pwc-archive/papers-with-abstracts huggingface dataset:
Processing, evaluating and understanding FMRI data with afni_proc.py
Authors: Richard C. Reynolds, Daniel R. Glen, Gang Chen, Ziad S. Saad, Robert W. Cox, Paul A. Taylor
Date: 2024-06-07 00:00:00

FMRI data are noisy, complicated to acquire, and typically go through many steps of processing before they are used in a study or clinical practice. Being able to visualize and understand the data from the start through the completion of processing, while being confident that each intermediate step was successful, is challenging. AFNI's afni_proc$.$py is a tool to create and run a processing pipeline for FMRI data. With its flexible features, afni_proc$.$py allows users to both control and evaluate their processing at a detailed level. It has been designed to keep users informed about all processing steps: it does not just process the data, but first outputs a fully commented processing script that the users can read, query, interpret and refer back to. Having this full provenance is important for being able to understand each step of processing; it also promotes transparency and reproducibility by keeping the record of individual-level processing and modeling specifics in a single, shareable place. Additionally, afni_proc$.$py creates pipelines that contain several automatic self-checks for potential problems during runtime. The output directory contains a dictionary of relevant quantities that can be programmatically queried for potential issues and a systematic, interactive quality control (QC) HTML. All of these features help users evaluate and understand their data and processing in detail. We describe these and other aspects of afni_proc$.$py here using a set of task-based and resting state FMRI example commands.
The Imaging Database for Epilepsy And Surgery (IDEAS)
Authors: Peter N. Taylor, Yujiang Wang, Callum Simpson, Vytene Janiukstyte, Jonathan Horsley, Karoline Leiberg, Beth Little, Harry Clifford, Sophie Adler, Sjoerd B. Vos, Gavin P Winston, Andrew W McEvoy, Anna Miserocchi, Jane de Tisi, John S Duncan
Date: 2024-06-10 00:00:00
Tasks: Lesion Detection, Surface Reconstruction

Magnetic resonance imaging (MRI) is a crucial tool to identify brain abnormalities in a wide range of neurological disorders. In focal epilepsy MRI is used to identify structural cerebral abnormalities. For covert lesions, machine learning and artificial intelligence algorithms may improve lesion detection if abnormalities are not evident on visual inspection. The success of this approach depends on the volume and quality of training data. Herein, we release an open-source dataset of preprocessed MRI scans from 442 individuals with drug-refractory focal epilepsy who had neurosurgical resections, and detailed demographic information. The MRI scan data includes the preoperative 3D T1 and where available 3D FLAIR, as well as a manually inspected complete surface reconstruction and volumetric parcellations. Demographic information includes age, sex, age of onset of epilepsy, location of surgery, histopathology of resected specimen, occurrence and frequency of focal seizures with and without impairment of awareness, focal to bilateral tonic-clonic seizures, number of anti-seizure medications (ASMs) at time of surgery, and a total of 1764 patient years of post-surgical follow up. Crucially, we also include resection masks delineated from post-surgical imaging. To demonstrate the veracity of our data, we successfully replicated previous studies showing long-term outcomes of seizure freedom in the range of around 50%. Our imaging data replicates findings of group level atrophy in patients compared to controls. Resection locations in the cohort were predominantly in the temporal and frontal lobes. We envisage our dataset, shared openly with the community, will catalyse the development and application of computational methods in clinical neurology.
Leveraging Hyperscanning EEG and VR Omnidirectional Treadmill to Explore Inter-Brain Synchrony in Collaborative Spatial Navigation
Authors: Chun-Hsiang Chuang, Po-Hsun Peng, Yi-Chieh Chen
Date: 2024-06-10 00:00:00
Tasks: EEG

Navigating through a physical environment to reach a desired location involves a complex interplay of cognitive, sensory, and motor functions. When navigating with others, experiencing a degree of behavioral and cognitive synchronization is both natural and ubiquitous. This synchronization facilitates a harmonious effort toward achieving a common goal, reflecting how individuals instinctively align their actions and thoughts in collaborative settings. Collaborative spatial tasks, which are crucial in daily and professional settings, require coordinated navigation and problem-solving skills. This study explores the neural mechanisms underlying such tasks by using hyperscanning electroencephalography (EEG) technology to examine brain dynamics in dyadic route planning within a virtual reality setting. By analyzing intra- and inter-brain couplings across delta, theta, alpha, beta, and gamma EEG bands using both functional and effective connectivity measures, we identified significant neural synchronization patterns associated with collaborative task performance in both leaders and followers. Functional intra-brain connectivity analyses revealed distinct neural engagement across EEG frequency bands, with increased delta couplings observed in both leaders and followers. Theta connectivity was particularly enhanced in followers, whereas the alpha band exhibited divergent patterns that indicate role-specific neural strategies. Inter-brain analysis revealed increased delta causality between interacting members but decreased theta and gamma couplings from followers to leaders. Additionally, inter-brain analysis indicated decreased couplings in faster-performing dyads, especially in theta bands. These insights enhance our understanding of the neural mechanisms driving collaborative spatial navigation and demonstrate the effectiveness of hyperscanning in studying complex brain-to-brain interactions.
The Integrated Information Theory needs Attention
Authors: Azenet Lopez, Carlos Montemayor
Date: 2024-06-10 00:00:00
Tasks: Philosophy

