Daily Papers

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.

Complex logical query answering (CLQA) is a recently emerged task of graph machine learning that goes beyond simple one-hop link prediction and solves a far more complex task of multi-hop logical reasoning over massive, potentially incomplete graphs in a latent space. The task received a significant traction in the community; numerous works expanded the field along theoretical and practical axes to tackle different types of complex queries and graph modalities with efficient systems. In this paper, we provide a holistic survey of CLQA with a detailed taxonomy studying the field from multiple angles, including graph types (modality, reasoning domain, background semantics), modeling aspects (encoder, processor, decoder), supported queries (operators, patterns, projected variables), datasets, evaluation metrics, and applications. Refining the CLQA task, we introduce the concept of Neural Graph Databases (NGDBs). Extending the idea of graph databases (graph DBs), NGDB consists of a Neural Graph Storage and a Neural Graph Engine. Inside Neural Graph Storage, we design a graph store, a feature store, and further embed information in a latent embedding store using an encoder. Given a query, Neural Query Engine learns how to perform query planning and execution in order to efficiently retrieve the correct results by interacting with the Neural Graph Storage. Compared with traditional graph DBs, NGDBs allow for a flexible and unified modeling of features in diverse modalities using the embedding store. Moreover, when the graph is incomplete, they can provide robust retrieval of answers which a normal graph DB cannot recover. Finally, we point out promising directions, unsolved problems and applications of NGDB for future research.

A network-based approach is presented to investigate the cerebrovascular flow patterns during atrial fibrillation (AF) with respect to normal sinus rhythm (NSR). AF, the most common cardiac arrhythmia with faster and irregular beating, has been recently and independently associated with the increased risk of dementia. However, the underlying hemodynamic mechanisms relating the two pathologies remain mainly undetermined so far; thus the contribution of modeling and refined statistical tools is valuable. Pressure and flow rate temporal series in NSR and AF are here evaluated along representative cerebral sites (from carotid arteries to capillary brain circulation), exploiting reliable artificially built signals recently obtained from an in silico approach. The complex network analysis evidences, in a synthetic and original way, a dramatic signal variation towards the distal/capillary cerebral regions during AF, which has no counterpart in NSR conditions. At the large artery level, networks obtained from both AF and NSR hemodynamic signals exhibit elongated and chained features, which are typical of pseudo-periodic series. These aspects are almost completely lost towards the microcirculation during AF, where the networks are topologically more circular and present random-like characteristics. As a consequence, all the physiological phenomena at microcerebral level ruled by periodicity - such as regular perfusion, mean pressure per beat, and average nutrient supply at cellular level - can be strongly compromised, since the AF hemodynamic signals assume irregular behaviour and random-like features. Through a powerful approach which is complementary to the classical statistical tools, the present findings further strengthen the potential link between AF hemodynamic and cognitive decline.

We propose a novel method called SHS-Net for oriented normal estimation of point clouds by learning signed hyper surfaces, which can accurately predict normals with global consistent orientation from various point clouds. Almost all existing methods estimate oriented normals through a two-stage pipeline, i.e., unoriented normal estimation and normal orientation, and each step is implemented by a separate algorithm. However, previous methods are sensitive to parameter settings, resulting in poor results from point clouds with noise, density variations and complex geometries. In this work, we introduce signed hyper surfaces (SHS), which are parameterized by multi-layer perceptron (MLP) layers, to learn to estimate oriented normals from point clouds in an end-to-end manner. The signed hyper surfaces are implicitly learned in a high-dimensional feature space where the local and global information is aggregated. Specifically, we introduce a patch encoding module and a shape encoding module to encode a 3D point cloud into a local latent code and a global latent code, respectively. Then, an attention-weighted normal prediction module is proposed as a decoder, which takes the local and global latent codes as input to predict oriented normals. Experimental results show that our SHS-Net outperforms the state-of-the-art methods in both unoriented and oriented normal estimation on the widely used benchmarks. The code, data and pretrained models are publicly available.

