Gene regulatory network (GRN) inference serves as a cornerstone for deciphering cellular decision-making processes. Early approaches rely exclusively on gene expression data, thus their predictive power remain fundamentally constrained by the vast combinatorial space of potential gene-gene interactions. Subsequent methods integrate prior knowledge to mitigate this challenge by restricting the solution space to biologically plausible interactions. However, we argue that the effectiveness of these approaches is contingent upon the precision of prior information and the reduction in the search space will circumscribe the models' potential for novel biological discoveries. To address these limitations, we introduce KINDLE, a three-stage framework that decouples GRN inference from prior knowledge dependencies.

Model fingerprinting has emerged as a powerful tool for model owners to identify their shared model given API access. In order to lower false discovery rate, fight fingerprint leakage, and defend against coalitions of model users attempting to bypass detection, we argue that scaling up the number of fingerprints one can embed into a model, i.e. Scalability of fingerprints, is critical. Hence, we pose scalability as a crucial requirement for fingerprinting schemes. We experiment with fingerprint design at a scale significantly larger than previously considered, and introduce a new method, dubbed Perinucleus sampling, to generate scalable, persistent, and harmless fingerprints. We demonstrate that this scheme can add 24,576 fingerprints to a Llama-3.1-8B

Test-time adaptation (TTA) methods have gained significant attention for enhancing the performance of vision-language models (VLMs) such as CLIP during inference, without requiring additional labeled data. However, current TTA researches generally suffer from major limitations such as duplication of baseline results, limited evaluation metrics, inconsistent experimental settings, and insufficient analysis. These problems hinder fair comparisons between TTA methods and make it difficult to assess their practical strengths and weaknesses. To address these challenges, we introduce TTA-VLM, a comprehensive benchmark for evaluating TTA methods on VLMs. Our benchmark implements 8 episodic TTA and 7 online TTA methods within a unified and reproducible framework, and evaluates them across 15 widely used datasets. Unlike prior studies focused solely on CLIP, we extend the evaluation to SigLIP--a model trained with a Sigmoid loss--and include training-time tuning methods such as CoOp, MaPLe, and TeCoA to assess generality. Beyond classification accuracy, TTA-VLM incorporates various evaluation metrics, including robustness, calibration, out-of-distribution detection, and stability, enabling a more holistic assessment of TTA methods. Through extensive experiments, we find that 1) existing TTA methods produce limited gains compared to the previous pioneering work; 2) current TTA methods exhibit poor collaboration with trainingtime fine-tuning methods; 3) accuracy gains frequently come at the cost of reduced model trustworthiness. We release TTA-VLM to provide fair comparison and comprehensive evaluation of TTA methods for VLMs, and we hope it encourages the community to develop more reliable and generalizable TTA strategies.

Boosting methods often achieve excellent classification accuracy, but can experience notable performance degradation in the presence of label noise. Existing robust methods for boosting provide theoretical robustness guarantees for certain types of label noise, and can exhibit only moderate performance degradation. However, previous theoretical results do not account for realistic types of noise and finite training sizes, and existing robust methods can provide unsatisfactory accuracies, even without noise. This paper presents methods for robust minimax boosting (RMBoost) that minimize worst-case error probabilities and are robust to general types of label noise. In addition, we provide finite-sample performance guarantees for RMBoost with respect to the error obtained without noise and with respect to the best possible error (Bayes risk). The experimental results corroborate that RMBoost is not only resilient to label noise but can also provide strong classification accuracy.

Pre-trained Large language models (LLMs) have shown impressive advancements in functional magnetic resonance imaging (fMRI) analysis and causal discovery. Considering the unique nature of the causal discovery field, which focuses on extracting causal graphs from observed data, research on LLMs in this field is still at an early exploratory stage. As a subfield of causal discovery, effective connectivity (EC) has received even less attention, and LLM-based approaches in EC remain unexplored. Existing LLM-based approaches for causal discovery typically rely on iterative querying to assess the causal influence between variable pairs, without any model adaptation or fine-tuning, making them ill-suited for handling the cross-modal gap and complex causal structures. To this end, we propose BrainECLLM, the first method to fine-tune LLMs for estimating brain EC from fMRI data. Specifically, multiscale decomposition mixing module decomposes fMRI time series data into short-term and long-term multiscale trends, then mixing them in bottom-up (fine to coarse) and top-down (coarse to fine) manner to extract multiscale temporal variations. And cross attention is applied with pre-trained word embeddings to ensure consistency between the fMRI input and pre-trained natural language. The experimental results on simulated and real resting-state fMRI datasets demonstrate that BrainEC-LLM can achieve superior performance when compared to state-of-the-art baselines. The code is available at https: //github.com/XiongWenXww/BrainEC-LLM.

