83 research outputs found
Advances of Machine Learning in Materials Science: Ideas and Techniques
In this big data era, the use of large dataset in conjunction with machine
learning (ML) has been increasingly popular in both industry and academia. In
recent times, the field of materials science is also undergoing a big data
revolution, with large database and repositories appearing everywhere.
Traditionally, materials science is a trial-and-error field, in both the
computational and experimental departments. With the advent of machine
learning-based techniques, there has been a paradigm shift: materials can now
be screened quickly using ML models and even generated based on materials with
similar properties; ML has also quietly infiltrated many sub-disciplinary under
materials science. However, ML remains relatively new to the field and is
expanding its wing quickly. There are a plethora of readily-available big data
architectures and abundance of ML models and software; The call to integrate
all these elements in a comprehensive research procedure is becoming an
important direction of material science research. In this review, we attempt to
provide an introduction and reference of ML to materials scientists, covering
as much as possible the commonly used methods and applications, and discussing
the future possibilities.Comment: 80 pages; 22 figures. To be published in Frontiers of Physics, 18,
xxxxx, (2023
Methodology of Algorithm Engineering
Research on algorithms has drastically increased in recent years. Various
sub-disciplines of computer science investigate algorithms according to
different objectives and standards. This plurality of the field has led to
various methodological advances that have not yet been transferred to
neighboring sub-disciplines. The central roadblock for a better knowledge
exchange is the lack of a common methodological framework integrating the
perspectives of these sub-disciplines. It is the objective of this paper to
develop a research framework for algorithm engineering. Our framework builds on
three areas discussed in the philosophy of science: ontology, epistemology and
methodology. In essence, ontology describes algorithm engineering as being
concerned with algorithmic problems, algorithmic tasks, algorithm designs and
algorithm implementations. Epistemology describes the body of knowledge of
algorithm engineering as a collection of prescriptive and descriptive
knowledge, residing in World 3 of Popper's Three Worlds model. Methodology
refers to the steps how we can systematically enhance our knowledge of specific
algorithms. The framework helps us to identify and discuss various validity
concerns relevant to any algorithm engineering contribution. In this way, our
framework has important implications for researching algorithms in various
areas of computer science
Application of multivariate statistics and machine learning to phenotypic imaging and chemical high-content data
Image-based high-content screens (HCS) hold tremendous promise for cell-based
phenotypic screens. Challenges related to HCS include not only storage and
management of data, but critical analysis of the complex image-based data. I
implemented a data storage and screen management framework and developed
approaches for data analysis of a number high-content microscopy screen formats.
I visualized and analysed pilot screens to develop a robust multi-parametric assay
for the identification of genes involved in DNA damage repair in HeLa cells.
Further, I developed and implemented new approaches for image processing and
screen data normalization. My analyses revealed that the ubiquitin ligase RNF8
plays a central role in DNA-damage response and that a related ubiquitin ligase
RNF168 causes the cellular and developmental phenotypes characteristic for the
RIDDLE syndrome. My approaches also uncovered a role for the MMS22LTONSL
complex in DSB repair and its role in the recombination-dependent repair
of stalled or collapsed replication forks.
The discovery of novel bioactive molecules is a challenge because the fraction of active
candidate molecules is usually small and confounded by noise in experimental
readouts. Cheminformatics can improve robustness of chemical high-throughput
screens and functional genomics data sets by taking structure-activity relationships
into account. I applied statistics, machine learning and cheminformatics
to different data sets to discern novel bioactive compounds. I showed that phenothiazines
and apomorphines are regulators for cell differentiation in murine
embryonic stem cells. Further, I pioneered computational methods for the identification of structural features that influence the degradation and retention of
compounds in the nematode C. elegans. I used chemoinformatics to assemble a
comprehensive screening library of previously approved drugs for redeployment
in new bioassays. A combination of chemical genetic interactions, cheminformatics
and machine learning allowed me to predict novel synergistic antifungal small
molecule combinations from sensitized screens with the drug library. In another
study on the biological effects of commonly prescribed psychoactive compounds,
I discovered a strong link between lipophilicity and bioactivity of compounds in
yeast and unexpected off-target effects that could account for unwanted side effects
in humans. I also investigated structure-activity relationships and assessed
the chemical diversity of a compound collection that was used to probe chemical-genetic
interactions in yeast. Finally, I have made these methods and tools available
to the scientific community, including an open source software package called
MolClass that allows researchers to make predictions about bioactivity of small
molecules based on their chemical structure
MECHANICAL ENERGY HARVESTER FOR POWERING RFID SYSTEMS COMPONENTS: MODELING, ANALYSIS, OPTIMIZATION AND DESIGN
Finding alternative power sources has been an important topic of study worldwide. It is vital to find substitutes for finite fossil fuels. Such substitutes may be termed renewable energy sources and infinite supplies. Such limitless sources are derived from ambient energy like wind energy, solar energy, sea waves energy; on the other hand, smart cities megaprojects have been receiving enormous amounts of funding to transition our lives into smart lives. Smart cities heavily rely on smart devices and electronics, which utilize small amounts of energy to run. Using batteries as the power source for such smart devices imposes environmental and labor cost issues. Moreover, in many cases, smart devices are in hard-to-access places, making accessibility for disposal and replacement difficult. Finally, battery waste harms the environment.
