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Deep Learning · Graph Neural Networks

Xinyu He, Dongqi Fu, Hanghang Tong, Ross Maciejewski, Jingrui He

Nowadays, temporal heterogeneous graphs attract much research and industrial attention for building the next-generation Relational Deep Learning models and applications, due to their informative structures and features. While providing timely and precise services like personalized recommendations and question answering, this rich information also introduces extra exposure risk for each node in the graph. The distinctive local topology, the abundant heterogeneous features, and the time dimension of the graph data are more prone to expose sensitive information and narrow down the scope of victim candidates, which calls for well-defined protection techniques on graphs. To this end, we propose a Temporal Heterogeneous Graph Generator balancing Privacy, Utility, and Efficiency, named THePUff. More specifically, we first propose a differential privacy algorithm to perturb the input temporal heterogeneous graph for protecting privacy, and then utilize both the perturbed graph and the original one in a generative adversarial setting for THePUff to learn and generate privacy-guaranteed and utility-preserved graph data in an efficient manner. We further propose 6 new metrics in the temporal setting to measure heterogeneous graph utility and privacy. Finally, based on temporal heterogeneous graph datasets with up to 1 million nodes and 20 million edges, the experiments show that THePUff generates utilizable temporal heterogeneous graphs with privacy protected, compared with state-of-the-art baselines.

Applications · Computer Vision

Haiyang Jiang, Tetsuichi Wazawa, Imari Sato, Takeharu Nagai, Yinqiang Zheng

Electron-multiplying charge-coupled device (EMCCD) has been instrumental in sensitive observations under low-light situations including astronomy, material science, and biology. Despite its ingenious designs to enhance target signals overcoming read-out circuit noises, produced images are not completely noise free, which could still cast a cloud on desired experiment outcomes, especially in fluorescence microscopy.Existing studies on EMCCD's noise model have been focusing on statistical characteristics in theory, yet unable to incorporate latest advancements in the field of computational photography, where physics-based noise models are utilized to guide deep learning processes, creating adaptive denoising algorithms for ordinary image sensors.Still, those models are not directly applicable to EMCCD.In this paper, we intend to pioneer EMCCD denoising by introducing a systematic study on physics-based noise model calibration procedures for an EMCCD camera, accurately estimating statistical features of observable noise components in experiments, which are then utilized to generate substantial amount of authentic training samples for one of the most recent neural networks.A first real-world test image dataset for EMCCD is captured, containing both images of ordinary daily scenes and those of microscopic contents.Benchmarking upon the testset and authentic microscopic images, we demonstrate distinct advantages of our model against previous methods for EMCCD and physics-based noise modeling, forging a promising new path for EMCCD denoising.

Probabilistic Methods · Everything Else

Domokos M. Kelen, Ádám Jung, Péter Kersch, Andras Benczur

Quantifying uncertainty is an essential part of predictive modeling, especially in the context of high-stakes decision-making. While classification output includes data uncertainty by design in the form of class probabilities, the regression task generally aims only to predict the expected value of the target variable. Probabilistic extensions often assume parametric distributions around the expected value, optimizing the likelihood over the resulting explicit densities. However, using parametric distributions can limit practical applicability, making it difficult for models to capture skewed, multi-modal, or otherwise complex distributions. In this paper, we propose optimizing a novel nondeterministic neural network regression architecture for loss functions derived from a sample-based approximation of the continuous ranked probability score (CRPS), enabling a truly distribution-free approach by learning to sample from the target's aleatoric distribution, rather than predicting explicit densities. Our approach allows the model to learn well-calibrated, arbitrary uni- and multivariate output distributions. We evaluate the method on a variety of synthetic and real-world tasks, including uni- and multivariate problems, function inverse approximation, and standard regression uncertainty benchmarks. Finally, we make all experiment code publicly available.

Social Aspects · Accountability, Transparency and Interpretability

Ruixuan HUANG, Shuai Wang

Concept activation vectors have been shown to take effects in safety concepts, efficiently and effectively guiding a considerable number of open-source large language models (LLMs) to respond positively to malicious instructions. In this blog, we aim to explore the capability boundaries of concept activation vectors in guiding various behaviors of LLMs through more extensive experiments. Our experiments demonstrate that this reasoning technique can low-costly transfer text styles and improve performance on specific tasks such as code generation.

