pwc-archive/papers-with-abstracts huggingface dataset:
Time-Integrated Spike-Timing-Dependent-Plasticity
Authors: William Gebhardt, Alexander G. Ororbia
Date: 2024-07-13 00:00:00

In this work, we propose time-integrated spike-timing-dependent plasticity (TI-STDP), a mathematical model of synaptic plasticity that allows spiking neural networks to continuously adapt to sensory input streams in an unsupervised fashion. Notably, we theoretically establish and formally prove key properties related to the synaptic adjustment mechanics that underwrite TI-STDP. Empirically, we demonstrate the efficacy of TI-STDP in simulations of jointly learning deeper spiking neural networks that process input digit pixel patterns, at both full image and patch-levels, comparing to two powerful historical instantations of STDP; trace-based STDP (TR-STDP) and event-based post-synaptic STDP (EV-STDP). Usefully, we demonstrate that not only are all forms of STDP capable of meaningfully adapting the synaptic efficacies of a multi-layer biophysical architecture, but that TI-STDP is notably able to do so without requiring the tracking of a large window of pre- and post-synaptic spike timings, the maintenance of additional parameterized traces, or the restriction of synaptic plasticity changes to occur within very narrow windows of time. This means that our findings show that TI-STDP can efficiently embody the benefits of models such as canonical STDP, TR-STDP, and EV-STDP without their costs or drawbacks. Usefully, our results further demonstrate the promise of using a spike-correlation scheme such as TI-STDP in conducting credit assignment in discrete pulse-based neuromorphic models, particularly those than acquire a lower-level distributed representation jointly with an upper-level, more abstract representation that self-organizes to cluster based on inherent cross-pattern similarities. We further demonstrate TI-STDP's effectiveness in adapting a simple neuronal circuit that learns a simple bi-level, part-whole hierarchy from sensory input patterns.
Transcranial low-level laser stimulation in near infrared-II region for brain safety and protection
Authors: Zhilin Li, Yongheng Zhao, Yiqing Hu, Yang Li, Keyao Zhang, Zhibing Gao, Lirou Tan, Hanli Liu, XiaoLi Li, Aihua Cao, Zaixu Cui, Chenguang Zhao
Date: 2024-07-13 00:00:00
Tasks: EEG, Electroencephalogram (EEG)

Background: The use of near-infrared lasers for transcranial photobiomodulation (tPBM) offers a non-invasive method for influencing brain activity and is beneficial for various neurological conditions. Objective: To investigate the safety and neuroprotective properties of tPBM using near-infrared (NIR)-II laser stimulation. Methods: We conducted thirteen experiments involving multidimensional and quantitative methods and measured serum neurobiomarkers, performed electroencephalogram (EEG) and magnetic resonance imaging (MRI) scans, assessed executive functions, and collected a subjective questionnaire. Results: Significant reductions (n=15) in neuron specific enolase (NSE) levels were observed after treatment, indicating neuroprotective effects. No structural or functional brain abnormalities were observed, confirming the safety of tPBM. Additionally, cognitive and executive functions were not impaired, with participants' feedback indicating minimal discomfort. Conclusions: Our data indicate that NIR-II tPBM is safe with specific parameters, highlighting its potential for brain protection.
Retrospective for the Dynamic Sensorium Competition for predicting large-scale mouse primary visual cortex activity from videos
Authors: Polina Turishcheva, Paul G. Fahey, Michaela Vystrčilová, Laura Hansel, Rachel Froebe, Kayla Ponder, Yongrong Qiu, Konstantin F. Willeke, Mohammad Bashiri, Ruslan Baikulov, Yu Zhu, Lei Ma, Shan Yu, Tiejun Huang, Bryan M. Li, Wolf De Wulf, Nina Kudryashova, Matthias H. Hennig, Nathalie L. Rochefort, Arno Onken, Eric Wang, Zhiwei Ding, Andreas S. Tolias, Fabian H. Sinz, Alexander S Ecker
Date: 2024-07-12 00:00:00
Tasks: Benchmarking, Pupil Dilation