Lifting 2D diffusion for 3D generation is a challenging problem due to the lack of geometric prior and the complex entanglement of materials and lighting in natural images. Existing methods have shown promise by first creating the geometry through score-distillation sampling (SDS) applied to rendered surface normals, followed by appearance modeling. However, relying on a 2D RGB diffusion model to optimize surface normals is suboptimal due to the distribution discrepancy between natural images and normals maps, leading to instability in optimization. In this paper, recognizing that the normal and depth information effectively describe scene geometry and be automatically estimated from images, we propose to learn a generalizable Normal-Depth diffusion model for 3D generation. We achieve this by training on the large-scale LAION dataset together with the generalizable image-to-depth and normal prior models. In an attempt to alleviate the mixed illumination effects in the generated materials, we introduce an albedo diffusion model to impose data-driven constraints on the albedo component. Our experiments show that when integrated into existing text-to-3D pipelines, our models significantly enhance the detail richness, achieving state-of-the-art results. Our project page is https://lingtengqiu.github.io/RichDreamer/.

While state-of-the-art monocular depth estimation approaches achieve impressive results in ideal settings, they are highly unreliable under challenging illumination and weather conditions, such as at nighttime or in the presence of rain. In this paper, we uncover these safety-critical issues and tackle them with md4all: a simple and effective solution that works reliably under both adverse and ideal conditions, as well as for different types of learning supervision. We achieve this by exploiting the efficacy of existing methods under perfect settings. Therefore, we provide valid training signals independently of what is in the input. First, we generate a set of complex samples corresponding to the normal training ones. Then, we train the model by guiding its self- or full-supervision by feeding the generated samples and computing the standard losses on the corresponding original images. Doing so enables a single model to recover information across diverse conditions without modifications at inference time. Extensive experiments on two challenging public datasets, namely nuScenes and Oxford RobotCar, demonstrate the effectiveness of our techniques, outperforming prior works by a large margin in both standard and challenging conditions. Source code and data are available at: https://md4all.github.io.

In industrial anomaly detection (IAD), accurately identifying defects amidst diverse anomalies and under varying imaging conditions remains a significant challenge. Traditional approaches often struggle with high false-positive rates, frequently misclassifying normal shadows and surface deformations as defects, an issue that becomes particularly pronounced in products with complex and intricate surface features. To address these challenges, we introduce PA-CLIP, a zero-shot anomaly detection method that reduces background noise and enhances defect detection through a pseudo-anomaly-based framework. The proposed method integrates a multiscale feature aggregation strategy for capturing detailed global and local information, two memory banks for distinguishing background information, including normal patterns and pseudo-anomalies, from true anomaly features, and a decision-making module designed to minimize false positives caused by environmental variations while maintaining high defect sensitivity. Demonstrated on the MVTec AD and VisA datasets, PA-CLIP outperforms existing zero-shot methods, providing a robust solution for industrial defect detection.

Transformer-based large language models (LLMs) have achieved great success with the growing model size. LLMs' size grows by 240times every two years, which outpaces the hardware progress and makes model inference increasingly costly. Model quantization is a promising approach to mitigate the widening gap between LLM size and hardware capacity. However, the existence of outliers, values with significant magnitudes, in LLMs makes existing quantization methods less effective. Prior outlier-aware quantization schemes adopt sparsity encoding techniques to separate outliers from normal values where the process requires global coordination (e.g., a global sparsity coordination list). This incurs complex encoding/decoding hardware logics and an extra orchestration controller for the computation between outlier and normal values. As such, it is not hardware-efficient and hence only achieves sub-optimal quantization benefits. We propose OliVe, an algorithm/architecture co-designed solution that adopts an outlier-victim pair (OVP) quantization and handles outlier values locally with low hardware overheads and high performance gains. The key insight of OliVe is that outliers are important while the normal values next to them are not. Thus those normal values (called victims) can be sacrificed to accommodate outliers. This enables a memory-aligned OVP encoding scheme, which can be efficiently integrated to the existing hardware accelerators like systolic array and tensor core. As a result, OliVe-based accelerator surpasses the existing outlier-aware accelerator, GOBO, by 4.5times speedup and 4.0times energy reduction, respectively, with a superior model accuracy.