To overcome these issues, vibration-based energy harvesters have been proposed and implemented. Vibration-based energy harvesters convert the dynamic or kinetic energy which is generated due to the motion of an object into electric energy. Energy transduction mechanisms can be delivered based on piezoelectric, electromagnetic, or electrostatic methods; the piezoelectric method is generally preferred to the other methods, particularly if the frequency fluctuations are considerable. In response, piezoelectric vibration-based energy harvesters (PVEHs), have been modeled and analyzed widely. However, there are two challenges with PVEH: the maximum amount of extractable voltage and the effective (operational) frequency bandwidth are often insufficient. In this dissertation, a new type of integrated multiple system comprised of a cantilever and spring-oscillator is proposed to improve and develop the performance of the energy harvester in terms of extractable voltage and effective frequency bandwidth. The new energy harvester model is proposed to supply sufficient energy to power low-power electronic devices like RFID components. Due to the temperature fluctuations, the thermal effect over the performance of the harvester is initially studied. To alter the resonance frequency of the harvester structure, a rotating element system is considered and analyzed. In the analytical-numerical analysis, Hamiltonâs principle along with Galerkinâs decomposition approach are adopted to derive the governing equations of the harvester motion and corresponding electric circuit. It is observed that integration of the spring-oscillator subsystem alters the boundary condition of the cantilever and subsequently reforms the resulting characteristic equation into a more complicated nonlinear transcendental equation. To find the resonance frequencies, this equation is solved numerically in MATLAB. It is observed that the inertial effects of the oscillator rendered to the cantilever via the restoring force effects of the spring significantly alter vibrational features of the harvester. Finally, the voltage frequency response function is analytically and numerically derived in a closed-from expression. Variations in parameter values enable the designer to mutate resonance frequencies and mode shape functions as desired. This is particularly important, since the generated energy from a PVEH is significant only if the excitation frequency coming from an external source matches the resonance (natural) frequency of the harvester structure. In subsequent sections of this work, the oscillator mass and spring stiffness are considered as the design parameters to maximize the harvestable voltage and effective frequency bandwidth, respectively. For the optimization, a genetic algorithm is adopted to find the optimal values. Since the voltage frequency response function cannot be implemented in a computer algorithm script, a suitable function approximator (regressor) is designed using fuzzy logic and neural networks. The voltage function requires manual assistance to find the resonance frequency and cannot be done automatically using computer algorithms. Specifically, to apply the numerical root-solver, one needs to manually provide the solver with an initial guess. Such an estimation is accomplished using a plot of the characteristic equation along with human visual inference. Thus, the entire process cannot be automated. Moreover, the voltage function encompasses several coefficients making the process computationally expensive. Thus, training a supervised machine learning regressor is essential. The trained regressor using adaptive-neuro-fuzzy-inference-system (ANFIS) is utilized in the genetic optimization procedure. The optimization problem is implemented, first to find the maximum voltage and second to find the maximum widened effective frequency bandwidth, which yields the optimal oscillator mass value along with the optimal spring stiffness value. As there is often no control over the external excitation frequency, it is helpful to design an adaptive energy harvester. This means that, considering a specific given value of the excitation frequency, energy harvester system parameters (oscillator mass and spring stiffness) need to be adjusted so that the resulting natural (resonance) frequency of the system aligns with the given excitation frequency. To do so, the given excitation frequency value is considered as the input and the system parameters are assumed as outputs which are estimated via the neural network fuzzy logic regressor. Finally, an experimental setup is implemented for a simple pure cantilever energy harvester triggered by impact excitations. Unlike the theoretical section, the experimental excitation is considered to be an impact excitation, which is a random process. The rationale for this is that, in the real world, the external source is a random trigger. Harmonic base excitations used in the theoretical chapters are to assess the performance of the energy harvester per standard criteria. To evaluate the performance of a proposed energy harvester model, the input excitation type consists of harmonic base triggers. In summary, this dissertation discusses several case studies and addresses key issues in the design of optimized piezoelectric vibration-based energy harvesters (PVEHs). First, an advanced model of the integrated systems is presented with equation derivations. Second, the proposed model is decomposed and analyzed in terms of mechanical and electrical frequency response functions. To do so, analytic-numeric methods are adopted. Later, influential parameters of the integrated system are detected. Then the proposed model is optimized with respect to the two vital criteria of maximum amount of extractable voltage and widened effective (operational) frequency bandwidth. Corresponding design (influential) parameters are found using neural network fuzzy logic along with genetic optimization algorithms, i.e., a soft computing method. The accuracy of the trained integrated algorithms is verified using the analytical-numerical closed-form expression of the voltage function. Then, an adaptive piezoelectric vibration-based energy harvester (PVEH) is designed. This final design pertains to the cases where the excitation (driving) frequency is given and constant, so the desired goal is to match the natural frequency of the system with the given driving frequency. In this response, a regressor using neural network fuzzy logic is designed to find the proper design parameters. Finally, the experimental setup is implemented and tested to report the maximum voltage harvested in each test execution
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.