Deep Learning · Graph Neural Networks

Jie Chen

Preconditioning is at the heart of iterative solutions of large, sparse linear systems of equations in scientific disciplines. Several algebraic approaches, which access no information beyond the matrix itself, are widely studied and used, but ill-conditioned matrices remain very challenging. We take a machine learning approach and propose using graph neural networks as a general-purpose preconditioner. They show attractive performance for many problems and can be used when the mainstream preconditioners perform poorly. Empirical evaluation on over 800 matrices suggests that the construction time of these graph neural preconditioners (GNPs) is more predictable and can be much shorter than that of other widely used ones, such as ILU and AMG, while the execution time is faster than using a Krylov method as the preconditioner, such as in inner-outer GMRES. GNPs have a strong potential for solving large-scale, challenging algebraic problems arising from not only partial differential equations, but also economics, statistics, graph, and optimization, to name a few.

Applications · Genetics, Cell Biology, Health, etc

Alessandro Palma, Till Richter, Hanyi Zhang, Manuel Lubetzki, Alexander Tong, Andrea Dittadi, Fabian Theis

Generative modeling of single-cell RNA-seq data is crucial for tasks like trajectory inference, batch effect removal, and simulation of realistic cellular data. However, recent deep generative models simulating synthetic single cells from noise operate on pre-processed continuous gene expression approximations, overlooking the discrete nature of single-cell data, which limits their effectiveness and hinders the incorporation of robust noise models. Additionally, aspects like controllable multi-modal and multi-label generation of cellular data remain underexplored. This work introduces CellFlow for Generation (CFGen), a flow-based conditional generative model that preserves the inherent discreteness of single-cell data. CFGen generates whole-genome multi-modal single-cell data reliably, improving the recovery of crucial biological data characteristics while tackling relevant generative tasks such as rare cell type augmentation and batch correction. We also introduce a novel framework for compositional data generation using Flow Matching. By showcasing CFGen on a diverse set of biological datasets and settings, we provide evidence of its value to the fields of computational biology and deep generative models.

Applications · Time Series

Daning Huang, Hanyang He, John Harlim, Yan Li

We address the problem of learning ordinary differential equations (ODEs) on manifolds. Existing machine learning methods, particularly those using neural networks, often struggle with high computational demands. To overcome this issue, we introduce a geometrically constrained operator-valued kernel that allows us to represent vector fields on tangent bundles of smooth manifolds. The construction of the kernel imposes the geometric constraints that are estimated from the data and ensures the computational feasibility for learning high dimensional systems of ODEs. Once the vector fields are estimated, e.g., by the kernel ridge regression, we need an ODE solver that guarantees the solution to stay on (or close to) the manifold. To overcome this issue, we propose a geometry-preserving ODE solver that approximates the exponential maps corresponding to the ODE solutions. We deduce a theoretical error bound for the proposed solver that guarantees the approximate solutions to lie on the manifold in the limit of large data. We verify the effectiveness of the proposed approach on high-dimensional dynamical systems, including the cavity flow problem, the beating and travelling waves in Kuramoto-Sivashinsky equations, and the reaction-diffusion dynamics.

