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1. Optimal decoding of neural dynamics occurs at mesoscale spatial and temporal resolutions

   https://doi.org/10.3389/fncel.2024.1287123  

   Samiei, Toktam ; Zou, Zhuowen ; Imani, Mohsen ; Nozari, Erfan ( February 2024 , Frontiers in Cellular Neuroscience)

   Jonathan R. Whitlock (Ed.)

   Understanding the neural code has been one of the central aims of neuroscience research for decades. Spikes are commonly referred to as the units of information transfer, but multi-unit activity (MUA) recordings are routinely analyzed in aggregate forms such as binned spike counts, peri-stimulus time histograms, firing rates, or population codes. Various forms of averaging also occur in the brain, from the spatial averaging of spikes within dendritic trees to their temporal averaging through synaptic dynamics. However, how these forms of averaging are related to each other or to the spatial and temporal units of information representation within the neural code has remained poorly understood.

   In this work we developed NeuroPixelHD, a symbolic hyperdimensional model of MUA, and used it to decode the spatial location and identity of static images shown ton= 9 mice in the Allen Institute Visual Coding—NeuroPixels dataset from large-scale MUA recordings. We parametrically varied the spatial and temporal resolutions of the MUA data provided to the model, and compared its resulting decoding accuracy.

   For almost all subjects, we found 125ms temporal resolution to maximize decoding accuracy for both the spatial location of Gabor patches (81 classes for patches presented over a 9×9 grid) as well as the identity of natural images (118 classes corresponding to 118 images) across the whole brain. This optimal temporal resolution nevertheless varied greatly between different regions, followed a sensory-associate hierarchy, and was significantly modulated by the central frequency of theta-band oscillations across different regions. Spatially, the optimal resolution was at either of two mesoscale levels for almost all mice: the area level, where the spiking activity of all neurons within each brain area are combined, and the population level, where neuronal spikes within each area are combined across fast spiking (putatively inhibitory) and regular spiking (putatively excitatory) neurons, respectively. We also observed an expected interplay between optimal spatial and temporal resolutions, whereby increasing the amount of averaging across one dimension (space or time) decreases the amount of averaging that is optimal across the other dimension, and vice versa.

   Our findings corroborate existing empirical practices of spatiotemporal binning and averaging in MUA data analysis, and provide a rigorous computational framework for optimizing the level of such aggregations. Our findings can also synthesize these empirical practices with existing knowledge of the various sources of biological averaging in the brain into a new theory of neural information processing in which theunit of informationvaries dynamically based on neuronal signal and noise correlations across space and time.

    

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2. A tale of three cities: uncovering human-urban interactions with geographic-context aware social media data

   https://doi.org/10.1007/s44212-022-00020-2  

   Yin, Junjun ; Chi, Guangqing ( December 2022 , Urban Informatics)

   Seeking spatiotemporal patterns about how citizens interact with the urban space is critical for understanding how cities function. Such interactions were studied in various forms focusing on patterns of people’s presence, action, and transition in the urban environment, which are defined as human-urban interactions in this paper. Using human activity datasets that utilize mobile positioning technology for tracking the locations and movements of individuals, researchers developed stochastic models to uncover preferential return behaviors and recurrent transitional activity structures in human-urban interactions. Ad-hoc heuristics and spatial clustering methods were applied to derive meaningful activity places in those studies. However, the lack of semantic meaning in the recorded locations makes it difficult to examine the details about how people interact with different activity places. In this study, we utilized geographic context-aware Twitter data to investigate the spatiotemporal patterns of people’s interactions with their activity places in different urban settings. To test consistency of our findings, we used geo-located tweets to derive the activity places in Twitter users’ location histories over three major U.S. metropolitan areas: Greater Boston Area, Chicago, and San Diego, where the geographic context of each location was inferred from its closest land use parcel. The results showed striking spatial and temporal similarities in Twitter users’ interactions with their activity places among the three cities. By using entropy-based predictability measures, this study not only confirmed the preferential return behaviors as people tend to revisit a few highly frequented places but also revealed detailed characteristics of those activity places.

    

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3. Learning 3D Dynamic Scene Representations for Robot Manipulation

   Xu, Zhenjia ; He, Zhanpeng ; Wu, Jiajun ; Song, Shuran ( November 2020 , Proceedings of the 2020 Conference on Robot Learning)

   3D scene representation for robot manipulation should capture three key object properties: permanency - objects that become occluded over time continue to exist; amodal completeness - objects have 3D occupancy, even if only partial observations are available; spatiotemporal continuity - the movement of each object is continuous over space and time. In this paper, we introduce 3D Dynamic Scene Representation (DSR), a 3D volumetric scene representation that simultaneously discovers, tracks, reconstructs objects, and predicts their dynamics while capturing all three properties. We further propose DSR-Net, which learns to aggregate visual observations over multiple interactions to gradually build and refine DSR. Our model achieves state-of-the-art performance in modeling 3D scene dynamics with DSR on both simulated and real data. Combined with model predictive control, DSR-Net enables accurate planning in downstream robotic manipulation tasks such as planar pushing. Code and data are available at dsr-net.cs.columbia.edu. 

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4. Estimating Hourly Population Distribution Patterns at High Spatiotemporal Resolution in Urban Areas Using Geo-Tagged Tweets and Dasymetric Mapping

   https://doi.org/10.4230/LIPIcs.GIScience.2021.I.10  

   Park, Jaehee ( September 2020 , 11th International Conference on Geographic Information Science (GIScience 2021))

   null (Ed.)

   This paper introduces a spatiotemporal analysis framework for estimating hourly changing population distribution patterns in urban areas using geo-tagged tweets (the messages containing users’ geospatial locations), land use data, and dasymetric maps. We collected geo-tagged social media (tweets) within the County of San Diego during one year (2015) by using Twitter’s Streaming Application Programming Interfaces (APIs). A semi-manual Twitter content verification procedure for data cleaning was applied first to separate tweets created by humans from non-human users (bots). The next step was to calculate the number of unique Twitter users every hour within census blocks. The final step was to estimate the actual population by transforming the numbers of unique Twitter users in each census block into estimated population densities with spatial and temporal factors using dasymetric maps. The temporal factor was estimated based on hourly changes of Twitter messages within San Diego County, CA. The spatial factor was estimated by using the dasymetric method with land use maps and 2010 census data. Comparing to census data, our methods can provide better estimated population in airports, shopping malls, sports stadiums, zoo and parks, and business areas during the day time. 

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5. 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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