Since the publication of the Society for Immunotherapy of Cancer\u27s (SITC) original cancer immunotherapy biomarkers resource document, there have been remarkable breakthroughs in cancer immunotherapy, in particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor immune activity. The most notable feature of these breakthroughs is the achievement of durable clinical responses in some patients, enabling long-term survival. These durable responses have been noted in tumor types that were not previously considered immunotherapy-sensitive, suggesting that all patients with cancer may have the potential to benefit from immunotherapy. However, a persistent challenge in the field is the fact that only a minority of patients respond to immunotherapy, especially those therapies that rely on endogenous immune activation such as checkpoint inhibitors and vaccination due to the complex and heterogeneous immune escape mechanisms which can develop in each patient. Therefore, the development of robust biomarkers for each immunotherapy strategy, enabling rational patient selection and the design of precise combination therapies, is key for the continued success and improvement of immunotherapy. In this document, we summarize and update established biomarkers, guidelines, and regulatory considerations for clinical immune biomarker development, discuss well-known and novel technologies for biomarker discovery and validation, and provide tools and resources that can be used by the biomarker research community to facilitate the continued development of immuno-oncology and aid in the goal of durable responses in all patients
Deep Learning Methods for Remote Sensing
Remote sensing is a field where important physical characteristics of an area are exacted using emitted radiation generally captured by satellite cameras, sensors onboard aerial vehicles, etc. Captured data help researchers develop solutions to sense and detect various characteristics such as forest fires, flooding, changes in urban areas, crop diseases, soil moisture, etc. The recent impressive progress in artificial intelligence (AI) and deep learning has sparked innovations in technologies, algorithms, and approaches and led to results that were unachievable until recently in multiple areas, among them remote sensing. This book consists of sixteen peer-reviewed papers covering new advances in the use of AI for remote sensing
On data-driven systems analyzing, supporting and enhancing usersâ interaction and experience
[EN]The research areas of Human-Computer Interaction and Software Architectures have
been traditionally treated separately, but in the literature, many authors made efforts to
merge them to build better software systems. One of the common gaps between software
engineering and usability is the lack of strategies to apply usability principles in the initial
design of software architectures. Including these principles since the early phases of software
design would help to avoid later architectural changes to include user experience
requirements. The combination of both fields (software architectures and Human-Computer
Interaction) would contribute to building better interactive software that should include the
best from both the systems and user-centered designs. In that combination, the software
architectures should enclose the fundamental structure and ideas of the system to offer the
desired quality based on sound design decisions.
Moreover, the information kept within a system is an opportunity to extract knowledge
about the system itself, its components, the software included, the users or the interaction
occurring inside. The knowledge gained from the information generated in a software
environment can be used to improve the system itself, its software, the usersâ experience, and
the results. So, the combination of the areas of Knowledge Discovery and Human-Computer
Interaction offers ideal conditions to address Human-Computer-Interaction-related
challenges. The Human-Computer Interaction focuses on human intelligence, the Knowledge
Discovery in computational intelligence, and the combination of both can raise the support
of human intelligence with machine intelligence to discover new insights in a world crowded
of data.
This Ph.D. Thesis deals with these kinds of challenges: how approaches like data-driven
software architectures (using Knowledge Discovery techniques) can help to improve the users'
interaction and experience within an interactive system. Specifically, it deals with how to
improve the human-computer interaction processes of different kind of stakeholders to
improve different aspects such as the user experience or the easiness to accomplish a specific
task.