Applications · Computer Vision

Onkar Susladkar, Jishu Sen Gupta, Chirag Sehgal, Sparsh Mittal, Rekha Singhal

The spatio-temporal complexity of video data presents significant challenges in tasks such as compression, generation, and inpainting. We present four key contributions to address the challenges of spatiotemporal video processing. First, we introduce the 3D Mobile Inverted Vector-Quantization Variational Autoencoder (3D-MBQ-VAE), which combines Variational Autoencoders (VAEs) with masked modeling to enhance spatiotemporal video compression. The model achieves superior temporal consistency and state-of-the-art (SOTA) reconstruction quality by employing a novel training strategy with full frame masking. Second, we present MotionAura, a text-to-video generation framework that utilizes vector-quantized diffusion models to discretize the latent space and capture complex motion dynamics, producing temporally coherent videos aligned with text prompts. Third, we propose a spectral transformer-based denoising network that processes video data in the frequency domain using the Fourier Transform. This method effectively captures global context and long-range dependencies for high-quality video generation and denoising. Lastly, we introduce a downstream task of Sketch Guided Video Inpainting. This task leverages Low-Rank Adaptation (LoRA) for parameter-efficient fine-tuning. Our models achieve SOTA performance on a range of benchmarks. Our work offers robust frameworks for spatiotemporal modeling and user-driven video content manipulation.

Reinforcement Learning · Deep RL

Yuhang Wang, Hanwei Guo, Sizhe Wang, Long Qian, Xuguang Lan

Model Predictive Control (MPC) has been demonstrated to be effective in continuous control tasks. When a world model and a value function are available, planning a sequence of actions ahead of time leads to a better policy. Existing methods typically obtain the value function and the corresponding policy in a model-free manner. However, we find that such an approach struggles with complex tasks, resulting in poor policy learning and inaccurate value estimation. To address this problem, we leverage the strengths of MPC itself. In this work, we introduce Bootstrapped Model Predictive Control (BMPC), a novel algorithm that performs policy learning in a bootstrapped manner. BMPC learns a network policy by imitating an MPC expert, and in turn, uses this policy to guide the MPC process. Combined with model-based TD-learning, our policy learning yields better value estimation and further boosts the efficiency of MPC. We also introduce a lazy reanalyze mechanism, which enables computationally efficient imitation learning. Our method achieves superior performance over prior works on diverse continuous control tasks. In particular, on challenging high-dimensional locomotion tasks, BMPC significantly improves data efficiency while also enhancing asymptotic performance and training stability, with comparable training time and smaller network sizes. Code is available at https://github.com/wertyuilife2/bmpc.

Yanjun Zhao, Sizhe Dang, Haishan Ye, Guang Dai, Yi Qian, Ivor Tsang

Fine-tuning large language models (LLMs) is necessary for specific downstream tasks, but classic first-order optimizer entails prohibitive GPU memory because of the back propagation. Recent works such as MeZO have turned to zeroth-order optimizers for fine-tuning, which reduce substantial memory by using two forward passes. However, heterogeneous curvatures across different parameter dimensions in LLMs often cause model convergence instability or even failure. In this work, we propose HiZOO, a diagonal Hessian informed Zeroth-Order Optimizer , which is the first work to leverage the diagonal Hessian to enhance ZOO for fine-tuning LLMs. We provide theoretical proof for HiZOO and visualize the optimization trajectories on test functions to illustrate how it improves convergence in handling heterogeneous curvatures. Extensive experiments on various models (RoBERTa, OPT, Phi-2 and LLama3, with 350M$\sim$66B parameters) indicate that HiZOO significantly reduces training steps and enhances model accuracy, while keeping the memory advantage of ZOO. For example, on SST2 task HiZOO achieves $8\times$ speedup and better accuracy over MeZO across different models. We also propose HiZOO-L, which reduces the Hessian memory cost to 10\% of the MeZO, while maintaining almost same performance. Compared with ZO-Adam, HiZOO-L achieves a 4.3\% improvement, just using 50\% of the GPU memory. Code is available at https://anonymous.4open.science/r/HiZOO-27F8.

Deep Learning · Large Language Models

Alex Kipnis, Konstantinos Voudouris, Luca Schulze Buschoff, Eric Schulz

Large Language Models (LLMs) vary in their abilities on a range of tasks. Initiatives such as the Open LLM Leaderboard aim to quantify these differences with several large benchmarks (sets of test items to which an LLM can respond either correctly or incorrectly). However, high correlations within and between benchmark scores suggest that (1) there exists a small set of common underlying abilities that these benchmarks measure, and (2) items tap into redundant information and the benchmarks may thus be considerably compressed. We use data from n > 5000 LLMs to identify the most informative items of six benchmarks, ARC, GSM8K, HellaSwag, MMLU, TruthfulQA and WinoGrande (with d = 28,632 items in total). From them we distill a sparse benchmark, metabench, that has less than 3% of the original size of all six benchmarks combined. This new sparse benchmark goes beyond point scores by yielding estimators of the underlying benchmark-specific abilities. We show that these estimators (1) can be used to reconstruct each original individual benchmark score with, on average, 1.24% root mean square error (RMSE), (2) reconstruct the original total score with 0.58% RMSE, and (3) have a single underlying common factor whose Spearman correlation with the total score is r = 0.94.