Extracting neural signals at the single motor neuron level provides an optimal control signal for neuroprosthetic applications. However, current algorithms to decompose motor units from high-density electromyography (HD-EMG) are timeconsuming and inconsistent, limiting their application to controlled scenarios in a research setting. We introduce MUelim, an algorithm for efficient motor unit decomposition that uses approximate joint diagonalization with a subtractive approach to rapidly identify and refine candidate sources. The algorithm incorporates an extend-lag procedure to augment data for enhanced source separability prior to diagonalization. By systematically iterating and eliminating redundant or noisy sources, MUelim achieves high decomposition accuracy while significantly reducing computational complexity, making it well-suited for real-time applications.

Out-of-distribution (OOD) fine-tuning has emerged as a promising approach for anomaly segmentation. Current OOD fine-tuning strategies typically employ global-level objectives, aiming to guide segmentation models to accurately predict a large number of anomaly pixels. However, these strategies often perform poorly on small anomalies. To address this issue, we propose an instance-level OOD fine-tuning framework, dubbed LNOIB (Leaving No OODInstance Behind). We start by theoretically analyzing why global-level objectives fail to segment small anomalies. Building on this analysis, we introduce a simple yet effective instancelevel objective. Moreover, we propose a feature separation objective to explicitly constrain the representations of anomalies, which are prone to be smoothed by their in-distribution (ID) surroundings. LNOIB integrates these objectives to enhance the segmentation of small anomalies and serves as a paradigm adaptable to existing OOD fine-tuning strategies, without introducing additional inference cost. Experimental results show that integrating LNOIB into various OOD fine-tuning strategies yields significant improvements, particularly in component-level results, highlighting its strength in comprehensive anomaly segmentation.

Out-of-distribution (OOD) detection and segmentation are crucial for deploying machine learning models in safety-critical applications such as autonomous driving and robot-assisted surgery. While prior research has primarily focused on unimodal image data, real-world applications are inherently multimodal, requiring the integration of multiple modalities for improved OOD detection. A key challenge is the lack of supervision signals from unknown data, leading to overconfident predictions on OOD samples. To address this challenge, we propose Feature Mixing, an extremely simple and fast method for multimodal outlier synthesis with theoretical support, which can be further optimized to help the model better distinguish between in-distribution (ID) and OOD data. Feature Mixing is modality-agnostic and applicable to various modality combinations. Additionally, we introduce CARLA-OOD, a novel multimodal dataset for OOD segmentation, featuring synthetic OOD objects across diverse scenes and weather conditions. Extensive experiments on SemanticKITTI, nuScenes, CARLA-OOD datasets, and the MultiOOD benchmark demonstrate that Feature Mixing achieves state-of-the-art performance with a 10 to 370 speedup.

Multi-label complementary label learning (MLCLL) is a weakly supervised paradigm that addresses multi-label learning (MLL) tasks using complementary labels (i.e., irrelevant labels) instead of relevant labels. Existing methods typically adopt an unbiased risk estimator (URE) under the assumption that complementary labels follow a uniform distribution. However, this assumption fails in realworld scenarios due to instance-specific annotation biases, making URE-based methods ineffective under such conditions.

Large language models are able to exploit in-context learning to access external knowledge beyond their training data through retrieval-augmentation. While promising, its inner workings remain unclear. In this work, we shed light on the mechanism of in-context retrieval augmentation for question answering by viewing a prompt as a composition of informational components. We propose an attributionbased method to identify specialized attention heads, revealing in-context heads that comprehend instructions and retrieve relevant contextual information, and parametric heads that store entities' relational knowledge. To better understand their roles, we extract function vectors and modify their attention weights to show how they can influence the answer generation process. Finally, we leverage the gained insights to trace the sources of knowledge used during inference, paving the way towards more safe and transparent language models.