The success of Large Language Models (LLMs) relies heavily on the huge amount of pre-training data learned in the pre-training phase. The opacity of the pre-training process and the training data causes the results of many benchmark tests to become unreliable. If any model has been trained on a benchmark test set, it can seriously hinder the health of the field. In order to automate and efficiently test the capabilities of large language models, numerous mainstream benchmarks adopt a multiple-choice format. As the swapping of the contents of multiple-choice options does not affect the meaning of the question itself, we propose a simple and effective data leakage detection method based on this property. Specifically, we shuffle the contents of the options in the data to generate the corresponding derived data sets, and then detect data leakage based on the model's log probability distribution over the derived data sets. If there is a maximum and outlier in the set of log probabilities, it indicates that the data is leaked. Our method is able to work under black-box conditions without access to model training data or weights, effectively identifying data leakage from benchmark test sets in model pre-training data, including both normal scenarios and complex scenarios where options may have been shuffled intentionally or unintentionally. Through experiments based on two LLMs and benchmark designs, we demonstrate the effectiveness of our method. In addition, we evaluate the degree of data leakage of 31 mainstream open-source LLMs on four benchmark datasets and give a ranking of the leaked LLMs for each benchmark, and we find that the Qwen family of LLMs has the highest degree of data leakage.

Privacy policies are long and complex documents that are difficult for users to read and understand, and yet, they have legal effects on how user data is collected, managed and used. Ideally, we would like to empower users to inform themselves about issues that matter to them, and enable them to selectively explore those issues. We present PrivacyQA, a corpus consisting of 1750 questions about the privacy policies of mobile applications, and over 3500 expert annotations of relevant answers. We observe that a strong neural baseline underperforms human performance by almost 0.3 F1 on PrivacyQA, suggesting considerable room for improvement for future systems. Further, we use this dataset to shed light on challenges to question answerability, with domain-general implications for any question answering system. The PrivacyQA corpus offers a challenging corpus for question answering, with genuine real-world utility.

People worldwide use language in subtle and complex ways to express emotions. While emotion recognition -- an umbrella term for several NLP tasks -- significantly impacts different applications in NLP and other fields, most work in the area is focused on high-resource languages. Therefore, this has led to major disparities in research and proposed solutions, especially for low-resource languages that suffer from the lack of high-quality datasets. In this paper, we present BRIGHTER-- a collection of multilabeled emotion-annotated datasets in 28 different languages. BRIGHTER covers predominantly low-resource languages from Africa, Asia, Eastern Europe, and Latin America, with instances from various domains annotated by fluent speakers. We describe the data collection and annotation processes and the challenges of building these datasets. Then, we report different experimental results for monolingual and crosslingual multi-label emotion identification, as well as intensity-level emotion recognition. We investigate results with and without using LLMs and analyse the large variability in performance across languages and text domains. We show that BRIGHTER datasets are a step towards bridging the gap in text-based emotion recognition and discuss their impact and utility.

This paper proposes ConsistDreamer - a novel framework that lifts 2D diffusion models with 3D awareness and 3D consistency, thus enabling high-fidelity instruction-guided scene editing. To overcome the fundamental limitation of missing 3D consistency in 2D diffusion models, our key insight is to introduce three synergetic strategies that augment the input of the 2D diffusion model to become 3D-aware and to explicitly enforce 3D consistency during the training process. Specifically, we design surrounding views as context-rich input for the 2D diffusion model, and generate 3D-consistent, structured noise instead of image-independent noise. Moreover, we introduce self-supervised consistency-enforcing training within the per-scene editing procedure. Extensive evaluation shows that our ConsistDreamer achieves state-of-the-art performance for instruction-guided scene editing across various scenes and editing instructions, particularly in complicated large-scale indoor scenes from ScanNet++, with significantly improved sharpness and fine-grained textures. Notably, ConsistDreamer stands as the first work capable of successfully editing complex (e.g., plaid/checkered) patterns. Our project page is at immortalco.github.io/ConsistDreamer.

