Seminar Talk from a SICSA visitor (Daniel Garijo) Friday 10 June, 11.00am

Accelerating Research Software Understandability Through Knowledge Capture

Daniel Garijo

Summary: Research Software is key to understand, reproduce and reuse existing work in many disciplines, ranging from Geosciences to Astronomy or Artificial Intelligence. However, research software is usually difficult to find, reuse, compare and understand due to its disconnected documentation (dispersed in manuals, readme files, web sites, and code comments) and a lack of structured metadata to describe it. These problems affect not only researchers, but also students who aim to compare published findings and policy makers seeking clarity on a scientific result. In this talk I will present the main research challenges and our recent efforts towards facilitating software understanding by automatically capturing Knowledge Graphs from software documentation and code.

Short bio: Dr. Daniel Garijo Verdejo is a Distinguished Researcher at the Ontology Engineering Group of Universidad Politécnica de Madrid (UPM). Previously, he held a Research Computer Scientist position at the Information Sciences Institute of the University of Southern California, in Los Angeles. Daniel’s research activities focus on e-Science and Knowledge Capture, specifically on how to increase the understandability of research software and scientific workflows by creating Knowledge Graph from their documentation and provenance (i.e., steps, outputs, inputs, intermediate results).

For this talk we will use a hybrid approach: In person (Jack Cole, 1.33) and online, via Teams.

If you wish to attend it would be helpful if you could register on eventbrite to let us know if you intend to attend in person or online

All Welcome!

Seminar – Phong Le, Amazon – 3rd March 2021

Can Language Models be Weak Annotators

We are happy to have Phong Le, from Amazon, talk on Teams on Wed 3 March at 12 noon on Teams.

Abstract

Deep language models e.g. BERT and GPT3 are the breakthrough in Natural Language Processing in the last 3 years. Being trained on massive raw text data, they capture useful priors for several tasks such as syntactic parsing, information extraction, and question answering. Moreover, they are capable of answering factual and commonsense cloze questions such as “Dante was born in _____”. In this talk, I will firstly give an overview about what language models “know”. I will then present our work on exploiting their knowledge as weak supervision for a specific task called relation classification.

Relation classification, the identification of a particular relation type between two entities in text, requires annotated data. Data annotation is either a manual process for supervised learning, or automated, using knowledge bases for distant learning. However, both methodologies are costly and time-consuming since they depend on intensive human labour for annotation or for knowledge base creation. Using language models as annotators, on the contrary, is very cheap but the annotation quality is low. We hence propose NoelA, an auto-encoder using a noisy channel, to improve the accuracy by learning from the low quality annotated data. NoelA outperforms BERT and a bootstrapping baseline on TACRED and reWIKI datasets.

Bio: I’m an applied scientist at Amazon Alexa. Before that, I was a tenure-track research fellow at the University of Manchester. I did a postdoc with Ivan Titov at the University of Edinburgh, and got a PhD from the University of Amsterdam under the supervision of (Jelle) Willem Zuidema. I’m interested in neural networks and deep learning. My current work is to employ them to solve natural language processing tasks such as entity linking, coreference resolution, and dependency parsing. I’m also interested in formal semantics, especially learning semantic parsing.

For more details, please visit my homepage https://sites.google.com/site/lephongxyz/

 

Please note the session will not be recorded, to preserve the like-for-like nature of physical seminars and also avoid any privacy/rights issues.

Event details

  • When: 3rd March 2021 12:00 - 3rd February 2021 13:00
  • Format: Seminar

Georgios Gerasimou (University of St Andrews): Frontiers in computational revealed preference analysis

RESCHEDULED: please note the changed date and a non-standard time!

Abstract: Prest is a recently published piece of open-source software for computational revealed preference analysis that provides novel ways to estimate decision makers’ preferences over choice alternatives by analysing their observable choice behaviour. This software is informed by classic as well as recent developments in economic revealed preference theory. Some of the recent developments take the form of models that are computationally complex. This complexity currently hinders the inclusion of these models in the Prest toolkit. The presentation will first aim to describe the primary ideas underpinning Prest and illustrate them with examples from its existing toolkit. It will then proceed with a discussion of some of the challenges pertaining to the expansion of that toolkit with more models and operations. The presentation will be self-contained and no prior background in economics will be necessary.

Speaker Bio: Georgios is a Reader in Economics at the University of St Andrews, working mainly on decision theory and revealed preference analysis. In the latter research programme, Georgios’ work aims to improve our understanding of people’s decision processes and preferences through theoretical, experimental/empirical as well as computational methods. Georgios co-developed the Prest software program for computational revealed preference analysis (https://prestsoftware.com/).

