talk, Hannes Werthner will briefly reflect on the history of computer science, and then discuss the need for an interdisciplinary response to these shortcomings. Such an answer is the Digital Humanism, which looks at this interplay of technology and humankind, it analyzes, and, most importantly, tries to influence the complex interplay of technology and humankind, for a better society and life. In the second part he will discuss this approach, and show what was achieved since its first workshop in 2019, and what lies ahead.
In the latest years, we have witnessed a growing number of media transmitted and stored on computers and mobile devices. For this reason, there is an actual need to employ smart compression algorithms to reduce the size of our media files. However, such techniques are often responsible for severe reduction of user perceived quality. In this talk we present several approaches we have developed to restore degraded images and videos to match their original quality, making use of Generative Adversarial Networks. The aim of the talk is to highlight the main features of our research work, including the advantages of our solution, the current challenges and the possible directions for future improvements.
Recommendation systems today are widely used across many applications such as in multimedia content platforms, social networks, and ecommerce, to provide suggestions to users that are most likely to fulfill their needs, thereby improving the user experience. Academic research, to date, largely focuses on the performance of recommendation models in terms of ranking quality or accuracy measures, which often don’t directly translate into improvements in the real-world. In this talk, we present some of the most interesting challenges that we face in the personalization efforts at Netflix. The goal of this talk is to sunshine challenging research problems in industrial recommendation systems and start a conversation about exciting areas of future research.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
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.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
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 .
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
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.
1. Nonequilibrium Network Dynamics
Inference, Fluctuation-Responses & Tipping Points
Marc Timme
with M. Thümler, J. Casadiego, H. Haehne et al.
Chair for Network Dynamics
TU Dresden, Institute for Theoretical Physics
Center for Advancing Electronics Dresden
Lakeside Labs, Klagenfurt
Cluster of Excellence Physics of Life
2. … in physics, engineering, …
• Disordered systems & stochastic processes
• Neuromorphic computing & network control
• Collective dynamics of energy systems
• Networked public mobility
• Quantum Synchronization
Nature Energy (2018)
Nature Comm. (2018)
Nature Phys. (2020)
Phys. Rev. Lett. (2020)
Phys. Rev. Lett. (2016)
Phys. Rev. Lett. (2012)
… in biology
• Information routing
• Distributed neural processing
• Protein scaling, gene regulation
• Inverse problems: structure dynamics?
Nature Phys. (2010)
Nature Phys. (2011)
Phys. Rev. Lett. (2012)
Nature Comm. (2020)
Nature Comm. (2021)
Phys. Rev. Lett. (2016)
Nature Comm. (2017b); Science Adv. (2017);
Phys. Rev. Lett. (2018b, 2019)
Science Adv. (2019)
Nature Comm. (2017a)
J. Neurosci. (2015)
Nature Comm. (2016)
… in socio-economics
• Interactions in social & financial dynamics
• Networked optimization & tech-driven behavior
Phys. Rev. Lett. (2018c)
Phys. Rev. Lett. (2018a)
4D Networks: Driven Distributed Discrete Dynamical Systems
3. Network function
fundamentally underlies
all aspects of our lives
social networks
neural circuits
gene & protein regulation
chemical reaction networks
transport & distribution networks
…
most are externally driven ➔ nonequilibrium collective dynamics
major questions unanswered to date:
A) How to deduce structural features from nonequilibrium dynamics?
B) How to describe & predict nonequilibrium* response properties?
(* nonlinear, nonstationary, distributed …) – in particular tipping points!
4. A) Network Dynamics as an Inverse Problem
network
noneq.
responses
input
observe collective responses → deduce structural features
?
5. What features of a networked system are most essential ?
network features
I) Network size
(# nodes or variables)
Haehne et al., Phys. Rev. Lett. 2019
II) Interaction topology
(who interacts with whom?)
Casadiego et al., Phys. Rev. Lett. 2018
Nature Comm. 2017
Nitzan et al., Science Adv. 2017
6. Infering Network Size from Perceptible Dynamics
input perceive
dynamics
from n units
What is #variables / network size N?
all units
perc. units
8. Simplest setting:
linear noiseless relaxation towards stable fixed point
fixed point
linearized dyn.
exact trajectory
observed time series
perceptible components
observe M times series each
for n perceptible units {1,…,n} (units {n+1,…,N} not perceptible)
sampled at k time points
9. Arrange time series data into a detection matrix
observe M times series
for n perceptible units
sampled at k times
collect M trajectories {1,…,m,…,M}
sample k time points
detection matrix
contains all information available
10. Deduce network size from detection matrix
known
(measured data)
unknown unknown (up to n entries)
→idea:
exploit rank inequality to deduce network size N
→ evaluate an increasing number M of trajectories
11. Increasing number M of evaluated trajectories reveals N
→ evaluate an increasing number M of trajectories
linear system linearized phase oscillator system
12. Generalization: anywhere in state space
nonlinear dynamics
near arbitrary point in state space
approximate flow
difference between two trajectories
→ detection matrix of identical form, now
15. Generic average nonequilibrium shift
internal dyn. + driving with zero average
here:
near fixed point
1-component & 1-frequency driving
example:
fluctuating input avg. response is shifted!
e
16. Shift or tipping?
fluctuating input avg. response is shifted!
response diverges!
large e = 6
even larger e = 8
e
i) Origin of the shift?
ii) How does shift depend on driving amplitude e?
iii) At which e do responses begin to diverge?
