Daily Papers

We consider fermions in a zero-temperature superconducting anti-de Sitter domain wall solution and find continuous bands of normal modes. These bands can be either partially filled or totally empty and gapped. We present a semi-classical argument which approximately captures the main features of the normal mode spectrum.

Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous uncertainty quantification (UQ) of its solution quality (e.g. interface RMSD or iRMSD). Results: We introduce a novel algorithm, Bayesian Active Learning (BAL), for optimization and UQ of such black-box functions and flexible protein docking. BAL directly models the posterior distribution of the global optimum (or native structures for protein docking) with active sampling and posterior estimation iteratively feeding each other. Furthermore, we use complex normal modes to represent a homogeneous Euclidean conformation space suitable for high-dimension optimization and construct funnel-like energy models for encounter complexes. Over a protein docking benchmark set and a CAPRI set including homology docking, we establish that BAL significantly improve against both starting points by rigid docking and refinements by particle swarm optimization, providing for one third targets a top-3 near-native prediction. BAL also generates tight confidence intervals with half range around 25% of iRMSD and confidence level at 85%. Its estimated probability of a prediction being native or not achieves binary classification AUROC at 0.93 and AUPRC over 0.60 (compared to 0.14 by chance); and also found to help ranking predictions. To the best of our knowledge, this study represents the first uncertainty quantification solution for protein docking, with theoretical rigor and comprehensive assessment. Source codes are available at https://github.com/Shen-Lab/BAL.

Model distillation has become essential for creating smaller, deployable language models that retain larger system capabilities. However, widespread deployment raises concerns about resilience to adversarial manipulation. This paper investigates vulnerability of distilled models to adversarial injection of biased content during training. We demonstrate that adversaries can inject subtle biases into teacher models through minimal data poisoning, which propagates to student models and becomes significantly amplified. We propose two propagation modes: Untargeted Propagation, where bias affects multiple tasks, and Targeted Propagation, focusing on specific tasks while maintaining normal behavior elsewhere. With only 25 poisoned samples (0.25% poisoning rate), student models generate biased responses 76.9% of the time in targeted scenarios - higher than 69.4% in teacher models. For untargeted propagation, adversarial bias appears 6x-29x more frequently in student models on unseen tasks. We validate findings across six bias types (targeted advertisements, phishing links, narrative manipulations, insecure coding practices), various distillation methods, and different modalities spanning text and code generation. Our evaluation reveals shortcomings in current defenses - perplexity filtering, bias detection systems, and LLM-based autorater frameworks - against these attacks. Results expose significant security vulnerabilities in distilled models, highlighting need for specialized safeguards. We propose practical design principles for building effective adversarial bias mitigation strategies.

Modern large language models (LLMs) often struggle to dynamically adapt their reasoning depth to varying task complexities, leading to suboptimal performance or inefficient resource utilization. To address this, we introduce DynamicMind, a novel tri-mode thinking system. DynamicMind empowers LLMs to autonomously select between Fast, Normal, and Slow thinking modes for zero-shot question answering (ZSQA) tasks through cognitive-inspired prompt engineering. Our framework's core innovations include: (1) expanding the established dual-process framework of fast and slow thinking into a tri-mode thinking system involving a normal thinking mode to preserve the intrinsic capabilities of LLM; (2) proposing the Thinking Density metric, which aligns computational resource allocation with problem complexity; and (3) developing the Thinking Mode Capacity (TMC) dataset and a lightweight Mind Router to predict the optimal thinking mode. Extensive experiments across diverse mathematical, commonsense, and scientific QA benchmarks demonstrate that DynamicMind achieves superior ZSQA capabilities while establishing an effective trade-off between performance and computational efficiency.

We introduce Metric3D v2, a geometric foundation model for zero-shot metric depth and surface normal estimation from a single image, which is crucial for metric 3D recovery. While depth and normal are geometrically related and highly complimentary, they present distinct challenges. SoTA monocular depth methods achieve zero-shot generalization by learning affine-invariant depths, which cannot recover real-world metrics. Meanwhile, SoTA normal estimation methods have limited zero-shot performance due to the lack of large-scale labeled data. To tackle these issues, we propose solutions for both metric depth estimation and surface normal estimation. For metric depth estimation, we show that the key to a zero-shot single-view model lies in resolving the metric ambiguity from various camera models and large-scale data training. We propose a canonical camera space transformation module, which explicitly addresses the ambiguity problem and can be effortlessly plugged into existing monocular models. For surface normal estimation, we propose a joint depth-normal optimization module to distill diverse data knowledge from metric depth, enabling normal estimators to learn beyond normal labels. Equipped with these modules, our depth-normal models can be stably trained with over 16 million of images from thousands of camera models with different-type annotations, resulting in zero-shot generalization to in-the-wild images with unseen camera settings. Our method enables the accurate recovery of metric 3D structures on randomly collected internet images, paving the way for plausible single-image metrology. Our project page is at https://JUGGHM.github.io/Metric3Dv2.