Event details

  • When: 17th February 2020 14:00 - 15:00
  • Where: Cole 1.33b
  • Series: School Seminar Series
  • Format: Seminar

Philippe Palanque (University of Toulouse): Harnessing Usability, UX and Dependability for Interactions in Safety Critical Contexts

Abstract: Innovation and creativity are the research drivers of the Human-Computer Interaction (HCI) community which is currently investing a vast amount of resources in the design and evaluation of “new” user interfaces and interaction techniques, leaving the correct functioning of these interfaces at the discretion of the helpless developers. In the area of formal methods and dependable systems the emphasis is usually put on the correct functioning of the system leaving its usability to secondary-level concerns (if at all addressed). However, designing interactive systems requires blending knowledge from these domains in order to provide operators with enjoyable, usable and dependable systems. The talk will present possible research directions and their benefits for combining several complementary approaches to engineer interactive critical systems. Due to their specificities, addressing this problem requires the definition of methods, notations, processes and tools to go from early informal requirements to deployed and maintained operational interactive systems. The presentation will highlight the benefits of (and the need for) an integrated framework for the iterative design of operators’ procedures and tasks, training material and the interactive system itself. The emphasis will be on interaction techniques specification and validation as their design is usually the main concern of HCI conferences. A specific focus will be on automation that is widely integrated in interactive systems both at interaction techniques level and at application level. Examples will be taken from interactive cockpits on large civil commercial aircrafts (such as the A380), satellite ground segment application and Air Traffic Control workstations.

Speaker Bio: Dr. Philippe Palanque is Professor in Computer Science at the University Toulouse 3 “Paul Sabatier” and is head of the Interactive Critical Systems group at the Institut de Recherche en Informatique de Toulouse (IRIT) in France. Since the late 80s he has been working on the development and application of formal description techniques for interactive system. He has worked for more than 10 years on research projects to improve interactive Ground Segment Systems at the Centre National d’Etudes Spatiales (CNES) and is also involved in the development of software architectures and user interface modeling for interactive cockpits in large civil aircraft (funded by Airbus). He was involved in the research network HALA! (Higher Automation Levels in Aviation) funded by SESAR programme which targets at building the future European air traffic management system. The main driver of Philippe’s research over the last 20 years has been to address in an even way Usability, Safety and Dependability in order to build trustable safety critical interactive systems. He is the secretary of the IFIP Working group 13.5 on Resilience, Reliability, Safety and Human Error in System Development, was steering committee chair of the CHI conference series at ACM SIGCHI and chair of the IFIP Technical Committee 13 on Human-Computer Interaction.

 

Event details

  • When: 3rd February 2020 11:00 - 12:00
  • Where: Cole 1.33a
  • Series: SACHI Seminar Series, School Seminar Series
  • Format: Seminar

Blindness seminar

The medical school is holding a Seminar on Wednesday 8th January @1400-1530
New tools and methods to prevent blindness.
Seminar room 1, Medical and Biological Sciences Building

  • Dr. Andrew Blaikie, St Andrews
    Arclight Project
  • Dr. Craig Robertson, CEO Epipole Ltd
    Hand held fundus cameras
  • Prof Congdon, Queen’s University Belfast
    Overview of Global Ophthalmology

Event details

  • When: 8th January 2020 14:00 - 15:30
  • Format: Seminar

Nguyen Dang (University of St Andrews): Hyper-Parameter Tuning for an evolutionary algorithm

Abstract: In this talk, I will present a case study to illustrate how automated algorithm configuration can be used to gain insights into theoretical results on an evolutionary algorithm, namely the (1+(λ,λ)) Genetic Algorithm. This work is a collaboration with Carola Doerr.

The (1+(λ,λ)) Genetic Algorithm is an evolutionary algorithm that has interesting theoretical properties. It is the first algorithm where the benefit of crossover operator is rigorously proved. It is also the first example where self-adjusting parameter choice is proved to outperform any static parameter choice. However, it is not very well understood how the hyper-parameter settings influences the overall performance of the algorithm. Analyzing such multi-dimensional dependencies precisely is at the edge of what running time analysis can offer. In this work, we make a step forward on this question by presenting an in-depth study of the algorithm’s hyper-parameters using techniques in automated algorithm configuration.

Speaker bio: Dr Nguyen Dang is a post-doc in the Constraint Programming group at the University of St Andrews. Her main research focus is on automated algorithm configuration, algorithm selection and their applications in various contexts. These techniques make use of statistical methods and machine learning for fine-tuning of algorithm parameters, assessing parameters’ importance and building algorithm portfolios. Another line of her research is about solving combinatorial optimisation problems using metaheuristic algorithms.