Deep Learning · Large Language Models

Yusu Qian, Hanrong Ye, Jean-Philippe Fauconnier, Peter Grasch, Yinfei Yang, Zhe Gan

Effective evaluation of Multimodal Large Language Models (MLLMs) is essential for understanding their capabilities and limitations. In this paper, we introduce MIA-Bench, a benchmark designed to assess MLLMs’ ability to strictly adhere to complex instructions. Our benchmark comprises a diverse set of 400 image-prompt pairs, each crafted to challenge the models’ compliance with layered instructions in generating accurate and contextually appropriate responses. Evaluation results from a wide array of state-of-the-art MLLMs reveal significant variations in performance, highlighting areas for improvement in instruction fidelity. Additionally, we create extra training data and explore supervised fine-tuning and direct preference optimization to enhance the models’ ability to strictly follow instructions without compromising performance on other tasks. We hope this benchmark not only serves as a tool for measuring MLLM adherence to instructions, but also guides future developments in MLLM training methods.

Deep Learning · Large Language Models

Dhruv Gautam, Spandan Garg, Jinu Jang, Neel Sundaresan, Roshanak Zilouchian Moghaddam

Recent advances in language model (LM) agents and function calling have enabled autonomous, feedback-driven systems to solve problems across various digital domains. To better understand the unique limitations of LM agents, we introduce RefactorBench, a benchmark consisting of 100 large handcrafted multi-file refactoring tasks in popular open-source repositories. Solving tasks within RefactorBench requires thorough exploration of dependencies across multiple files and strong adherence to relevant instructions. Every task is defined by 3 natural language instructions of varying specificity and is mutually exclusive, allowing for the creation of longer combined tasks on the same repository. Baselines on RefactorBench reveal that current LM agents struggle with simple compositional tasks, solving only 22\% of tasks with base instructions, in contrast to a human developer with short time constraints solving 87\%. Through trajectory analysis, we identify various unique failure modes of LM agents, and further explore the failure mode of tracking past actions. By adapting a baseline agent to condition on representations of state, we achieve a 43.9\% improvement in solving RefactorBench tasks. We further extend our state-aware approach to encompass entire digital environments and outline potential directions for future research. RefactorBench aims to support the study of LM agents by providing a set of real-world, multi-hop tasks within the realm of code.

Theory · Learning Theory

Wenhao Xu, Xuefeng Gao, Xuedong He

Risk-sensitive linear quadratic regulator is one of the most fundamental problems in risk-sensitive optimal control. In this paper, we study online adaptive control of risk-sensitive linear quadratic regulator in the finite horizon episodic setting. We propose a simple least-squares greedy algorithm and show that it achieves $\widetilde{\mathcal{O}}(\log N)$ regret under a specific identifiability assumption, where $N$ is the total number of episodes. If the identifiability assumption is not satisfied, we propose incorporating exploration noise into the least-squares-based algorithm, resulting in an algorithm with $\widetilde{\mathcal{O}}(\sqrt{N})$ regret. To our best knowledge, this is the first set of regret bounds for episodic risk-sensitive linear quadratic regulator. Our proof relies on perturbation analysis of less-standard Riccati equations for risk-sensitive linear quadratic control, and a delicate analysis of the loss in the risk-sensitive performance criterion due to applying the suboptimal controller in the online learning process.