Understanding how biological visual systems process information is challenging because of the nonlinear relationship between visual input and neuronal responses. Artificial neural networks allow computational neuroscientists to create predictive models that connect biological and machine vision. Machine learning has benefited tremendously from benchmarks that compare different model on the same task under standardized conditions. However, there was no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we established the Sensorium 2023 Benchmark Competition with dynamic input, featuring a new large-scale dataset from the primary visual cortex of ten mice. This dataset includes responses from 78,853 neurons to 2 hours of dynamic stimuli per neuron, together with the behavioral measurements such as running speed, pupil dilation, and eye movements. The competition ranked models in two tracks based on predictive performance for neuronal responses on a held-out test set: one focusing on predicting in-domain natural stimuli and another on out-of-distribution (OOD) stimuli to assess model generalization. As part of the NeurIPS 2023 competition track, we received more than 160 model submissions from 22 teams. Several new architectures for predictive models were proposed, and the winning teams improved the previous state-of-the-art model by 50%. Access to the dataset as well as the benchmarking infrastructure will remain online at www.sensorium-competition.net.
Invariant inter-subject relational structures in the human visual cortex
Authors: Ofer Lipman, Shany Grossman, Doron Friedman, Yacov Hel-Or, Rafael Malach
Date: 2024-07-11 00:00:00

It is a fundamental behavior that different individuals see the world in a largely similar manner. This is an essential basis for humans' ability to cooperate and communicate. However, what are the neuronal properties that underlie these inter-subject commonalities of our visual world? Finding out what aspects of neuronal coding remain invariant across individuals' brains will shed light not only on this fundamental question but will also point to the neuronal coding scheme as the basis of visual perception. Here, we address this question by obtaining intracranial recordings from three cohorts of patients taking part in a different visual recognition task (overall 19 patients and 244 high-order visual contacts included in the analyses) and examining the neuronal coding scheme most consistent across individuals' visual cortex. Our results highlight relational coding - expressed by the set of similarity distances between profiles of pattern activations - as the most consistent representation across individuals. Alternative coding schemes, such as population vector coding or linear coding, failed to achieve similar inter-subject consistency. Our results thus support relational coding as the central neuronal code underlying individuals' shared perceptual content in the human brain.
Psychology of Artificial Intelligence: Epistemological Markers of the Cognitive Analysis of Neural Networks
Authors: Michael Pichat
Date: 2024-07-04 00:00:00
Tasks: Attribute

What is the "nature" of the cognitive processes and contents of an artificial neural network? In other words, how does an artificial intelligence fundamentally "think," and in what form does its knowledge reside? The psychology of artificial intelligence, as predicted by Asimov (1950), aims to study this AI probing and explainability-sensitive matter. This study requires a neuronal level of cognitive granularity, so as not to be limited solely to the secondary macro-cognitive results (such as cognitive and cultural biases) of synthetic neural cognition. A prerequisite for examining the latter is to clarify some epistemological milestones regarding the cognitive status we can attribute to its phenomenology.
Latent Diffusion for Neural Spiking Data
Authors: Jaivardhan Kapoor, Auguste Schulz, Julius Vetter, Felix Pei, Richard Gao, Jakob H. Macke
Date: 2024-06-27 00:00:00

Modern datasets in neuroscience enable unprecedented inquiries into the relationship between complex behaviors and the activity of many simultaneously recorded neurons. While latent variable models can successfully extract low-dimensional embeddings from such recordings, using them to generate realistic spiking data, especially in a behavior-dependent manner, still poses a challenge. Here, we present Latent Diffusion for Neural Spiking data (LDNS), a diffusion-based generative model with a low-dimensional latent space: LDNS employs an autoencoder with structured state-space (S4) layers to project discrete high-dimensional spiking data into continuous time-aligned latents. On these inferred latents, we train expressive (conditional) diffusion models, enabling us to sample neural activity with realistic single-neuron and population spiking statistics. We validate LDNS on synthetic data, accurately recovering latent structure, firing rates, and spiking statistics. Next, we demonstrate its flexibility by generating variable-length data that mimics human cortical activity during attempted speech. We show how to equip LDNS with an expressive observation model that accounts for single-neuron dynamics not mediated by the latent state, further increasing the realism of generated samples. Finally, conditional LDNS trained on motor cortical activity during diverse reaching behaviors can generate realistic spiking data given reach direction or unseen reach trajectories. In summary, LDNS simultaneously enables inference of low-dimensional latents and realistic conditional generation of neural spiking datasets, opening up further possibilities for simulating experimentally testable hypotheses.
Multi-object Data Integration in the Study of Primary Progressive Aphasia
Authors: Rene Gutierrez, Rajarshi Guhaniyogi, Aaron Scheffler, Maria Luisa Gorno-Tempini, Maria Luisa Mandelli, Giovanni Battistella
Date: 2024-06-26 00:00:00
Tasks: Data Integration