The Integrated Information Theory (IIT) might be our current best bet at a scientific explanation of phenomenal consciousness. IIT focuses on the distinctively subjective and phenomenological aspects of conscious experience. Currently, it offers the fundaments of a formal account, but future developments shall explain the qualitative structures of every possible conscious experience. But this ambitious project is hindered by one fundamental limitation. IIT fails to acknowledge the crucial roles of attention in generating phenomenally conscious experience and shaping its contents. Here, we argue that IIT urgently needs an account of attention. Without this account, IIT cannot explain important informational differences between different kinds of experiences. Furthermore, though some IIT proponents celebratedly endorse a double dissociation between consciousness and attention, close analysis reveals that such as dissociation is in fact incompatible with IIT. Notably, the issues we raise for IIT will likely arise for many internalist theories of conscious contents in philosophy, especially theories with primitivist inclinations. Our arguments also extend to the recently popularized structuralist approaches. Overall, our discussion highlights how considerations about attention are indispensable for scientific as well as philosophical theorizing about conscious experience.
From First-order to Higher-order Interactions: Enhanced Representation of Homotopic Functional Connectivity through Control of Intervening Variables
Authors: Behdad Khodabandehloo, Payam Jannatdoust, Babak Nadjar Araabi
Date: 2024-06-09 00:00:00
Tasks: Functional Connectivity

The brain's complex functionality emerges from network interactions that go beyond dyadic connections, with higher-order interactions significantly contributing to this complexity. One method of capturing higher-order interactions is through traversing the brain network using random walks. The efficacy of these random walks depends on the defined mutual interactions between two brain entities. More precise capture of higher-order interactions enables a better reflection of the brain's intrinsic neurophysiological characteristics. One well-established neurophysiological concept is Homotopic Functional Connectivity (HoFC), which illustrates the synchronized spontaneous activity between corresponding regions in the brain's left and right hemispheres. We employ node2vec, a random walk node embedding approach, alongside resting-state fMRI from the Human Connectome Project (HCP) to obtain higher-order feature vectors. We assess the efficacy of different functional connectivity parameterizations using HoFC. The results indicates that the quality of capturing higher-order interactions largely depends on the statistical dependency measure between brain regions. Higher-order interactions defined by partial correlation, better reflects HoFC compare to other statistical associations. In this case of first-order interactions, tangent space embedding more effectively demonstrates HoFC. The findings validate HoFC and underscore the importance of functional connectivity construction method in capturing intrinsic characteristics of the human brain.
Continuous Attractor Networks for Laplace Neural Manifolds
Authors: Bryan C. Daniels, Marc W. Howard
Date: 2024-06-06 00:00:00

Many cognitive models, including those for predicting the time of future events, can be mapped onto a particular form of neural representation in which activity across a population of neurons is restricted to manifolds that specify the Laplace transform of functions of continuous variables. These populations coding Laplace transform are associated with another population that inverts the transform, approximating the original function. This paper presents a neural circuit that uses continuous attractor dynamics to represent the Laplace transform of a delta function evolving in time. One population places an edge at any location along a 1-D array of neurons; another population places a bump at a location corresponding to the edge. Together these two populations can estimate a Laplace transform of delta functions in time along with an approximate inverse transform. Building the circuit so the edge moves at an appropriate speed enables the network to represent events as a function of log time. Choosing the connections appropriately within the edge network make the network states map onto Laplace transform with exponential change as a function of time. In this paper we model a learned temporal association in which one stimulus predicts another at some fixed delay $T$. Shortly after $t=0$ the first stimulus recedes into the past. The Laplace Neural Manifold representing the past maintains the Laplace transform $\exp(-st)$. Another Laplace Neural Manifold represents the predicted future. At $t=0$, the second stimulus is represented a time $T$ in the future. At each moment between 0 and $T$, firing over the Laplace transform predicting the future changes as $\exp[-s(T-t)]$. Despite exponential growth in firing, the circuit is robust to noise, making it a practical means to implement Laplace Neural Manifolds in populations of neurons for a variety of cognitive models.
Experimental Measurement of Assembly Indices are Required to Determine The Threshold for Life
Authors: Sara I. Walker, Cole Mathis, Stuart Marshall, Leroy Cronin
Date: 2024-06-10 00:00:00

