Daily Papers

We performed variability analysis of the multiwavelength light curves for the flat-spectrum radio quasar PKS 0727-11. Using the generalized Lomb-Scargle periodogram, we identified a possible quasi-periodic oscillation (QPO) of sim 168.6 days (persisted for 6 cycles, with a significance of 3.8sigma) in the gamma-ray light curve during the flare period (MJD 54687-55738). It is the first time that periodic variations have been detected in this source, and further supported by other methods: weighted wavelet z-transform, phase dispersion minimization, REDFIT, autoregressive integrated moving average model, and structure function analysis. Cross-correlation analysis shows that there is a strong correlation between multi-band light variations, indicating that gamma-ray and radio flares may originate from the same disturbance, and the distance between the emission regions of gamma-ray and radio flares is calculated based on the time lag. We demonstrate that QPO arising from the non-ballistic helical jet motion driven by the orbital motion in a supermassive binary black hole is a plausible physical explanation. In this scenario, the estimated mass of the primary black hole is Msim3.66times10^8-5.79times10^{9}M_odot.

There is renewed interest in modeling and understanding the nervous system of the nematode Caenorhabditis elegans (C. elegans), as this small model system provides a path to bridge the gap between nervous system structure (connectivity) and function (physiology). However, existing physiology datasets, whether involving passive recording or stimulation, are in distinct formats, and connectome datasets require preprocessing before analysis can commence. Here we compile and homogenize datasets of neural activity and connectivity. Our neural activity dataset is derived from 11 C. elegans neuroimaging experiments, while our connectivity dataset is compiled from 9 connectome annotations based on 3 primary electron microscopy studies and 1 signal propagation study. Physiology datasets, collected under varying protocols, measure calcium fluorescence in labeled subsets of the worm's 300 neurons. Our preprocessing pipeline standardizes these datasets by consistently ordering labeled neurons and resampling traces to a common sampling rate, yielding recordings from approximately 900 worms and 250 uniquely labeled neurons. The connectome datasets, collected from electron microscopy reconstructions, represent the entire nervous system as a graph of connections. Our collection is accessible on HuggingFace, facilitating analysis of the structure-function relationship in biology using modern neural network architectures and enabling cross-lab and cross-animal comparisons.

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

The local structure of V_{2}O_{3}, an archetypal strongly correlated electron system that displays a metal-insulator transition around 160 K, has been investigated via pair distribution function (PDF) analysis of neutron and x-ray total scattering data. The rhombohedral-to-monoclinic structural phase transition manifests as an abrupt change on all length scales in the observed PDF. No monoclinic distortions of the local structure are found above the transition, although coexisting regions of phase-separated rhombohedral and monoclinic symmetry are observed between 150 K and 160 K. This lack of structural fluctuations above the transition contrasts with the known presence of magnetic fluctuations in the high-temperature state, suggesting that the lattice degree of freedom plays a secondary role behind the spin degree of freedom in the transition mechanism.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

We investigate the internal structure of language model computations using causal analysis and demonstrate two motifs: (1) a form of adaptive computation where ablations of one attention layer of a language model cause another layer to compensate (which we term the Hydra effect) and (2) a counterbalancing function of late MLP layers that act to downregulate the maximum-likelihood token. Our ablation studies demonstrate that language model layers are typically relatively loosely coupled (ablations to one layer only affect a small number of downstream layers). Surprisingly, these effects occur even in language models trained without any form of dropout. We analyse these effects in the context of factual recall and consider their implications for circuit-level attribution in language models.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

What fundamental properties of reward functions enable efficient sparse-reward reinforcement learning? We address this question through the lens of low-rank structure in reward matrices, showing that such structure induces a sharp transition from exponential to polynomial sample complexity, the first result of this kind for sparse-reward RL. We introduce Policy-Aware Matrix Completion (PAMC), which connects matrix completion theory with reinforcement learning via a new analysis of policy-dependent sampling. Our framework provides: (i) impossibility results for general sparse reward observation, (ii) reward-free representation learning from dynamics, (iii) distribution-free confidence sets via conformal prediction, and (iv) robust completion guarantees that degrade gracefully when low-rank structure is only approximate. Empirically, we conduct a pre-registered evaluation across 100 systematically sampled domains, finding exploitable structure in over half. PAMC improves sample efficiency by factors between 1.6 and 2.1 compared to strong exploration, structured, and representation-learning baselines, while adding only about 20 percent computational overhead.These results establish structural reward learning as a promising new paradigm, with immediate implications for robotics, healthcare, and other safety-critical, sample-expensive applications.