Deep neural networks (DNNs) are widely deployed on real-world devices. Concerns regarding their security have gained great attention from researchers. Recently, a new weight modification attack called bit flip attack (BFA) was proposed, which exploits memory fault inject techniques such as row hammer to attack quantized models in the deployment stage. With only a few bit flips, the target model can be rendered useless as a random guesser or even be implanted with malicious functionalities. In this work, we seek to further reduce the number of bit flips. We propose a training-assisted bit flip attack, in which the adversary is involved in the training stage to build a high-risk model to release. This high-risk model, obtained coupled with a corresponding malicious model, behaves normally and can escape various detection methods. The results on benchmark datasets show that an adversary can easily convert this high-risk but normal model to a malicious one on victim's side by flipping only one critical bit on average in the deployment stage. Moreover, our attack still poses a significant threat even when defenses are employed. The codes for reproducing main experiments are available at https://github.com/jianshuod/TBA.

Proteins are dynamic molecular machines whose biological functions, spanning enzymatic catalysis, signal transduction, and structural adaptation, are intrinsically linked to their motions. Designing proteins with targeted dynamic properties, however, remains a challenge due to the complex, degenerate relationships between sequence, structure, and molecular motion. Here, we introduce VibeGen, a generative AI framework that enables end-to-end de novo protein design conditioned on normal mode vibrations. VibeGen employs an agentic dual-model architecture, comprising a protein designer that generates sequence candidates based on specified vibrational modes and a protein predictor that evaluates their dynamic accuracy. This approach synergizes diversity, accuracy, and novelty during the design process. Via full-atom molecular simulations as direct validation, we demonstrate that the designed proteins accurately reproduce the prescribed normal mode amplitudes across the backbone while adopting various stable, functionally relevant structures. Notably, generated sequences are de novo, exhibiting no significant similarity to natural proteins, thereby expanding the accessible protein space beyond evolutionary constraints. Our work integrates protein dynamics into generative protein design, and establishes a direct, bidirectional link between sequence and vibrational behavior, unlocking new pathways for engineering biomolecules with tailored dynamical and functional properties. This framework holds broad implications for the rational design of flexible enzymes, dynamic scaffolds, and biomaterials, paving the way toward dynamics-informed AI-driven protein engineering.

In this paper, we present a novel insider attack called Matryoshka, which employs an irrelevant scheduled-to-publish DNN model as a carrier model for covert transmission of multiple secret models which memorize the functionality of private ML data stored in local data centers. Instead of treating the parameters of the carrier model as bit strings and applying conventional steganography, we devise a novel parameter sharing approach which exploits the learning capacity of the carrier model for information hiding. Matryoshka simultaneously achieves: (i) High Capacity -- With almost no utility loss of the carrier model, Matryoshka can hide a 26x larger secret model or 8 secret models of diverse architectures spanning different application domains in the carrier model, neither of which can be done with existing steganography techniques; (ii) Decoding Efficiency -- once downloading the published carrier model, an outside colluder can exclusively decode the hidden models from the carrier model with only several integer secrets and the knowledge of the hidden model architecture; (iii) Effectiveness -- Moreover, almost all the recovered models have similar performance as if it were trained independently on the private data; (iv) Robustness -- Information redundancy is naturally implemented to achieve resilience against common post-processing techniques on the carrier before its publishing; (v) Covertness -- A model inspector with different levels of prior knowledge could hardly differentiate a carrier model from a normal model.

Deep learning models are intrinsically sensitive to distribution shifts in the input data. In particular, small, barely perceivable perturbations to the input data can force models to make wrong predictions with high confidence. An common defense mechanism is regularization through adversarial training which injects worst-case perturbations back into training to strengthen the decision boundaries, and to reduce overfitting. In this context, we perform an investigation of 3x3 convolution filters that form in adversarially-trained models. Filters are extracted from 71 public models of the linf-RobustBench CIFAR-10/100 and ImageNet1k leaderboard and compared to filters extracted from models built on the same architectures but trained without robust regularization. We observe that adversarially-robust models appear to form more diverse, less sparse, and more orthogonal convolution filters than their normal counterparts. The largest differences between robust and normal models are found in the deepest layers, and the very first convolution layer, which consistently and predominantly forms filters that can partially eliminate perturbations, irrespective of the architecture. Data & Project website: https://github.com/paulgavrikov/cvpr22w_RobustnessThroughTheLens

Static word embeddings are ubiquitous in computational social science applications and contribute to practical decision-making in a variety of fields including law and healthcare. However, assessing the statistical uncertainty in downstream conclusions drawn from word embedding statistics has remained challenging. When using only point estimates for embeddings, researchers have no streamlined way of assessing the degree to which their model selection criteria or scientific conclusions are subject to noise due to sparsity in the underlying data used to generate the embeddings. We introduce a method to obtain approximate, easy-to-use, and scalable reconstruction error variance estimates for GloVe (Pennington et al., 2014), one of the most widely used word embedding models, using an analytical approximation to a multivariate normal model. To demonstrate the value of embeddings with variance (GloVe-V), we illustrate how our approach enables principled hypothesis testing in core word embedding tasks, such as comparing the similarity between different word pairs in vector space, assessing the performance of different models, and analyzing the relative degree of ethnic or gender bias in a corpus using different word lists.