This article focuses on a multi-modal imaging data application where structural/anatomical information from gray matter (GM) and brain connectivity information in the form of a brain connectome network from functional magnetic resonance imaging (fMRI) are available for a number of subjects with different degrees of primary progressive aphasia (PPA), a neurodegenerative disorder (ND) measured through a speech rate measure on motor speech loss. The clinical/scientific goal in this study becomes the identification of brain regions of interest significantly related to the speech rate measure to gain insight into ND patterns. Viewing the brain connectome network and GM images as objects, we develop an integrated object response regression framework of network and GM images on the speech rate measure. A novel integrated prior formulation is proposed on network and structural image coefficients in order to exploit network information of the brain connectome while leveraging the interconnections among the two objects. The principled Bayesian framework allows the characterization of uncertainty in ascertaining a region being actively related to the speech rate measure. Our framework yields new insights into the relationship of brain regions associated with PPA, offering a deeper understanding of neuro-degenerative patterns of PPA. The supplementary file adds details about posterior computation and additional empirical results.
Is GPT-4 conscious?
Authors: Izak Tait, Joshua Bensemann, Ziqi Wang
Date: 2024-06-19 00:00:00

GPT-4 is often heralded as a leading commercial AI offering, sparking debates over its potential as a steppingstone toward artificial general intelligence. But does it possess consciousness? This paper investigates this key question using the nine qualitative measurements of the Building Blocks theory. GPT-4's design, architecture and implementation are compared to each of the building blocks of consciousness to determine whether it has achieved the requisite milestones to be classified as conscious or, if not, how close to consciousness GPT-4 is. Our assessment is that, while GPT-4 in its native configuration is not currently conscious, current technological research and development is sufficient to modify GPT-4 to have all the building blocks of consciousness. Consequently, we argue that the emergence of a conscious AI model is plausible in the near term. The paper concludes with a comprehensive discussion of the ethical implications and societal ramifications of engineering conscious AI entities.
Brain Dialogue Interface (BDI): A User-Friendly fMRI Model for Interactive Brain Decoding
Authors: Heng Huang, Lin Zhao, Zihao Wu, Xiaowei Yu, Jing Zhang, Xintao Hu, Dajiang Zhu, Tianming Liu
Date: 2024-06-17 00:00:00
Tasks: Brain Decoding

Brain decoding techniques are essential for understanding the neurocognitive system. Although numerous methods have been introduced in this field, accurately aligning complex external stimuli with brain activities remains a formidable challenge. To alleviate alignment difficulties, many studies have simplified their models by employing single-task paradigms and establishing direct links between brain/world through classification strategies. Despite improvements in decoding accuracy, this strategy frequently encounters issues with generality when adapting these models to various task paradigms. To address this issue, this study introduces a user-friendly decoding model that enables dynamic communication with the brain, as opposed to the static decoding approaches utilized by traditional studies. The model functions as a brain simulator, allowing for interactive engagement with the brain and enabling the decoding of a subject's experiences through dialogue-like queries. Uniquely, our model is trained in a completely unsupervised and task-free manner. Our experiments demonstrate the feasibility and versatility of our proposed method. Notably, our model demonstrates exceptional capabilities in signal compression, successfully representing the entire brain signal of approximately 185,751 voxels with just 32 signals. Furthermore, we show how our model can integrate seamlessly with multimodal models, thus enhancing the potential for controlling brain decoding through textual or image inputs.
Bayesian Theory of Consciousness as Exchangeable Emotion-Cognition Inference
Authors: Xin Li
Date: 2024-05-17 00:00:00
Tasks: Hippocampus, Navigate, Specificity