Event details

  • When: 11th February 2020 14:00 - 15:00
  • Where: Cole 1.33b
  • Series: School Seminar Series
  • Format: Seminar

Matt Blackledge (Institute of Cancer Research): Clinical Computational Imaging: Perspectives in Oncology

Abstract: There is an ever-increasing burden on imaging departments to deliver high-throughput assessment of medical images.  MRI in particular provides the advantage of full-body coverage and and a variety of quantitative imaging techniques, such as diffusion-weighted MRI, that can offer potent biomarkers for disease response and prognosis; with the advent of accelerated imaging techniques, many quantitative images can now be acquired in a single patient scan.  Increases in computational power and the advent of methodologies such as deep-learning may help to deliver on the promise of truly personalised, image-guided therapies; by helping clinicians to better understand the complexities within multi-parametric MRI it may be possible to derive a non-invasive “digital biopsy” that can be monitored during treatment.  In this presentation, we will review recent developments within the Computational Imaging group at the Institute of Cancer Research and Royal Marsden Hospital, demonstrating how novel algorithms and deep learning can be used to assist in the response assessment of advanced prostate cancer and soft-tissue sarcoma.

Speaker Bio: Dr Matt Blackledge is the team-leader of computational imaging at the ICR, where he has been developing computational techniques in MRI for over a decade.  He is funded by both CRUK and Sarcoma UK to innovate novel approaches to image analysis from MRI and X-ray CT to improve cancer patient outcomes in a variety of disease types.  He is particularly interested in how AI can be used to (i) further accelerate MR-image acquisition, (ii) understand cancer heterogeneity in images, and (iii) probe the link between quantitative imaging biomarkers and their underlying biology.

 

Event details

  • When: 4th February 2020 14:00 - 15:00
  • Where: Cole 1.33b
  • Series: School Seminar Series
  • Format: Seminar

School seminar: Interactions between Group Theory, Cyber Security, Artificial Intelligence, and Quantum Computation – talk by Delaram Kahrobaei (York)

Abstract:

In this talk, I explore how group theory playing a crucial role in cyber security and quantum computation. At the same time, how computer science for example machine learning algorithms and computational complexity could help group theorists to tackle their open problems, as such this could help with cryptanalysis of the proposed primitives.

Symmetry is present in all forms in the natural and biological structures as well as man-made environments. Computational symmetry applies group-theory to create algorithms that model and analyze symmetry in real data set. The use of symmetry groups in optimizing the formulation of signal processing and machine learning algorithms can greatly enhance the impact of these algorithms in many fields of science and engineering where highly complex symmetries exist.

At the same time, Machine Learning techniques could help with solving long standing group theoretic problems. For example, in the paper [J. Gryak (University of Michigan, Data Science Institute), R. Haralick (The City University of New York, the prize recipient of International Association for Pattern Recognition), D. Kahrobaei, Solving the Conjugacy Decision Problem via Machine Learning, Experimental Mathematics, Taylor & Francis (2019)] the authors use machine learning techniques to solve the conjugacy decision problem in a variety of groups. Beyond their utilitarian worth, the developed methods provide the computational group theorist a new digital “sketchpad” with which one can explore the structure of groups and other algebraic objects, and perhaps yielding heretofore unknown mathematical relationships.

Graph theoretic problems have been of interest of theoretical computer scientists for many years, especially the computational complexity problems for such algorithmic problems. Such studies have been fruitful for one of the millennium problems (P vs NP) of the Clay Math Institute. Since graph groups are uniquely defined by a finite simplicial graph and vice versa, it is clear that there is a natural connection between algorithmic graph theoretic problems and group theoretic problems for graph groups. Since the graph theoretic problems have been of central importance in complexity theory, it is natural to consider some of these graph theoretic problems via their equivalent formulation as group theoretic problems about graph groups. The theme of the paper [Algorithmic problems in right-angled Artin groups: Complexity and applications, R. Flores, D. Kahrobaei, T. Koberda, J. of Algebra, Elsevier 2019.] is to convert graph theoretic problems for finite graphs into group theoretic ones for graph groups (a.k.a. right-angled Artin) groups, and to investigate the graph theory algebraically. In doing so, new approaches to resolving problems in complexity theory become apparent. The authors are primarily motivated by the fact that some of these group theoretic problems can be used for cryptographic purposes, such as authentication schemes, secret sharing schemes, and key exchange problems.

In the past couple of decades many groups have been proposed for cryptography, for instance: polycyclic groups for public-key exchanges, digital signatures, secret sharing schemes (Eick, Kahrobaei), hyperbolic groups for private key encryption (Chatterji-Kahrobaei), p-groups for multilinear maps (Kahrobaei, Tortora, Tota) among others. [J. Gryak, D. Kahrobaei, The Status of the Polycyclic Group-Based Cryptography: A Survey and Open Problems, Groups Complexity Cryptology, De Gruyter (2016).]