Assembly Theory (AT) was developed to help distinguish living from non-living systems. The theory is simple as it posits that the amount of selection or Assembly is a function of the number of complex objects where their complexity can be objectively determined using assembly indices. The assembly index of a given object relates to the number of recursive joining operations required to build that object and can be not only rigorously defined mathematically but can be experimentally measured. In pervious work we outlined the theoretical basis, but also extensive experimental measurements that demonstrated the predictive power of AT. These measurements showed that is a threshold in assembly indices for organic molecules whereby abiotic chemical systems could not randomly produce molecules with an assembly index greater or equal than 15. In a recent paper by Hazen et al [1] the authors not only confused the concept of AT with the algorithms used to calculate assembly indices, but also attempted to falsify AT by calculating theoretical assembly indices for objects made from inorganic building blocks. A fundamental misunderstanding made by the authors is that the threshold is a requirement of the theory, rather than experimental observation. This means that exploration of inorganic assembly indices similarly requires an experimental observation, correlated with the theoretical calculations. Then and only then can the exploration of complex inorganic molecules be done using AT and the threshold for living systems, as expressed with such building blocks, be determined. Since Hazen et al.[1] present no experimental measurements of assembly theory, their analysis is not falsifiable.
Advances in Machine Learning, Statistical Methods, and AI for Single-Cell RNA Annotation Using Raw Count Matrices in scRNA-seq Data
Authors: Megha Patel, Nimish Magre, Himanshi Motwani, Nik Bear Brown
Date: 2024-06-07 00:00:00

Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the resolution of individual cells, providing unprecedented insights into cellular heterogeneity and complex biological systems. This paper reviews various advanced computational and machine learning techniques tailored for the analysis of scRNA-seq data, emphasizing their roles in different stages of the data processing pipeline.
Tree balance in phylogenetic models
Authors: Sophie J. Kersting, Kristina Wicke, Mareike Fischer
Date: 2024-06-07 00:00:00
Tasks: Diversity

Tree shape statistics, particularly measures of tree (im)balance, play an important role in the analysis of the shape of phylogenetic trees. With applications ranging from testing evolutionary models to studying the impact of fertility inheritance and selection, or tumor development and language evolution, the assessment of measures of tree balance is important. Currently, a multitude of at least 30 (im)balance indices can be found in the literature, alongside numerous other tree shape statistics. This diversity prompts essential questions: How can we assist researchers in choosing only a small number of indices to mitigate the challenges of multiple testing? Is there a preeminent balance index tailored to specific tasks? This research expands previous studies on the examination of index power, encompassing almost all established indices and a broader array of alternative models, such as a variety of trait-based models. Our investigation reveals distinct groups of balance indices better suited for different tree models, suggesting that decisions on balance index selection can be enhanced with prior knowledge. Furthermore, we present the \textsf{R} software package \textsf{poweRbal} which allows the inclusion of new indices and models, thus facilitating future research on the power of tree shape statistics.
Classical Myelo-Proliferative Neoplasms emergence and development based on real life incidence and mathematical modeling
Authors: Ana Fernández Baranda, Vincent Bansaye, Evelyne Lauret, Morgane Mounier, Valérie Ugo, Sylvie Méléard, Stéphane Giraudier
Date: 2024-06-10 00:00:00

Mathematical modeling offers the opportunity to test hypothesis concerning Myeloproliferative emergence and development. We tested different mathematical models based on a training cohort (n=264 patients) (Registre de la c\^ote d'Or) to determine the emergence and evolution times before JAK2V617F classical Myeloproliferative disorders (respectively Polycythemia Vera and Essential Thrombocytemia) are diagnosed. We dissected the time before diagnosis as two main periods: the time from embryonic development for the JAK2V617F mutation to occur, not disappear and enter in proliferation, and a second time corresponding to the expansion of the clonal population until diagnosis. We demonstrate using progressively complexified models that the rate of active mutation occurrence is not constant and doesn't just rely on individual variability, but rather increases with age and takes a median time of 63.1+/-13 years. A contrario, the expansion time can be considered as constant: 8.8 years once the mutation has emerged. Results were validated in an external cohort (national FIMBANK Cohort, n=1248 patients). Analyzing JAK2V617F Essential Thrombocytema versus Polycythemia Vera, we noticed that the first period of time (rate of active homozygous mutation occurrence) for PV takes approximatively 1.5 years more than for ET to develop when the expansion time was quasi-similar. In conclusion, our multi-step approach and the ultimate time-dependent model of MPN emergence and development demonstrates that the emergence of a JAK2V617F mutation should be linked to an aging mechanism, and indicates a 8-9 years period of time to develop a full MPN.
Accurate stochastic simulation algorithm for multiscale models of infectious diseases
Authors: Yuan Yin, Jennifer A. Flegg, Mark B. Flegg
Date: 2024-06-07 00:00:00

