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1. Trajectories in epistemic network analysis

   https://doi.org/https://doi.org/10.1007/978-3-030-67788-6_8  

   Brohinsky, Jais ; Marquart, Cody ; Wang, Junting ; Ruis, Andrew R ; Shaffer, David W. ( January 2021 , Advances in Quantitative Ethnography: Second International Conference, ICQE 2020, Malibu, CA, USA, February 1-3, 2021, Proceedings)

   Ruis, Andrew R. ; Lee, Seung B. (Ed.)

   While quantitative ethnographers have used epistemic network analysis (ENA) to model trajectories that show change in network structure over time, visualizing trajectory models in a way that facilitates accurate interpretation has been a significant challenge. As a result, ENA has predominantly been used to construct aggregate models, which can obscure key differences in how network structures change over time. This study reports on the development and testing of a new approach to visualizing ENA trajectories. It documents the challenges associated with visualizing ENA trajectory models, the features constructed to address those challenges, and the design decisions that aid in the interpretation of trajectory models. To test this approach, we compare ENA trajectory models with aggregate models using a dataset with previously published results and known temporal features. This comparison focuses on interpretability and consistency with prior qualitative analysis, and we show that ENA trajectories are able to represent information unavailable in aggregate models and facilitate interpretations consistent with qualitative findings. This suggests that this approach to ENA trajectories is an effective tool for representing change in network structure over time. 

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2. The Deep Learning Epilepsy Detection Challenge: Design, Implementation, and Test of a New Crowd-Sourced AI Challenge Ecosystem

   Kiral, Isabell ; Roy, Subhrajit ; Mummert, Todd ; Braz, Alan ; Tsay, Jason ; Tang, Jianbin ; Asif, Umar ; Schaffter, Thomas ; Mehmet, Eren ; Picone, Joseph ; et al ( April 2019 , Challenges in Machine Learning Competitions for All (CiML))

   null (Ed.)