Most of the current cryptosystems are based on number theoretic problems such discrete logarithm problem (DLP) for example Diffie-Hellman key-exchange. Recently there has been some natural connections between algorithmic number theoretic and algorithmic group theoretic problems. For example, it has been shown that for a different subfamily of metabelian groups the conjugacy search problem reduces to the DLP. [J. Gryak, D. Kahrobaei, C. Martinez-Perez, On the conjugacy problem in certain metabelian groups, Glasgow Math. J., Cambridge Univ. Press (2019).]

In August 2015 the National Security Agency (NSA) announced plans to upgrade security standards; the goal is to replace all deployed cryptographic protocols with quantum secure protocols. This transition requires a new security standard to be accepted by the National Institute of Standards and Technology (NIST).

One goal of cryptography, as it relates to complexity theory, is to analyze the complexity assumptions used as the basis for various cryptographic protocols and schemes. A central question is determining how to generate intractible instances of these problems upon which to implement an actual cryptographic scheme. The candidates for these instances must be platforms in which the hardness assumption is still reasonable. Determining if the group-based cryptographic schemes are quantum-safe begins with determining the groups in which these hardness assumptions are invalid in the quantum setting.

In what follows we address the quantum complexity of the Hidden Subgroup Problem (HSP) to determine the groups in which the hardness assumption still stands. The Hidden Subgroup Problem (HSP) asks the following: given a description of a group G and a function f from G to X for some finite set X is guaranteed to be strictly H-periodic, i.e. constant and distinct on left (resp. right) cosets of a subgroup H < G, find a generating set for H.

Group-based cryptography could be shown to be post-quantum if the underlying security problem is NP-complete or unsolvable; firstly, we need to analyze the problem’s equivalence to HSP, then analyze the applicability of Grover’s search problem. [K. Horan, D. Kahrobaei, Hidden Subgroup Problem and Post-quantum Group-based Cryptography, Springer Lecture Notes in Computer Science 10931, 2018].

Speaker Bio:

I am currently the Chair of Cyber Security at the University of York, a position I have held since November 2018. While at York, I founded and am the director of the York Interdisciplinary Center for Cyber Security. Before coming to York, I was Full Professor at the City University of New York (CUNY) in New York City. I was at CUNY for 12 years, among other duties, I supervised 7 PhD computer science and mathematics students. In addition to my position at York, I am also an Adjunct Professor of Computer Science at the Center for Cyber Security at New York University (NYU). I have been an adjunct at NYU since 2016. I was a lecturer in Pure Mathematics at the University of St Andrews before New York.

I am an associate editor of the of the Advances of Mathematics of Communication, published by the American Institute of Mathematical Sciences, the chief editor of the International Journal of Computer Mathematics: Computer Systems Theory, Taylor & Francis, and an associate editor of SIAM Journal on Applied Algebra and Geometry, The Society for Industrial and Applied Mathematics. I also have entrepreneurial experience as President and Co-founder of Infoshield, Inc., a computer security company.

My main research area is Post-Quantum Algebraic Cryptography, Information Security, Data Science, Applied Algebra. My research has been supported by grants from the US military: US Office of Naval Research, Canadian New Frontiers in Research Fund Exploration, American Association of Advancement in Sciences, National Science Foundation, National Security Agency, Maastricht-York Investment Fund, Research Foundation of CUNY, London Mathematical Society, the Edinburgh Mathematical Society, Swiss National Foundation, Institut Henri Poincare, and the Association for Women in Mathematics. I have 70 publications in prestigious journals and conference proceedings and several US patents. I have given about 240 invited talks in conferences and seminars around the world.

Event details

  • When: 28th January 2020 14:00 - 15:00
  • Where: Cole 1.33b
  • Series: School Seminar Series
  • Format: Seminar

Rob Stewart (Heriot-Watt University): Reliable Parallel Computing using Model Checking

Abstract:

This talk will demonstrate how model checking based verification of compilers and runtime systems can increase the confidence of parallel execution of programming languages, using two case studies.

As HPC systems continue to increase in scale, their mean time between failure decreases meaning reliability has become a major concern. I will present HdpH-RS, a parallel HPC language. HdpH-RS has a formal semantics, and a fault tolerant work stealing scheduler that has been verified with the SPIN model checker. At embedded scale, program transformations on stateful dynamic code can introduce bugs, race conditions and deadlock. I will present a parallel refactoring tool for the CAL dataflow language. It is integrated with the TINA model checker that we use to identify parallelisable cyclo-static actors in dynamic dataflow programs.

The broader aim of this work is to integrate automated formal verification into parallelising compilers and parallel runtime systems for heterogeneous architectures.

Speaker bio: Dr Rob Stewart is an Assistant Professor at Heriot-Watt University. He’s interested in formalising, verifying and implementing dataflow, functional and domain specific programming languages for manycore architectures and programmable hardware.

Event details

  • When: 19th November 2019 14:00 - 15:00
  • Where: Cole 1.33b
  • Series: School Seminar Series
  • Format: Seminar