Yongqi Ding, Lin Zuo, Mengmeng Jing, Pei He, Hanpu Deng

Spiking neural networks (SNNs) exhibit superior energy efficiency but suffer from limited performance. In this paper, we consider SNNs as ensembles of temporal subnetworks that share architectures and weights, and highlight a crucial issue that affects their performance: excessive differences in initial states (neuronal membrane potentials) across timesteps lead to unstable subnetwork outputs, resulting in degraded performance. To mitigate this, we promote the consistency of the initial membrane potential distribution and output through membrane potential smoothing and temporally adjacent subnetwork guidance, respectively, to improve overall stability and performance. Moreover, membrane potential smoothing facilitates forward propagation of information and backward propagation of gradients, mitigating the notorious temporal gradient vanishing problem. Our method requires only minimal modification of the spiking neurons without adapting the network structure, making our method generalizable and showing consistent performance gains in 1D speech, 2D object, and 3D point cloud recognition tasks. In particular, on the challenging CIFAR10-DVS dataset, we achieved 83.20\% accuracy with only four timesteps. This provides valuable insights into unleashing the potential of SNNs.

Deep Learning · Generative Models and Autoencoders

Jiachen Li, Qian Long, Jian (Skyler) Zheng, Xiaofeng Gao, Robinson Piramuthu, Wenhu Chen, William Wang

In this paper, we focus on enhancing a diffusion-based text-to-video (T2V) model during the post-training phase by distilling a highly capable consistency model from a pretrained T2V model. Our proposed method, T2V-Turbo-v2, introduces a significant advancement by integrating various supervision signals, including high-quality training data, reward model feedback, and conditional guidance, into the consistency distillation process. Through comprehensive ablation studies, we highlight the crucial importance of tailoring datasets to specific learning objectives and the effectiveness of learning from diverse reward models for enhancing both the visual quality and text-video alignment. Additionally, we highlight the vast design space of conditional guidance strategies, which centers on designing an effective energy function to augment the teacher ODE solver. We demonstrate the potential of this approach by extracting motion guidance from the training datasets and incorporating it into the ODE solver, showcasing its effectiveness in improving the motion quality of the generated videos with the improved motion-related metrics from VBench and T2V-CompBench. Empirically, our T2V-Turbo-v2 establishes a new state-of-the-art result on VBench, **with a Total score of 85.13**, surpassing proprietary systems such as Gen-3 and Kling.

Deep Learning · Graph Neural Networks

Xingbo Fu, Yinhan He, Jundong Li

Pre-training powerful Graph Neural Networks (GNNs) with unlabeled graph data in a self-supervised manner has emerged as a prominent technique in recent years. However, inevitable objective gaps often exist between pre-training and downstream tasks. To bridge this gap, graph prompt tuning techniques design and learn graph prompts by manipulating input graphs or reframing downstream tasks as pre-training tasks without fine-tuning the pre-trained GNN models. While recent graph prompt tuning methods have proven effective in adapting pre-trained GNN models for downstream tasks, they overlook the crucial role of edges in graph prompt design, which can significantly affect the quality of graph representations for downstream tasks.In this study, we propose EdgePrompt, a simple yet effective graph prompt tuning method from the perspective of edges. Unlike previous studies that design prompt vectors on node features, EdgePrompt manipulates input graphs by learning additional prompt vectors for edges and incorporates the edge prompts through message passing in the pre-trained GNN models to better embed graph structural information for downstream tasks. Our method is compatible with prevalent GNN architectures pre-trained under various pre-training strategies and is universal for different downstream tasks.We provide comprehensive theoretical analyses of our method regarding its capability of handling node classification and graph classification as downstream tasks.Extensive experiments on ten graph datasets under four pre-training strategies demonstrate the superiority of our proposed method against six baselines. Our code is available at https://github.com/xbfu/EdgePrompt.