   The DeepLearningEpilepsyDetectionChallenge: design, implementation, andtestofanewcrowd-sourced AIchallengeecosystem Isabell Kiral*, Subhrajit Roy*, Todd Mummert*, Alan Braz*, Jason Tsay, Jianbin Tang, Umar Asif, Thomas Schaffter, Eren Mehmet, The IBM Epilepsy Consortium◊ , Joseph Picone, Iyad Obeid, Bruno De Assis Marques, Stefan Maetschke, Rania Khalaf†, Michal Rosen-Zvi† , Gustavo Stolovitzky† , Mahtab Mirmomeni† , Stefan Harrer† * These authors contributed equally to this work † Corresponding authors: rkhalaf@us.ibm.com, rosen@il.ibm.com, gustavo@us.ibm.com, mahtabm@au1.ibm.com, sharrer@au.ibm.com ◊ Members of the IBM Epilepsy Consortium are listed in the Acknowledgements section J. Picone and I. Obeid are with Temple University, USA. T. Schaffter is with Sage Bionetworks, USA. E. Mehmet is with the University of Illinois at Urbana-Champaign, USA. All other authors are with IBM Research in USA, Israel and Australia. Introduction This decade has seen an ever-growing number of scientific fields benefitting from the advances in machine learning technology and tooling. More recently, this trend reached the medical domain, with applications reaching from cancer diagnosis [1] to the development of brain-machine-interfaces [2]. While Kaggle has pioneered the crowd-sourcing of machine learning challenges to incentivise data scientists from around the world to advance algorithm and model design, the increasing complexity of problem statements demands of participants to be expert data scientists, deeply knowledgeable in at least one other scientific domain, and competent software engineers with access to large compute resources. People who match this description are few and far between, unfortunately leading to a shrinking pool of possible participants and a loss of experts dedicating their time to solving important problems. Participation is even further restricted in the context of any challenge run on confidential use cases or with sensitive data. Recently, we designed and ran a deep learning challenge to crowd-source the development of an automated labelling system for brain recordings, aiming to advance epilepsy research. A focus of this challenge, run internally in IBM, was the development of a platform that lowers the barrier of entry and therefore mitigates the risk of excluding interested parties from participating. The challenge: enabling wide participation With the goal to run a challenge that mobilises the largest possible pool of participants from IBM (global), we designed a use case around previous work in epileptic seizure prediction [3]. In this “Deep Learning Epilepsy Detection Challenge”, participants were asked to develop an automatic labelling system to reduce the time a clinician would need to diagnose patients with epilepsy. Labelled training and blind validation data for the challenge were generously provided by Temple University Hospital (TUH) [4]. TUH also devised a novel scoring metric for the detection of seizures that was used as basis for algorithm evaluation [5]. In order to provide an experience with a low barrier of entry, we designed a generalisable challenge platform under the following principles: 1. No participant should need to have in-depth knowledge of the specific domain. (i.e. no participant should need to be a neuroscientist or epileptologist.) 2. No participant should need to be an expert data scientist. 3. No participant should need more than basic programming knowledge. (i.e. no participant should need to learn how to process fringe data formats and stream data efficiently.) 4. No participant should need to provide their own computing resources. In addition to the above, our platform should further • guide participants through the entire process from sign-up to model submission, • facilitate collaboration, and • provide instant feedback to the participants through data visualisation and intermediate online leaderboards. The platform The architecture of the platform that was designed and developed is shown in Figure 1. The entire system consists of a number of interacting components. (1) A web portal serves as the entry point to challenge participation, providing challenge information, such as timelines and challenge rules, and scientific background. The portal also facilitated the formation of teams and provided participants with an intermediate leaderboard of submitted results and a final leaderboard at the end of the challenge. (2) IBM Watson Studio [6] is the umbrella term for a number of services offered by IBM. Upon creation of a user account through the web portal, an IBM Watson Studio account was automatically created for each participant that allowed users access to IBM's Data Science Experience (DSX), the analytics engine Watson Machine Learning (WML), and IBM's Cloud Object Storage (COS) [7], all of which will be described in more detail in further sections. (3) The user interface and starter kit were hosted on IBM's Data Science Experience platform (DSX) and formed the main component for designing and testing models during the challenge. DSX allows for real-time collaboration on shared notebooks between team members. A starter kit in the form of a Python notebook, supporting the popular deep learning libraries TensorFLow [8] and PyTorch [9], was provided to all teams to guide them through the challenge process. Upon instantiation, the starter kit loaded necessary python libraries and custom functions for the invisible integration with COS and WML. In dedicated spots in the notebook, participants could write custom pre-processing code, machine learning models, and post-processing algorithms. The starter kit provided instant feedback about participants' custom routines through data visualisations. Using the notebook only, teams were able to run the code on WML, making use of a compute cluster of IBM's resources. The starter kit also enabled submission of the final code to a data storage to which only the challenge team had access. (4) Watson Machine Learning provided access to shared compute resources (GPUs). Code was bundled up automatically in the starter kit and deployed to and run on WML. WML in turn had access to shared storage from which it requested recorded data and to which it stored the participant's code and trained models. (5) IBM's Cloud Object Storage held the data for this challenge. Using the starter kit, participants could investigate their results as well as data samples in order to better design custom algorithms. (6) Utility Functions were loaded into the starter kit at instantiation. This set of functions included code to pre-process data into a more common format, to optimise streaming through the use of the NutsFlow and NutsML libraries [10], and to provide seamless access to the all IBM services used. Not captured in the diagram is the final code evaluation, which was conducted in an automated way as soon as code was submitted though the starter kit, minimising the burden on the challenge organising team. Figure 1: High-level architecture of the challenge platform Measuring success The competitive phase of the "Deep Learning Epilepsy Detection Challenge" ran for 6 months. Twenty-five teams, with a total number of 87 scientists and software engineers from 14 global locations participated. All participants made use of the starter kit we provided and ran algorithms on IBM's infrastructure WML. Seven teams persisted until the end of the challenge and submitted final solutions. The best performing solutions reached seizure detection performances which allow to reduce hundred-fold the time eliptologists need to annotate continuous EEG recordings. Thus, we expect the developed algorithms to aid in the diagnosis of epilepsy by significantly shortening manual labelling time. Detailed results are currently in preparation for publication. Equally important to solving the scientific challenge, however, was to understand whether we managed to encourage participation from non-expert data scientists. Figure 2: Primary occupation as reported by challenge participants Out of the 40 participants for whom we have occupational information, 23 reported Data Science or AI as their main job description, 11 reported being a Software Engineer, and 2 people had expertise in Neuroscience. Figure 2 shows that participants had a variety of specialisations, including some that are in no way related to data science, software engineering, or neuroscience. No participant had deep knowledge and experience in data science, software engineering and neuroscience. Conclusion Given the growing complexity of data science problems and increasing dataset sizes, in order to solve these problems, it is imperative to enable collaboration between people with differences in expertise with a focus on inclusiveness and having a low barrier of entry. We designed, implemented, and tested a challenge platform to address exactly this. Using our platform, we ran a deep-learning challenge for epileptic seizure detection. 87 IBM employees from several business units including but not limited to IBM Research with a variety of skills, including sales and design, participated in this highly technical challenge. 

