pwc-archive/papers-with-abstracts huggingface dataset:
JanusDNA: A Powerful Bi-directional Hybrid DNA Foundation Model
Authors: Qihao Duan, Bingding Huang, Zhenqiao Song, Irina Lehmann, Lei Gu, Roland Eils, Benjamin Wild
Date: 2025-05-22 00:00:00
Tasks: GPU, Long-range modeling, Mamba, Mixture-of-Experts

Large language models (LLMs) have revolutionized natural language processing and are increasingly applied to other sequential data types, including genetic sequences. However, adapting LLMs to genomics presents significant challenges. Capturing complex genomic interactions requires modeling long-range dependencies within DNA sequences, where interactions often span over 10,000 base pairs, even within a single gene, posing substantial computational burdens under conventional model architectures and training paradigms. Moreover, standard LLM training approaches are suboptimal for DNA: autoregressive training, while efficient, supports only unidirectional understanding. However, DNA is inherently bidirectional, e.g., bidirectional promoters regulate transcription in both directions and account for nearly 11% of human gene expression. Masked language models (MLMs) allow bidirectional understanding but are inefficient, as only masked tokens contribute to the loss per step. To address these limitations, we introduce JanusDNA, the first bidirectional DNA foundation model built upon a novel pretraining paradigm that combines the optimization efficiency of autoregressive modeling with the bidirectional comprehension of masked modeling. JanusDNA adopts a hybrid Mamba, Attention and Mixture of Experts (MoE) architecture, combining long-range modeling of Attention with efficient sequential learning of Mamba. MoE layers further scale model capacity via sparse activation while keeping computational cost low. Notably, JanusDNA processes up to 1 million base pairs at single nucleotide resolution on a single 80GB GPU. Extensive experiments and ablations show JanusDNA achieves new SOTA results on three genomic representation benchmarks, outperforming models with 250x more activated parameters. Code: https://github.com/Qihao-Duan/JanusDNA
The global communication pathways of the human brain transcend the cortical-subcortical-cerebellar division
Authors: Julian Schulte, Mario Senden, Gustavo Deco, Xenia Kobeleva, Gorka Zamora-López
Date: 2025-05-28 00:00:00

Understanding how cortex, subcortex and cerebellum integrate is a major challenge for neuroscience, however, studies of the brain's structural connectivity have mostly focused on cortico-cortical links. Here, we used diffusion imaging to construct the structural connectome of the entire human brain including 360 cortical, 233 subcortical, and 125 cerebellar regions of interest (ROIs). We found that the brain forms a modular and hierarchical network architecture, organized into modules of mixed cortical, subcortical and/or cerebellar regions, and whose cross-modular pathways are centralized through highly connected hub ROIs (a `rich-club'). This global rich-club is subcortically dominated and, surprisingly, composed of hub ROIs from all subcortical structures rather than one region like the thalamus, centralizing the communication pathways. This study improves our understanding of the human brain's organization. It provides structural evidence to question the prevalent cortico-centric notion by revealing a connectome centered at the subcortex but made of transversal pathways.
Self-orthogonalizing attractor neural networks emerging from the free energy principle
Authors: Tamas Spisak, Karl Friston
Date: 2025-05-28 00:00:00

Attractor dynamics are a hallmark of many complex systems, including the brain. Understanding how such self-organizing dynamics emerge from first principles is crucial for advancing our understanding of neuronal computations and the design of artificial intelligence systems. Here we formalize how attractor networks emerge from the free energy principle applied to a universal partitioning of random dynamical systems. Our approach obviates the need for explicitly imposed learning and inference rules and identifies emergent, but efficient and biologically plausible inference and learning dynamics for such self-organizing systems. These result in a collective, multi-level Bayesian active inference process. Attractors on the free energy landscape encode prior beliefs; inference integrates sensory data into posterior beliefs; and learning fine-tunes couplings to minimize long-term surprise. Analytically and via simulations, we establish that the proposed networks favor approximately orthogonalized attractor representations, a consequence of simultaneously optimizing predictive accuracy and model complexity. These attractors efficiently span the input subspace, enhancing generalization and the mutual information between hidden causes and observable effects. Furthermore, while random data presentation leads to symmetric and sparse couplings, sequential data fosters asymmetric couplings and non-equilibrium steady-state dynamics, offering a natural extension to conventional Boltzmann Machines. Our findings offer a unifying theory of self-organizing attractor networks, providing novel insights for AI and neuroscience.
Do Large Language Models Think Like the Brain? Sentence-Level Evidence from fMRI and Hierarchical Embeddings
Authors: Yu Lei, Xingyang Ge, Yi Zhang, Yiming Yang, Bolei Ma
Date: 2025-05-28 00:00:00
Tasks: Sentence