Several research actions and experiments support this investigation. These research
actions included performing a systematic literature review and mapping of the literature that
was aimed at finding how the software architectures in the literature have been used to
support, analyze or enhance the human-computer interaction. Also, the actions included work
on four different research scenarios that presented common challenges in the Human-
Computer Interaction knowledge area. The case studies that fit into the scenarios selected
were chosen based on the Human-Computer Interaction challenges they present, and on the
authorsâ accessibility to them. The four case studies were: an educational laboratory virtual world, a Massive Open Online Course and the social networks where the students discuss
and learn, a system that includes very large web forms, and an environment where
programmers develop code in the context of quantum computing. The development of the
experiences involved the review of more than 2700 papers (only in the literature review
phase), the analysis of the interaction of 6000 users in four different contexts or the analysis
of 500,000 quantum computing programs.
As outcomes from the experiences, some solutions are presented regarding the minimal
software artifacts to include in software architectures, the behavior they should exhibit, the
features desired in the extended software architecture, some analytic workflows and
approaches to use, or the different kinds of feedback needed to reinforce the usersâ interaction
and experience.
The results achieved led to the conclusion that, despite this is not a standard practice in
the literature, the software environments should embrace Knowledge Discovery and datadriven
principles to analyze and respond appropriately to the usersâ needs and improve or
support the interaction. To adopt Knowledge Discovery and data-driven principles, the
software environments need to extend their software architectures to cover also the challenges
related to Human-Computer Interaction. Finally, to tackle the current challenges related to
the usersâ interaction and experience and aiming to automate the software response to usersâ
actions, desires, and behaviors, the interactive systems should also include intelligent
behaviors through embracing the Artificial Intelligence procedures and techniques
On Data-driven systems analyzing, supporting and enhancing usersâ interaction and experience
Tesis doctoral en inglés y resumen extendido en español[EN] The research areas of Human-Computer Interaction and Software Architectures have been traditionally treated separately, but in the literature, many authors made efforts to merge them to build better software systems. One of the common gaps between software engineering and usability is the lack of strategies to apply usability principles in the initial design of software architectures. Including these principles since the early phases of software design would help to avoid later architectural changes to include user experience requirements. The combination of both fields (software architectures and Human-Computer Interaction) would contribute to building better interactive software that should include the best from both the systems and user-centered designs. In that combination, the software architectures should enclose the fundamental structure and ideas of the system to offer the desired quality based on sound design decisions.
Moreover, the information kept within a system is an opportunity to extract knowledge about the system itself, its components, the software included, the users or the interaction occurring inside. The knowledge gained from the information generated in a software environment can be used to improve the system itself, its software, the usersâ experience, and the results. So, the combination of the areas of Knowledge Discovery and Human-Computer Interaction offers ideal conditions to address Human-Computer-Interaction-related challenges. The Human-Computer Interaction focuses on human intelligence, the Knowledge Discovery in computational intelligence, and the combination of both can raise the support of human intelligence with machine intelligence to discover new insights in a world crowded of data.
This Ph.D. Thesis deals with these kinds of challenges: how approaches like data-driven software architectures (using Knowledge Discovery techniques) can help to improve the users' interaction and experience within an interactive system. Specifically, it deals with how to improve the human-computer interaction processes of different kind of stakeholders to improve different aspects such as the user experience or the easiness to accomplish a specific task.
Several research actions and experiments support this investigation. These research actions included performing a systematic literature review and mapping of the literature that was aimed at finding how the software architectures in the literature have been used to support, analyze or enhance the human-computer interaction. Also, the actions included work on four different research scenarios that presented common challenges in the Human-Computer Interaction knowledge area. The case studies that fit into the scenarios selected were chosen based on the Human-Computer Interaction challenges they present, and on the authorsâ accessibility to them. The four case studies were: an educational laboratory virtual world, a Massive Open Online Course and the social networks where the students discuss and learn, a system that includes very large web forms, and an environment where programmers develop code in the context of quantum computing. The development of the experiences involved the review of more than 2700 papers (only in the literature review phase), the analysis of the interaction of 6000 users in four different contexts or the analysis of 500,000 quantum computing programs.
As outcomes from the experiences, some solutions are presented regarding the minimal software artifacts to include in software architectures, the behavior they should exhibit, the features desired in the extended software architecture, some analytic workflows and approaches to use, or the different kinds of feedback needed to reinforce the usersâ interaction and experience.
The results achieved led to the conclusion that, despite this is not a standard practice in the literature, the software environments should embrace Knowledge Discovery and data-driven principles to analyze and respond appropriately to the usersâ needs and improve or support the interaction. To adopt Knowledge Discovery and data-driven principles, the software environments need to extend their software architectures to cover also the challenges related to Human-Computer Interaction. Finally, to tackle the current challenges related to the usersâ interaction and experience and aiming to automate the software response to usersâ actions, desires, and behaviors, the interactive systems should also include intelligent behaviors through embracing the Artificial Intelligence procedures and techniques
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