This paper proposes a unified framework in which consciousness emerges as a cycle-consistent, affectively anchored inference process, recursively structured by the interaction of emotion and cognition. Drawing from information theory, optimal transport, and the Bayesian brain hypothesis, we formalize emotion as a low-dimensional structural prior and cognition as a specificity-instantiating update. This emotion-cognition cycle minimizes joint uncertainty by aligning emotionally weighted priors with context-sensitive cognitive appraisals. Subjective experience thus arises as the informational footprint of temporally extended, affect-modulated simulation. We introduce the Exchangeable Integration Theory of Consciousness (EITC), modeling conscious episodes as conditionally exchangeable samples drawn from a latent affective self-model. This latent variable supports integration, via a unified cause-effect structure with nonzero irreducibility, and differentiation, by preserving contextual specificity across episodes. We connect this architecture to the Bayesian theory of consciousness through Rao-Blackwellized inference, which stabilizes inference by marginalizing latent self-structure while enabling adaptive updates. This mechanism ensures coherence, prevents inference collapse, and supports goal-directed simulation. The formal framework builds on De Finetti's exchangeability theorem, integrated information theory, and KL-regularized optimal transport. Overall, consciousness is reframed as a recursive inference process, shaped by emotion, refined by cognition, stabilized through exchangeability, and unified through a latent self-model that integrates experience across time.
A Numerical Comparison of Petri Net and Ordinary Differential Equation SIR Component Models
Authors: Trevor Reckell, Beckett Sterner, Petar Jevtić, Reggie Davidrajuh
Date: 2024-07-13 00:00:00
Tasks: Epidemiology, valid

Petri nets are a promising modeling framework for epidemiology, including the spread of disease across populations or within an individual. In particular, the Susceptible-Infectious-Recovered (SIR) compartment model is foundational for population epidemiological modeling and has been implemented in several prior Petri net studies. However, the SIR model is generally stated as a system of ordinary differential equations (ODEs) with continuous time and variables, while Petri nets are discrete event simulations. To our knowledge, no prior study has investigated the numerical equivalence of Petri net SIR models to the classical ODE formulation. We introduce crucial numerical techniques for implementing SIR models in the GPenSim package for Petri net simulations. We show that these techniques are critical for Petri net SIR models and show a relative root mean squared error of less than 1% compared to ODE simulations for biologically relevant parameter ranges. We conclude that Petri nets provide a valid framework for modeling SIR-type dynamics using biologically relevant parameter values provided that the other PN structures we outline are also implemented.
Fence decompositions and cherry covers in non-binary phylogenetic networks
Authors: Joan Carles Pons, Pau Vives López, Yukihiro Murakami, Leo van Iersel
Date: 2024-07-11 00:00:00
Tasks: ARC

Reticulate evolution can be modelled using phylogenetic networks. Tree-based networks, which are one of the more general classes of phylogenetic networks, have recently gained eminence for its ability to represent evolutionary histories with an underlying tree structure. To better understand tree-based networks, numerous characterizations have been proposed, based on tree embeddings, matchings, and arc partitions. Here, we build a bridge between two arc partition characterizations, namely maximal fence decompositions and cherry covers. Results on cherry covers have been found for general phylogenetic networks. We first show that the number of cherry covers is the same as the number of support trees (underlying tree structure of tree-based networks) for a given semibinary network. Maximal fence decompositions have only been defined thus far for binary networks (constraints on vertex degrees). We remedy this by generalizing fence decompositions to non-binary networks, and using this, we characterize semi-binary tree-based networks in terms of forbidden structures. Furthermore, we give an explicit enumeration of cherry covers of semi-binary networks, by studying its fence decomposition. Finally, we prove that it is possible to characterize semi-binary tree-child networks, a subclass of tree-based networks, in terms of the number of their cherry covers.
Methods for quantifying self-organization in biology: a forward-looking survey and tutorial
Authors: Alexandria Volkening
Date: 2024-07-15 00:00:00
Tasks: Topological Data Analysis