Understanding whether large language models (LLMs) and the human brain converge on similar computational principles remains a fundamental and important question in cognitive neuroscience and AI. Do the brain-like patterns observed in LLMs emerge simply from scaling, or do they reflect deeper alignment with the architecture of human language processing? This study focuses on the sentence-level neural mechanisms of language models, systematically investigating how hierarchical representations in LLMs align with the dynamic neural responses during human sentence comprehension. By comparing hierarchical embeddings from 14 publicly available LLMs with fMRI data collected from participants, who were exposed to a naturalistic narrative story, we constructed sentence-level neural prediction models to precisely identify the model layers most significantly correlated with brain region activations. Results show that improvements in model performance drive the evolution of representational architectures toward brain-like hierarchies, particularly achieving stronger functional and anatomical correspondence at higher semantic abstraction levels.
Flexible Tool Selection through Low-dimensional Attribute Alignment of Vision and Language
Authors: Guangfu Hao, Haojie Wen, Liangxuna Guo, Yang Chen, Yanchao Bi, Shan Yu
Date: 2025-05-28 00:00:00
Tasks: Attribute

Flexible tool selection reflects a complex cognitive ability that distinguishes humans from other species, yet computational models that capture this ability remain underdeveloped. We developed a framework using low-dimensional attribute representations to bridge visual tool perception and linguistic task understanding. We constructed a comprehensive dataset (ToolNet) containing 115 common tools labeled with 13 carefully designed attributes spanning physical, functional, and psychological properties, paired with natural language scenarios describing tool usage. Visual encoders (ResNet or ViT) extract attributes from tool images while fine-tuned language models (GPT-2, LLaMA, DeepSeek) derive required attributes from task descriptions. Our approach achieves 74% accuracy in tool selection tasks-significantly outperforming direct tool matching (20%) and smaller multimodal models (21%-58%), while approaching performance of much larger models like GPT-4o (73%) with substantially fewer parameters. Ablation studies revealed that manipulation-related attributes (graspability, hand-relatedness, elongation) consistently prove most critical across modalities. This work provides a parameter-efficient, interpretable solution that mimics human-like tool cognition, advancing both cognitive science understanding and practical applications in tool selection tasks.
Visual Large Language Models Exhibit Human-Level Cognitive Flexibility in the Wisconsin Card Sorting Test
Authors: Guangfu Hao, Frederic Alexandre, Shan Yu
Date: 2025-05-28 00:00:00

Cognitive flexibility has been extensively studied in human cognition but remains relatively unexplored in the context of Visual Large Language Models (VLLMs). This study assesses the cognitive flexibility of state-of-the-art VLLMs (GPT-4o, Gemini-1.5 Pro, and Claude-3.5 Sonnet) using the Wisconsin Card Sorting Test (WCST), a classic measure of set-shifting ability. Our results reveal that VLLMs achieve or surpass human-level set-shifting capabilities under chain-of-thought prompting with text-based inputs. However, their abilities are highly influenced by both input modality and prompting strategy. In addition, we find that through role-playing, VLLMs can simulate various functional deficits aligned with patients having impairments in cognitive flexibility, suggesting that VLLMs may possess a cognitive architecture, at least regarding the ability of set-shifting, similar to the brain. This study reveals the fact that VLLMs have already approached the human level on a key component underlying our higher cognition, and highlights the potential to use them to emulate complex brain processes.
Organizational Regularities in Recurrent Neural Networks
Authors: Claus Metzner, Achim Schilling, Andreas Maier, Patrick Krauss
Date: 2025-05-28 00:00:00

