Filtering Step Remaining Instances Raw images collected 7.5Mimages After deduplication and car detection 4.9M images Initial car bounding boxes 13.22M boxes After score/size thresholding 6.97M boxes After Qwen2.5-7B

Precision and Recall are fundamental metrics in machine learning tasks where both accurate predictions and comprehensive coverage are essential, such as in multi-label learning, language generation, medical studies, and recommender systems. A key challenge in these settings is the prevalence of one-sided feedback, where only positive examples are observed during training--e.g., in multi-label tasks like tagging people in Facebook photos, we may observe only a few tagged individuals, without knowing who else appears in the image. To address learning under such partial feedback, we introduce a Probably Approximately Correct (PAC) framework in which hypotheses are set functions that map each input to a set of items, extending beyond single-label predictions and generalizing classical binary, multi-class, and multi-label models. Our results reveal sharp statistical and algorithmic separations from standard settings: classical methods such as Empirical Risk Minimization provably fail, even for simple hypothesis classes. We develop new algorithms that learn from positive data alone, achieving optimal sample complexity in the realizable case, and establishing multiplicative--rather than additive--approximation guarantees in the agnostic case, where achieving additive regret is impossible.

Accurate network estimation serves as the cornerstone for understanding complex systems across scientific domains, from decoding gene regulatory networks in systems biology to identifying social relationship patterns in computational sociology. Modern applications demand methods that simultaneously address two critical challenges: capturing nonlinear dependencies between variables and reconstructing inherent hierarchical structures where higher-level entities coordinate lower-level components (e.g., functional pathways organizing gene clusters). Traditional Gaussian graphical models fundamentally fail in these aspects due to their restrictive linear assumptions and flat network representations. We propose NNBLNet, a neural network-based learning framework for bi-level network inference. The core innovation lies in hierarchical selection layers that enforce structural consistency between high-level coordinator groups and their constituent low-level connections via adaptive sparsity constraints. This architecture is integrated with a compositional neural network architecture that learn cross-level association patterns through constrained nonlinear transformations, explicitly preserving hierarchical dependencies while overcoming the representational limitations of linear methods. Crucially, we establish formal theoretical guarantees for the consistent recovery of both high-level connections and their internal low-level structures under general statistical regimes. Extensive validation demonstrates NNBLNet's effectiveness across synthetic and real-world scenarios, achieving superior F1 scores compared to competitive methods and particularly beneficial for complex systems analysis through its interpretable bi-level structure discovery.

Invariant object recognition-the ability to identify objects despite changes in appearance-is a hallmark of visual processing in the brain, yet its understanding remains a central challenge in systems neuroscience. Artificial neural networks trained to predict neural responses to visual stimuli ("digital twins") could provide a powerful framework for studying such complex computations in silico. However, while current models accurately capture single-neuron responses within individual visual areas, their ability to reproduce how populations of neurons represent object identity, and how these representations transform across the cortical hierarchy, remains largely unexplored. Here we examine key functional signatures observed experimentally and find that current models account for hierarchical changes in basic single-neuron properties, such as receptive field size, but fail to capture more complex population-level phenomena, particularly invariant object representations. To address this gap, we introduce a biologically inspired hierarchical readout scheme that mirrors cortical anatomy, modeling each visual area as a projection from a distinct depth within a shared core network. This approach significantly improves the prediction of population-level representational transformations, outperforming standard models that use only the final layer, as well as alternatives with modified architecture, regularization, and loss function. Our results suggest that incorporating anatomical information provides a strong inductive bias in digital twin models, enabling them to better capture general principles of brain function.

The growing adoption of machine learning models for biological sequences has intensified the need for interpretable predictions, with Shapley values emerging as a theoretically grounded standard for model explanation. While effective for local explanations of individual input sequences, scaling Shapley-based interpretability to extract global biological insights requires evaluating thousands of sequences--incurring exponential computational cost per query. We introduce SHAP zero, a novel algorithm that amortizes the cost of Shapley value computation across large-scale biological datasets. After a one-time model sketching step, SHAP zero enables near-zero marginal cost for future queries by uncovering an underexplored connection between Shapley values, high-order feature interactions, and the sparse Fourier transform of the model. Applied to models of guide RNA efficacy, DNA repair outcomes, and protein fitness, SHAP zero explains predictions orders of magnitude faster than existing methods, recovering rich combinatorial interactions previously inaccessible at scale. This work opens the door to principled, efficient, and scalable interpretability for black-box sequence models in biology.