From flocking birds to schooling fish, organisms interact to form collective dynamics across the natural world. Self-organization is present at smaller scales as well: cells interact and move during development to produce patterns in fish skin, and wound healing relies on cell migration. Across these examples, scientists are interested in shedding light on the individual behaviors informing spatial group dynamics and in predicting the patterns that will emerge under altered agent interactions. One challenge to these goals is that images of self-organization -- whether empirical or generated by models -- are qualitative. To get around this, there are many methods for transforming qualitative pattern data into quantitative information. In this tutorial chapter, I survey some methods for quantifying self-organization, including order parameters, pair correlation functions, and techniques from topological data analysis. I also discuss some places that I see as especially promising for quantitative data, modeling, and data-driven approaches to continue meeting in the future.
AI Detectors are Poor Western Blot Classifiers: A Study of Accuracy and Predictive Values
Authors: Romain-Daniel Gosselin
Date: 2024-07-14 00:00:00
Tasks: Articles, Specificity

The recent rise of generative artificial intelligence (GenAI) capable of creating scientific images presents a challenge in the fight against academic fraud. This study evaluates the efficacy of three free web-based AI detectors in identifying AI-generated images of Western blots, which is a very common technique in biology. We tested these detectors on a collection of artificial Western blot images (n=48) that were created using ChatGPT 4 DALLE 3 and on authentic Western blots (n=48) that were sampled from articles published within four biology journals in 2015; this was before the rise of generative AI based on large language models. The results reveal that the sensitivity (0.9583 for Is It AI, 0.1875 for Hive Moderation, and 0.7083 for Illuminarty) and specificity (0.5417 for Is It AI, 0.8750 for Hive Moderation, and 0.4167 for Illuminarty) are very different. Positive predictive values (PPV) across various AI prevalence were low, for example reaching 0.1885 for Is It AI, 0.1429 for Hive Moderation, and 0.1189 for Illuminarty at an AI prevalence of 0.1. This highlights the difficulty in confidently determining image authenticity based on the output of a single detector. Reducing the size of Western blots from four to two lanes reduced test sensitivities and increased test specificities but did not markedly affect overall detector accuracies and also only slightly improved the PPV of one detector (Is It AI). These findings strongly argue against the use of free AI detectors to detect fake scientific images, and they demonstrate the urgent need for more robust detection tools that are specifically trained on scientific content such as Western blot images.
DMRIntTk: integrating different DMR sets based on density peak clustering
Authors: Wenjin Zhang, Wenlong Jie, Wanxin Cui, Guihua Duan, You Zou, Xiaoqing Peng
Date: 2024-07-14 00:00:00
Tasks: Clustering

\textbf{Background}: Identifying differentially methylated regions (DMRs) is a basic task in DNA methylation analysis. However, due to the different strategies adopted, different DMR sets will be predicted on the same dataset, which poses a challenge in selecting a reliable and comprehensive DMR set for downstream analysis. \textbf{Results}: Here, we develop DMRIntTk, a toolkit for integrating DMR sets predicted by different methods on a same dataset. In DMRIntTk, the genome is segmented into bins and the reliability of each DMR set at different methylation thresholds is evaluated. Then, the bins are weighted based on the covered DMR sets and integrated into DMRs by using a density peak clustering algorithm. To demonstrate the practicality of DMRIntTk, DMRIntTk was applied to different scenarios, including different tissues with relatively large methylation differences, cancer tissues versus normal tissues with medium methylation differences, and disease tissues versus normal tissues with subtle methylation differences. The results show that DMRIntTk can effectively trim the regions with small methylation differences in the original DMR sets and therefore it can enhance the proportion of DMRs with higher methylation differences. In addition, the overlap analysis suggests that the integrated DMR sets are quite comprehensive, and the functional analysis indicates the integrated disease-related DMR sets are significantly enriched in biological pathways, which are associated with the pathological mechanisms of the diseases. \textbf{Conclusions}: Conclusively, DMRIntTk can help researchers obtaining a reliable and comprehensive DMR set from many prediction methods. \textbf{Keywords}:{Differentially methylated regions, Methylation array, Cancer-related differentially methylated regions, Tissue-specific differentially methylated regions, Density peak clustering.}