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3. Multimodality as universality: Designing inclusive accessibility to graphical information

   https://doi.org/10.3389/feduc.2023.1071759  

   Doore, Stacy A. ; Dimmel, Justin ; Kaplan, Toni M. ; Guenther, Benjamin A. ; Giudice, Nicholas A. ( April 2023 , Frontiers in Education)

   Graphical representations are ubiquitous in the learning and teaching of science, technology, engineering, and mathematics (STEM). However, these materials are often not accessible to the over 547,000 students in the United States with blindness and significant visual impairment, creating barriers to pursuing STEM educational and career pathways. Furthermore, even when such materials are made available to visually impaired students, access is likely through literalized modes (e.g., braille, verbal description), which is problematic as these approaches (1) do not directly convey spatial information and (2) are different from the graphic-based materials used by students without visual impairment. The purpose of this study was to design and evaluate a universally accessible system for communicating graphical representations in STEM classes. By combining a multisensory vibro-audio interface and an app running on consumer mobile hardware, the system is meant to work equally well for all students, irrespective of their visual status. We report the design of the experimental system and the results of an experiment where we compared learning performance with the system to traditional (visual or tactile) diagrams for sighted participants (n = 20) and visually impaired participants (n =9) respectively. While the experimental multimodal diagrammatic system (MDS) did result in significant learning gains for both groups of participants, the results also revealed no statistically significant differences in the capacity for learning from graphical information across both comparison groups. Likewise, there were no statistically significant differences in the capacity for learning from graphical information between the stimuli presented through the experimental system and the traditional (visual or tactile) diagram control conditions, across either participant group. These findings suggest that both groups were able to learn graphical information from the experimental system as well as traditional diagram presentation materials. This learning modality was supported without the need for conversion of the diagrams to make them accessible for participants who required tactile materials. The system also provided additional multisensory information for sighted participants to interpret and answer questions about the diagrams. Findings are interpreted in terms of new universal design principles for producing multisensory graphical representations that would be accessible to all learners.

    

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4. GraphBLAST: A High-Performance Linear Algebra-based Graph Framework on the GPU

   https://doi.org/10.1145/3466795  

   Yang, Carl ; Buluç, Aydın ; Owens, John D. ( January 2021 , ACM transactions on mathematical software)

   null (Ed.)

   High-performance implementations of graph algorithms are challenging to implement on new parallel hardware such as GPUs because of three challenges: (1) the difficulty of coming up with graph building blocks, (2) load imbalance on parallel hardware, and (3) graph problems having low arithmetic intensity. To address some of these challenges, GraphBLAS is an innovative, on-going effort by the graph analytics community to propose building blocks based on sparse linear algebra, which allow graph algorithms to be expressed in a performant, succinct, composable, and portable manner. In this paper, we examine the performance challenges of a linear-algebra-based approach to building graph frameworks and describe new design principles for overcoming these bottlenecks. Among the new design principles is exploiting input sparsity, which allows users to write graph algorithms without specifying push and pull direction.Exploiting output sparsityallows users to tell the backend which values of the output in a single vectorized computation they do not want computed. Load-balancing is an important feature for balancing work amongst parallel workers. We describe the important load-balancing features for handling graphs with different characteristics. The design principles described in this paper have been implemented in “GraphBLAST”, the first high-performance linear algebra-based graph framework on NVIDIA GPUs that is open-source. The results show that on a single GPU, GraphBLAST has on average at least an order of magnitude speedup over previous GraphBLAS implementations SuiteSparse andGBTL, comparable performance to the fastest GPU hardwired primitives and shared-memory graph frameworks Ligra and Gunrock, and better performance than any other GPU graph framework ,while offering a simpler and more concise programming model. 

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5. The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling

   https://doi.org/10.1073/pnas.2022598118  

   Gates, Alexander J. ; Brattig Correia, Rion ; Wang, Xuan ; Rocha, Luis M. ( March 2021 , Proceedings of the National Academy of Sciences)

   null (Ed.)

   The ability to map causal interactions underlying genetic control and cellular signaling has led to increasingly accurate models of the complex biochemical networks that regulate cellular function. These network models provide deep insights into the organization, dynamics, and function of biochemical systems: for example, by revealing genetic control pathways involved in disease. However, the traditional representation of biochemical networks as binary interaction graphs fails to accurately represent an important dynamical feature of these multivariate systems: some pathways propagate control signals much more effectively than do others. Such heterogeneity of interactions reflects canalization—the system is robust to dynamical interventions in redundant pathways but responsive to interventions in effective pathways. Here, we introduce the effective graph, a weighted graph that captures the nonlinear logical redundancy present in biochemical network regulation, signaling, and control. Using 78 experimentally validated models derived from systems biology, we demonstrate that 1) redundant pathways are prevalent in biological models of biochemical regulation, 2) the effective graph provides a probabilistic but precise characterization of multivariate dynamics in a causal graph form, and 3) the effective graph provides an accurate explanation of how dynamical perturbation and control signals, such as those induced by cancer drug therapies, propagate in biochemical pathways. Overall, our results indicate that the effective graph provides an enriched description of the structure and dynamics of networked multivariate causal interactions. We demonstrate that it improves explainability, prediction, and control of complex dynamical systems in general and biochemical regulation in particular. 

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