Previous work has shown that the dynamical regime of Recurrent Neural Networks (RNNs) - ranging from oscillatory to chaotic and fixpoint behavior - can be controlled by the global distribution of weights in connection matrices with statistically independent elements. However, it remains unclear how network dynamics respond to organizational regularities in the weight matrix, as often observed in biological neural networks. Here, we investigate three such regularities: (1) monopolar output weights per neuron, in accordance with Dale's principle, (2) reciprocal symmetry between neuron pairs, as in Hopfield networks, and (3) modular structure, where strongly connected blocks are embedded in a background of weaker connectivity. We construct weight matrices in which the strength of each regularity can be continuously tuned via control parameters, and analyze how key dynamical signatures of the RNN evolve as a function of these parameters. Moreover, using the RNN for actual information processing in a reservoir computing framework, we study how each regularity affects performance. We find that Dale monopolarity and modularity significantly enhance task accuracy, while Hopfield reciprocity tends to reduce it by promoting early saturation, limiting reservoir flexibility.
Early Assessment of Artificial Lower Extremity Sensory Response Times and Proprioceptive Acuity via Sensory Cortex Electrical Stimulation
Authors: Won Joon Sohn, Jeffrey Lim, Po T. Wang, Susan J. Shaw, Michelle Armacost, Hui Gong, Brian Lee, Darrin Lee, Payam Heydari, Richard A. Andersen, Charles Y. Liu, Zoran Nenadic, An H. Do
Date: 2025-05-28 00:00:00

Bi-directional brain computer interfaces (BD-BCIs) may restore brain-controlled walking and artificial leg sensation after spinal cord injury. Current BD-BCIs provide only simplistic "tingling" feedback, which lacks proprioceptive information to perceive critical gait events (leg swing, double support). This information must also be perceived adequately fast to facilitate timely motor responses. Here, we investigated utilizing primary sensory cortex (S1) direct cortical electrical stimulation (DCES) to deliver leg proprioceptive information and measured response times to artificial leg sensations. Subjects with subdural electrocorticogram electrodes over S1 leg areas participated in two tasks: (1) Proprioceptive acuity: subjects identified the difference between DCES-induced percepts emulating various leg swing speeds; (2) Sensory response: measuring subjects' reaction time to DCES-induced leg sensations, with DCES-hand, visual and auditory control conditions. Three subjects were recruited. Only one completed the proprioceptive assessment, achieving 80%, 70%, 60%, and 53% accuracy in discriminating between fast/slow, fast/medium, medium/slow, and same speeds, respectively (p-value=1.9x10$^{-5}$). Response times for leg/hand percepts were 1007$\pm$413/599$\pm$171 ms, visual leg/hand responses were 528$\pm$137/384$\pm$84 ms, and auditory leg/hand responses were 393$\pm$106/352$\pm$93 ms, respectively. These results suggest proprioceptive information can be delivered artificially, but perception may be significantly delayed. Future work should address improving acuity, reducing response times, and expanding sensory modalities.
Optimizing fMRI Data Acquisition for Decoding Natural Speech with Limited Participants
Authors: Louis Jalouzot, Alexis Thual, Yair Lakretz, Christophe Pallier, Bertrand Thirion
Date: 2025-05-27 00:00:00