In the infectious disease literature, significant effort has been devoted to studying dynamics at a single scale. For example, compartmental models describing population-level dynamics are often formulated using differential equations. In cases where small numbers or noise play a crucial role, these differential equations are replaced with memoryless Markovian models, where discrete individuals can be members of a compartment and transition stochastically. Classic stochastic simulation algorithms, such as the next reaction method, can be employed to solve these Markovian models exactly. The intricate coupling between models at different scales underscores the importance of multiscale modelling in infectious diseases. However, several computational challenges arise when the multiscale model becomes non-Markovian. In this paper, we address these challenges by developing a novel exact stochastic simulation algorithm. We apply it to a showcase multiscale system where all individuals share the same deterministic within-host model while the population-level dynamics are governed by a stochastic formulation. We demonstrate that as long as the within-host information is harvested at a reasonable resolution, the novel algorithm will always be accurate. Furthermore, our implementation is still efficient even at finer resolutions. Beyond infectious disease modelling, the algorithm is widely applicable to other multiscale systems, providing a versatile, accurate, and computationally efficient framework.
Hybrid metapopulation agent-based epidemiological models for efficient insight on the individual scale: a contribution to green computing
Authors: Julia Bicker, René Schmieding, Michael Meyer-Hermann, Martin J. Kühn
Date: 2024-06-06 00:00:00

Emerging infectious diseases and climate change are two of the major challenges in 21st century. Although over the past decades, highly-resolved mathematical models have contributed in understanding dynamics of infectious diseases and are of great aid when it comes to finding suitable intervention measures, they may need substantial computational effort and produce significant CO2 emissions. Two popular modeling approaches for mitigating infectious disease dynamics are agent-based and population-based models. Agent-based models (ABMs) offer a microscopic view and are thus able to capture heterogeneous human contact behavior and mobility patterns. However, insights on individual-level dynamics come with high computational effort that scales with the number of agents. On the other hand, population-based models using e.g. ordinary differential equations (ODEs) are computationally efficient even for large populations due to their complexity being independent of the population size. Yet, population-based models are restricted in their granularity as they assume a (to some extent) homogeneous and well-mixed population. To manage the trade-off between computational complexity and level of detail, we propose spatial- and temporal-hybrid models that use ABMs only in an area or time frame of interest. To account for relevant influences to disease dynamics, e.g., from outside, due to commuting activities, we use population-based models, only adding moderate computational costs. Our hybridization approach demonstrates significant reduction in computational effort by up to 98% -- without losing the required depth in information in the focus frame. Concluding, hybrid epidemiological models can provide insights on the individual scale where necessary, using aggregated models where possible, thereby making a contribution to green computing.
Overcoming Limitations in Artificial Intelligence-based Prostate Cancer Detection through Better Datasets and a Bayesian Approach to Aggregate Panel Predictions
Authors: T. J. Hart, Chloe Engler Hart, Spencer Hopson, Paul M. Urie, Dennis Della Corte
Date: 2024-06-10 00:00:00
Tasks: Diagnostic, whole slide images

Despite considerable progress in developing artificial intelligence (AI) algorithms for prostate cancer detection from whole slide images, the clinical applicability of these models remains limited due to variability in pathological annotations and existing dataset limitations. This article proposes a novel approach to overcome these challenges by leveraging a Bayesian framework to seamlessly integrate new data, and present results as a panel of annotations. The framework is demonstrated by integrating a Bayesian prior with one trained AI model to generate a distribution of Gleason patterns for each pixel of an image. It is shown that using this distribution of Gleason patterns rather than a ground-truth label can improve model applicability, mitigate errors, and highlight areas of interest for pathologists. Additionally, we present a high-quality, hand-curated dataset of prostate histopathological images annotated at the gland level by trained pre-medical students and verified by an expert pathologist. We highlight the potential of this adaptive and uncertainty-aware framework for developing clinically deployable AI tools that can support pathologists in accurate prostate cancer grading, improve diagnostic accuracy, and create positive patient outcomes.
Application of Black-Litterman Bayesian in Statistical Arbitrage
Authors: Qiqin Zhou
Date: 2024-06-10 00:00:00
Tasks: Portfolio Optimization

\begin{abstract} In this paper, we integrated the statistical arbitrage strategy, pairs trading, into the Black-Litterman model and constructed efficient mean-variance portfolios. Typically, pairs trading underperforms under volatile or distressed market condition because the selected asset pairs fail to revert to equilibrium within the investment horizon. By enhancing this strategy with the Black-Litterman portfolio optimization, we achieved superior performance compared to the S\&P 500 market index under both normal and extreme market conditions. Furthermore, this research presents an innovative idea of incorporating traditional pairs trading strategies into the portfolio optimization framework in a scalable and systematic manner.