(tipping point)
- nonlinearity of f(x)
- nonlinearly, at least like e2
- yes, we develop
non-standard perturb. theory
17. i) Nonlinear origin of the shift
asymptotic series for “small” e
substitute into ODE…
… and collect orders of e
➔ zero contribution to shift
➔ lowest-order
nonzero contribution
is nonlinear
18. ii) Predicting shift in 2nd order in e
substitute ➔
➔
shift scales (at least) quadratically
e.g. 2x the driving amplitude → 4x the response shift
tipping point
19. iii) How to predict tipping point?
key observation:
standard perturbation theory
cannot capture tipping at any order
(polynomials defined for all e)
How to predict it?
idea: non-tipping solutions stay local near fixed point
➔ zero average rate of change
solve for
- exactly or
- by expanding integrand: modified perturbation theory
20. Tipping point prediction – 1D example
solve for ➔
with Bessel function
➔
finite domain
implies critical e
21. Tipping point prediction – power grid model
shift
so far:
limited prediction for simple system
also for networks
- nonlinear shift
- finite-e tipping
22. Summary Part A
How to find network size from nonequilibrium time series?
Haehne et al., Phys. Rev. Lett. 2019 & Boerner et al., in prep.
network dynamics as an inverse problem (blackbox approach)
suitably arrange all time series data in detection matrix
exploit rank inequality by sequentially considering various M
open challenges:
• robust rank detection?
• how many perceived nodes necessary?
• multi-dim. units?
• combine time series data from different state space regions?
23. Summary Part B
Fluctuation-induced nonlinear shift & tipping
Thuemler et al., MNTS, in press 2022 & in prep. 2022
→ revealed non-trivial average response shift
→ nonlinear origin
→ quantify shift by 2nd order perturbation theory
→ finite-order perturbation theory
incapable of predicting tipping point
→ new framework for predicting tipping point
open challenges:
• understand errors & increase accuracy of tipping pt. prediction
• understand distributedness
of nonlinear responses across a network
24. Thank you to
Questions and comments welcome!
my colleagues, collaborators &
Network Dynamics team
you all for your attention & interest
http://networkdynamics.info
25. Arrange time series data into a detection matrix
observe M times series
for n perceptible units
sampled at k times
mth measured trajectory, {1,…,m,…,M}
sample at k time points
detection matrix
contains all information available
26. Technically: detect gap in singular value spectrum
linear system linearized phase oscillator system
linear system nonlinear system
27. Summary Part II
Nonlinear Dynamics ➔ Interaction Topology
• introduced explicit dependency matrices
(explicit, uniquely multiplies system state, relates to incidence matrix)
• exploit concepts of dynamics space to obtain linear restricting equations
• ARNI (algorithm for revealing network interactions)
for block-sparse and block-dense solutions
• event spaces yield networks from event times
(not shown)
• from statistics of time series only
Casadiego et al., Nature Comm. (2017)
Casadiego et al., Phys. Rev. Lett. (2018)
Nitzan et al., Science Adv. (2017)
29. How to obtain a model for given system?
• take from literature (= from someone else)
• do it yourself (use the data!)
Topical Review: Timme & Casadiego J. Phys. A (2014)
30. A) Standard: System’s Dynamics as a Forward Problem
system
model
predict
dynamics
input
model of system constituents → predicts dynamics
fixed points, stability,
response functions,
bifurcations, …
31. Systems Dynamics as an Inverse Problem
system
model
observe
dynamics
input
observe system dynamics → deduce system constituents
32. Part II Model-free inference of network interactions
nonlinear network dynamical system
derive linear system
of constraint equations
→ group sparse inference problem
develop suitable group sparse algorithm
33. Model-free inference of network interactions
3-point interaction
incidence matrix
define explicit dependency matrix such that
1 if and only if RHSi does explicitly depend on xj
0 otherwise
for each i, is a diagonal matrix with
34. Explicit Dependency Matrix (cont’d)
➔
useful features for systems of differential equations:
• multiplies system state on RHS of DE
• explicitely appears exactly once
• related to incidence matrix in graph theory
Casadiego et al. Nature Comm. (2017)
35. exploit: derivative zero iff independent of coordinate
Dynamics space = state space x space of 1st derivatives
zi = (x, dxi/dt=Fi(x))
36. Action of Explicit Dependency Matrix in order expansions
naturally multiplies each dependency in each order
→ appears as linear coefficients in restricting equations
40. Reconstruction Performance
only type of function, not function itself is relevant for successful reconstruction
Casadiego et al., Nature Comm. (2017)
45. Reconstruction from noisy time series
of a subset of units
deterministic transient trajectory
noisy transient trajectory
• N=100
• fraction R of observed units
• noise-driven dynamics
➔ still reasonable performance
46. From complex to more complex settings
so far:
- uniform request rates
- infinitely large busses
now:
- arbitrary request rate distribution
- finite-capacity of busses