Post-merger gravitational wave echoes provide a unique opportunity to probe the near-horizon structure of astrophysical black holes, that may be modified due to non-perturbative quantum gravity phenomena. However, since the waveform is subject to large theoretical uncertainties, it is necessary to develop model-agnostic search methods for detecting echoes from observational data. A promising strategy is to identify the characteristic quasinormal modes (QNMs) associated with echoes, {\it in frequency space}, which complements existing searches of quasiperiodic pulses in time. In this study, we build upon our previous work targeting these modes by incorporating relative phase information to optimize the Bayesian search algorithm. Using a new phase-marginalized likelihood, the performance can be significantly improved for well-resolved QNMs. This enables an efficient model-agnostic search for QNMs of different shapes by using a simple search template. To demonstrate the robustness of the search algorithm, we construct four complementary benchmarks for the echo waveform that span a diverse range of different theoretical possibilities for the near-horizon structure. We then validate our Bayesian search algorithms by injecting the benchmark models into different realizations of Gaussian noise. Using two types of phase-marginalized likelihoods, we find that the search algorithm can efficiently detect the corresponding QNMs. Therefore, our search strategy provides a concrete Bayesian and model-agnostic approach to "quantum black hole seismology".

We present AERO, a audio super-resolution model that processes speech and music signals in the spectral domain. AERO is based on an encoder-decoder architecture with U-Net like skip connections. We optimize the model using both time and frequency domain loss functions. Specifically, we consider a set of reconstruction losses together with perceptual ones in the form of adversarial and feature discriminator loss functions. To better handle phase information the proposed method operates over the complex-valued spectrogram using two separate channels. Unlike prior work which mainly considers low and high frequency concatenation for audio super-resolution, the proposed method directly predicts the full frequency range. We demonstrate high performance across a wide range of sample rates considering both speech and music. AERO outperforms the evaluated baselines considering Log-Spectral Distance, ViSQOL, and the subjective MUSHRA test. Audio samples and code are available at https://pages.cs.huji.ac.il/adiyoss-lab/aero

Deep learning has become an area of interest in most scientific areas, including physical sciences. Modern networks apply real-valued transformations on the data. Particularly, convolutions in convolutional neural networks discard phase information entirely. Many deterministic signals, such as seismic data or electrical signals, contain significant information in the phase of the signal. We explore complex-valued deep convolutional networks to leverage non-linear feature maps. Seismic data commonly has a lowcut filter applied, to attenuate noise from ocean waves and similar long wavelength contributions. Discarding the phase information leads to low-frequency aliasing analogous to the Nyquist-Shannon theorem for high frequencies. In non-stationary data, the phase content can stabilize training and improve the generalizability of neural networks. While it has been shown that phase content can be restored in deep neural networks, we show how including phase information in feature maps improves both training and inference from deterministic physical data. Furthermore, we show that the reduction of parameters in a complex network outperforms larger real-valued networks.

Complex vector modes, entangled in spin and orbital angular momentum, are opening burgeoning opportunities for a wide variety of applications. Importantly, the flexible manipulation the various properties of such beams will pave the way to novel applications. As such, in this manuscript, we demonstrate a longitudinal spin-orbit separation of complex vector modes propagating in free space. To achieve this we employed the recently demonstrated circular Airy Gaussian vortex vector (CAGVV) modes, which feature a self-focusing property. More precisely, by properly manipulating the intrinsic parameters of CAGVV modes, the strong coupling between the two constituting orthogonal components of CAGVV mode undergo a spin-orbit separation along the propagation direction namely, while one polarisation component, focuses at a specific plane, the other focuses at a different plane. Such spin-orbit separation, which we demonstrated by numerical simulations and corroborated experimentally, can be adjusted on-demand by simply changing the initial parameters of CAGVV modes. Our findings will be of great relevance, for example in optical tweezers, to manipulate micro- or nano-particles at two different parallel planes.