Deep Learning · Graph Neural Networks

Seong Ho Pahng, Sahand Hormoz

Graph Neural Networks (GNNs) traditionally employ a message-passing mechanism that resembles diffusion over undirected graphs, which often leads to homogenization of node features and reduced discriminative power in tasks such as node classification. Our key insight for addressing this limitation is to assign fuzzy edge directions---that can vary continuously from node $i$ pointing to node $j$ to vice versa---to the edges of a graph so that features can preferentially flow in one direction between nodes to enable long-range information transmission across the graph. We also introduce a novel complex-valued Laplacian for directed graphs with fuzzy edges where the real and imaginary parts represent information flow in opposite directions. Using this Laplacian, we propose a general framework, called Continuous Edge Direction (CoED) GNN, for learning on graphs with fuzzy edges and prove its expressivity limits using a generalization of the Weisfeiler-Leman (WL) graph isomorphism test for directed graphs with fuzzy edges. Our architecture aggregates neighbor features scaled by the learned edge directions and processes the aggregated messages from in-neighbors and out-neighbors separately alongside the self-features of the nodes. Since continuous edge directions are differentiable, they can be learned jointly with the GNN weights via gradient-based optimization. CoED GNN is particularly well-suited for graph ensemble data where the graph structure remains fixed but multiple realizations of node features are available, such as in gene regulatory networks, web connectivity graphs, and power grids. We demonstrate through extensive experiments on both synthetic and real graph ensemble datasets that learning continuous edge directions significantly improves performance both for undirected and directed graphs compared with existing methods.

Theory · Deep Learning

Alireza Mousavi-Hosseini, Adel Javanmard, Murat A Erdogdu

Recently, there have been numerous studies on feature learning with neural networks, specifically on learning single- and multi-index models where the target is a function of a low-dimensional projection of the input. Prior works have shown that in high dimensions, the majority of the compute and data resources are spent on recovering the low-dimensional projection; once this subspace is recovered, the remainder of the target can be learned independently of the ambient dimension. However, implications of feature learning in adversarial settings remain unexplored. In this work, we take the first steps towards understanding adversarially robust feature learning with neural networks. Specifically, we prove that the hidden directions of a multi-index model offer a Bayes optimal low-dimensional projection for robustness against $\ell_2$-bounded adversarial perturbations under the squared loss, assuming that the multi-index coordinates are statistically independent from the rest of the coordinates. Therefore, robust learning can be achieved by first performing standard feature learning, then robustly tuning a linear readout layer on top of the standard representations. In particular, we show that adversarially robust learning is just as easy as standard learning. Specifically, the additional number of samples needed to robustly learn multi-index models when compared to standard learning, does not depend on dimensionality.

Applications · Computer Vision

Xiandong Zou, Mingzhu Shen, Christos-Savvas Bouganis, Yiren Zhao

Low-Rank Adaptation (LoRA) has emerged as a widely adopted technique in text-to-image models, enabling precise rendering of multiple distinct elements, such as characters and styles, in multi-concept image generation. However, current approaches face significant challenges when composing these LoRAs for multi-concept image generation, particularly as the number of LoRAs increases, resulting in diminished generated image quality. In this paper, we initially investigate the role of LoRAs in the denoising process through the lens of the Fourier frequency domain.Based on the hypothesis that applying multiple LoRAs could lead to "semantic conflicts", we have conducted empirical experiments and find that certain LoRAs amplify high-frequency features such as edges and textures, whereas others mainly focus on low-frequency elements, including the overall structure and smooth color gradients.Building on these insights, we devise a frequency domain based sequencing strategy to determine the optimal order in which LoRAs should be integrated during inference. This strategy offers a methodical and generalizable solution compared to the naive integration commonly found in existing LoRA fusion techniques.To fully leverage our proposed LoRA order sequence determination method in multi-LoRA composition tasks, we introduce a novel, training-free framework, Cached Multi-LoRA (CMLoRA), designed to efficiently integrate multiple LoRAs while maintaining cohesive image generation.With its flexible backbone for multi-LoRA fusion and a non-uniform caching strategy tailored to individual LoRAs, CMLoRA has the potential to reduce semantic conflicts in LoRA composition and improve computational efficiency.Our experimental evaluations demonstrate that CMLoRA outperforms state-of-the-art training-free LoRA fusion methods by a significant margin -- it achieves an average improvement of $2.19$% in CLIPScore, and $11.25%$% in MLLM win rate compared to LoraHub, LoRA Composite, and LoRA Switch.