This paper proposes X2-DFD, an eXplainable and eXtendable framework based on multimodal large-language models (MLLMs) for deepfake detection, consisting of three key stages (see Figure 1). The first stage, Model Feature Assessment, systematically evaluates the detectability of forgery-related features for the MLLM, generating a prioritized ranking of features based on their intrinsic importance to the model. The second stage, Explainable Dataset Construction, consists of two key modules: Strong Feature Strengthening, which is designed to enhance the model's existing detection and explanation capabilities by reinforcing its well-learned features, and Weak Feature Supplementing, which addresses gaps by integrating specific feature detectors (e.g., low-level artifact analyzers) to compensate for the MLLM's limitations. The third stage, Fine-tuning and Inference, involves finetuning the MLLM on the constructed dataset and deploying it for final detection and explanation. By integrating these three stages, our approach enhances the MLLM's strengths while supplementing its weaknesses, ultimately improving both the detectability and explainability. Extensive experiments and ablations, followed by a comprehensive human study, validate the improved performance of our approach compared to the original MLLMs. More encouragingly, our framework is designed to be plug-and-play, allowing it to seamlessly integrate with future more advanced MLLMs and specific feature detectors, leading to continual improvement and extension to face the challenges of rapidly evolving deepfakes.

As we increase the number of features in the SAE, hierarchical features tend to split into finer features ("math" may split into "algebra", "geometry", etc.), a phenomenon referred to as feature splitting. However, we show that sparse decomposition and splitting of hierarchical features is not robust. Specifically, we show that seemingly monosemantic features fail to fire where they should, and instead get "absorbed" into their children features. We coin this phenomenon feature absorption, and show that it is caused by optimizing for sparsity in SAEs whenever the underlying features form a hierarchy. We introduce a metric to detect absorption in SAEs, and validate our findings empirically on hundreds of LLM SAEs. Our investigation suggests that varying SAE sizes or sparsity is insufficient to solve this issue. We discuss the implications of feature absorption in SAEs and some potential approaches to solve the fundamental theoretical issues before SAEs can be used for interpreting LLMs robustly and at scale.

In enterprise settings, organizational data is segregated, siloed and carefully protected by elaborate access control frameworks. These access control structures can completely break down if an LLM fine-tuned on the siloed data serves requests, for downstream tasks, from individuals with disparate access privileges. We propose Permissioned LLMs (PermLLM), a new class of LLMs that superimpose the organizational data access control structures on query responses they generate. We formalize abstractions underpinning the means to determine whether access control enforcement happens correctly over LLM query responses. Our formalism introduces the notion of a relevant response that can be used to prove whether a PermLLM mechanism has been implemented correctly. We also introduce a novel metric, called access advantage, to empirically evaluate the efficacy of a PermLLM mechanism. We introduce three novel PermLLM mechanisms that build on Parameter Efficient Fine-Tuning to achieve the desired access control. We furthermore present two instantiations of access advantage-(i) Domain Distinguishability Index (DDI) based on Membership Inference Attacks, and (ii) Utility Gap Index (UGI) based on LLM utility evaluation. We demonstrate the efficacy of our PermLLM mechanisms through extensive experiments on five public datasets (GPQA, RCV1, SimpleQA, WMDP, and PubMedQA), in addition to evaluating the validity of DDI and UGI metrics themselves for quantifying access control in LLMs.

Over the last decade, ransomware detection has become a central topic in cybersecurity research. Due to ransomware's direct interaction with storage devices, analyzing I/O streams has become an effective detection method and represents a vital area of focus for research. A major challenge in this field is the lack of publicly accessible data featuring individual command labeling. To address this problem, we introduce the Command LEvel Annotated Ransomware (CLEAR) dataset, a large-scale collection of storage devices' stream data. The dataset comprises 1,045 TiB of I/O traffic data, featuring malicious traffic from 137 ransomware variants.

Real-world objects frequently undergo state transformations. From an apple being cut into pieces to a butterfly emerging from its cocoon, tracking through these changes is important for understanding real-world objects and dynamics. However, existing methods often lose track of the target object after transformation, due to significant changes in object appearance. To address this limitation, we introduce the task of Track Any State: tracking objects through transformations while detecting and describing state changes, accompanied by a new benchmark dataset, VOST-TAS. To tackle this problem, we present TubeletGraph, a zero-shot system that recovers missing objects after transformation and maps out how object states are evolving over time. TubeletGraph first identifies potentially overlooked tracks, and determines whether they should be integrated based on semantic and proximity priors. Then, it reasons about the added tracks and generates a state graph describing each observed transformation. TubeletGraph achieves state-of-the-art tracking performance under transformations, while demonstrating deeper understanding of object transformations and promising capabilities in temporal grounding and semantic reasoning for complex object transformations. Code, additional results, and the benchmark dataset are available at https://tubelet-graph.github.io.