Modern machine learning algorithms, especially deep learning based techniques, typically involve careful hyperparameter tuning to achieve the best performance. Despite the surge of intense interest in practical techniques like Bayesian optimization and random search based approaches to automating this laborious and compute intensive task, the fundamental learning theoretic complexity of tuning hyperparameters for deep neural networks is poorly understood. Inspired by this glaring gap, we initiate the formal study of hyperparameter tuning complexity in deep learning through a recently introduced data driven setting. We assume that we have a series of deep learning tasks, and we have to tune hyperparameters to do well on average over the distribution of tasks. A major difficulty is that the utility function as a function of the hyperparameter is very volatile and furthermore, it is given implicitly by an optimization problem over the model parameters. To tackle this challenge, we introduce a new technique to characterize the discontinuities and oscillations of the utility function on any fixed problem instance as we vary the hyperparameter; our analysis relies on subtle concepts including tools from differential/algebraic geometry and constrained optimization. This can be used to show that the learning theoretic complexity of the corresponding family of utility functions is bounded. We instantiate our results and provide sample complexity bounds for concrete applications tuning a hyperparameter that interpolates neural activation functions and setting the kernel parameter in graph neural networks.

Conventional music structure analysis algorithms aim to divide a song into segments and to group them with abstract labels (e.g., 'A', 'B', and 'C'). However, explicitly identifying the function of each segment (e.g., 'verse' or 'chorus') is rarely attempted, but has many applications. We introduce a multi-task deep learning framework to model these structural semantic labels directly from audio by estimating "verseness," "chorusness," and so forth, as a function of time. We propose a 7-class taxonomy (i.e., intro, verse, chorus, bridge, outro, instrumental, and silence) and provide rules to consolidate annotations from four disparate datasets. We also propose to use a spectral-temporal Transformer-based model, called SpecTNT, which can be trained with an additional connectionist temporal localization (CTL) loss. In cross-dataset evaluations using four public datasets, we demonstrate the effectiveness of the SpecTNT model and CTL loss, and obtain strong results overall: the proposed system outperforms state-of-the-art chorus-detection and boundary-detection methods at detecting choruses and boundaries, respectively.

In this study, we investigate the protection offered by federated learning algorithms against eavesdropping adversaries. In our model, the adversary is capable of intercepting model updates transmitted from clients to the server, enabling it to create its own estimate of the model. Unlike previous research, which predominantly focuses on safeguarding client data, our work shifts attention protecting the client model itself. Through a theoretical analysis, we examine how various factors, such as the probability of client selection, the structure of local objective functions, global aggregation at the server, and the eavesdropper's capabilities, impact the overall level of protection. We further validate our findings through numerical experiments, assessing the protection by evaluating the model accuracy achieved by the adversary. Finally, we compare our results with methods based on differential privacy, underscoring their limitations in this specific context.

In the pursuit to understand the intricacies of human brain's visual processing, reconstructing dynamic visual experiences from brain activities emerges as a challenging yet fascinating endeavor. While recent advancements have achieved success in reconstructing static images from non-invasive brain recordings, the domain of translating continuous brain activities into video format remains underexplored. In this work, we introduce NeuroCine, a novel dual-phase framework to targeting the inherent challenges of decoding fMRI data, such as noises, spatial redundancy and temporal lags. This framework proposes spatial masking and temporal interpolation-based augmentation for contrastive learning fMRI representations and a diffusion model enhanced by dependent prior noise for video generation. Tested on a publicly available fMRI dataset, our method shows promising results, outperforming the previous state-of-the-art models by a notable margin of {20.97%}, {31.00%} and {12.30%} respectively on decoding the brain activities of three subjects in the fMRI dataset, as measured by SSIM. Additionally, our attention analysis suggests that the model aligns with existing brain structures and functions, indicating its biological plausibility and interpretability.

Recent works on structured text translation remain limited to the sentence level, as they struggle to effectively handle the complex document-level XML or HTML structures. To address this, we propose Format Reinforcement Learning (FormatRL), which employs Group Relative Policy Optimization on top of a supervised fine-tuning model to directly optimize novel structure-aware rewards: 1) TreeSim, which measures structural similarity between predicted and reference XML trees and 2) Node-chrF, which measures translation quality at the level of XML nodes. Additionally, we apply StrucAUC, a fine-grained metric distinguishing between minor errors and major structural failures. Experiments on the SAP software-documentation benchmark demonstrate improvements across six metrics and an analysis further shows how different reward functions contribute to improvements in both structural and translation quality.