We investigate optimal strategies for decoding perceived natural speech from fMRI data acquired from a limited number of participants. Leveraging Lebel et al. (2023)'s dataset of 8 participants, we first demonstrate the effectiveness of training deep neural networks to predict LLM-derived text representations from fMRI activity. Then, in this data regime, we observe that multi-subject training does not improve decoding accuracy compared to single-subject approach. Furthermore, training on similar or different stimuli across subjects has a negligible effect on decoding accuracy. Finally, we find that our decoders better model syntactic than semantic features, and that stories containing sentences with complex syntax or rich semantic content are more challenging to decode. While our results demonstrate the benefits of having extensive data per participant (deep phenotyping), they suggest that leveraging multi-subject for natural speech decoding likely requires deeper phenotyping or a substantially larger cohort.
Capturing Aperiodic Temporal Dynamics of EEG Signals through Stochastic Fluctuation Modeling
Authors: Yuhao Sun, Zhiyuan Ma, Xinke Shen, Jinhao Li, Guan Wang, Sen Song
Date: 2025-05-25 00:00:00
Tasks: EEG

Electrophysiological brain signals, such as electroencephalography (EEG), exhibit both periodic and aperiodic components, with the latter often modeled as 1/f noise and considered critical to cognitive and neurological processes. Although various theoretical frameworks have been proposed to account for aperiodic activity, its scale-invariant and long-range temporal dependency remain insufficiently explained. Drawing on neural fluctuation theory, we propose a novel framework that parameterizes intrinsic stochastic neural fluctuations to account for aperiodic dynamics. Within this framework, we introduce two key parameters-self-similarity and scale factor-to characterize these fluctuations. Our findings reveal that EEG fluctuations exhibit self-similar and non-stable statistical properties, challenging the assumptions of conventional stochastic models in neural dynamical modeling. Furthermore, the proposed parameters enable the reconstruction of EEG-like signals that faithfully replicate the aperiodic spectrum, including the characteristic 1/f spectral profile, and long range dependency. By linking structured neural fluctuations to empirically observed aperiodic EEG activity, this work offers deeper mechanistic insights into brain dynamics, resulting in a more robust biomarker candidate than the traditional 1/f slope, and provides a computational methodology for generating biologically plausible neurophysiological signals.
Multi-Modal Spectral Parametrization Method (MMSPM) for analyzing EEG activity with distinct scaling regimes
Authors: Frigyes Samuel Racz, John Milton, Juan Luis Cabrera, Gábor Csukly, José del R. Millán
Date: 2025-05-23 00:00:00
Tasks: EEG

Aperiodic neural activity has been the subject of intense research interest lately as it could reflect on the cortical excitation/inhibition ratio, which is suspected to be affected in numerous clinical conditions. This phenomenon is characterized via the aperiodic scaling exponent $\beta$, equal to the spectral slope following log-log transformation of power spectra. Despite recent progress, however, most current methods do not take into consideration the plausible multimodal nature in the power spectra of neurophysiological recordings - i.e., $\beta$ might be different in low- ($\beta_{lo}$) and high-frequency ($\beta_{hi}$) regimes -, especially in case of $|\beta_{lo}|>|\beta_{hi}|$. Here we propose an algorithm, the multi-modal spectral parametrization method (MMSPM) that aims to account for this issue. MMSPM estimates $\beta_{lo}$ and $\beta_{hi}$ separately using a constrained, piece-wise regression technique, and also assesses if they are significantly different or instead the spectrum is indeed unimodal and can be characterized simply with broadband $\beta$. Here we present the MMSPM algorithm and evaluate its performance in silico on simulated power spectra. Then, we use MMSPM on resting-state electroencephalography (EEG) data collected from 19 young, healthy volunteers, as well as on a separate dataset of EEG recordings from 30 schizophrenia patients and 31 healthy controls, and demonstrate that broadband (0.1-100 Hz and 0.5-45 Hz) EEG spectra can indeed present a bimodality pattern with significantly steeper low-range ($<\sim2$ Hz) and flatter high-range scaling regimes (i.e., $|\beta_{lo}|>|\beta_{hi}|$). Clinical relevance: The MMSPM method characterizes aperiodic neural activity in distinct scaling regimes, which can be relevant in numerous pathological conditions such as dementia or schizophrenia.
ConnectomeDiffuser: Generative AI Enables Brain Network Construction from Diffusion Tensor Imaging
Authors: Xuhang Chen, Michael Kwok-Po Ng, Kim-Fung Tsang, Chi-Man Pun, Shuqiang Wang
Date: 2025-05-23 00:00:00
Tasks: Diagnostic

Brain network analysis plays a crucial role in diagnosing and monitoring neurodegenerative disorders such as Alzheimer's disease (AD). Existing approaches for constructing structural brain networks from diffusion tensor imaging (DTI) often rely on specialized toolkits that suffer from inherent limitations: operator subjectivity, labor-intensive workflows, and restricted capacity to capture complex topological features and disease-specific biomarkers. To overcome these challenges and advance computational neuroimaging instrumentation, ConnectomeDiffuser is proposed as a novel diffusion-based framework for automated end-to-end brain network construction from DTI. The proposed model combines three key components: (1) a Template Network that extracts topological features from 3D DTI scans using Riemannian geometric principles, (2) a diffusion model that generates comprehensive brain networks with enhanced topological fidelity, and (3) a Graph Convolutional Network classifier that incorporates disease-specific markers to improve diagnostic accuracy. ConnectomeDiffuser demonstrates superior performance by capturing a broader range of structural connectivity and pathology-related information, enabling more sensitive analysis of individual variations in brain networks. Experimental validation on datasets representing two distinct neurodegenerative conditions demonstrates significant performance improvements over other brain network methods. This work contributes to the advancement of instrumentation in the context of neurological disorders, providing clinicians and researchers with a robust, generalizable measurement framework that facilitates more accurate diagnosis, deeper mechanistic understanding, and improved therapeutic monitoring of neurodegenerative diseases such as AD.
Transformer brain encoders explain human high-level visual responses
Authors: Hossein Adeli, Minni Sun, Nikolaus Kriegeskorte
Date: 2025-05-22 00:00:00

A major goal of neuroscience is to understand brain computations during visual processing in naturalistic settings. A dominant approach is to use image-computable deep neural networks trained with different task objectives as a basis for linear encoding models. However, in addition to requiring tuning a large number of parameters, the linear encoding approach ignores the structure of the feature maps both in the brain and the models. Recently proposed alternatives have focused on decomposing the linear mapping to spatial and feature components but focus on finding static receptive fields for units that are applicable only in early visual areas. In this work, we employ the attention mechanism used in the transformer architecture to study how retinotopic visual features can be dynamically routed to category-selective areas in high-level visual processing. We show that this computational motif is significantly more powerful than alternative methods in predicting brain activity during natural scene viewing, across different feature basis models and modalities. We also show that this approach is inherently more interpretable, without the need to create importance maps, by interpreting the attention routing signal for different high-level categorical areas. Our approach proposes a mechanistic model of how visual information from retinotopic maps can be routed based on the relevance of the input content to different category-selective regions.
Brain volume predicts survival of colliding-spreading messages on mammal brain networks
Authors: Yan Hao, Tate Tower, Hannah Lax, Marc-Thorsten Hütt, Daniel J. Graham
Date: 2025-05-21 00:00:00

White matter in mammal brains forms a densely interconnected communication network. Due to high edge density, along with continuous generation and spread of messages, brain networks must contend with congestion, which may limit polysynaptic message survival in complex ways. Here we study congestion with a colliding-spreading model, a synchronous Markovian process where messages arriving coincidentally at a node are deleted, while surviving messages spread to all nearest neighbors. Numerical simulations on a large sample of mammal connectomes demonstrate that message survival follows a positively skewed lognormal-like distribution for all connectomes tested. This distribution mirrors empirical distributions of interareal distances and edge weights. However, the distribution of message survival is an emergent property of system dynamics and graph topology alone; it does not require interareal distances or edge weights. We then show that message survival is well predicted by log brain volume (r = -0.64) across species. Thus, messages survive longer in small compared to large mammals, in accordance with the notion that larger brains become more modular. Chimpanzee showed the lowest message survival among the animals tested. We describe structural properties that may play a role in generating these dynamics and we discuss implications of our results for brain function and evolution.