DeepNLP/ICML-2024-Accepted-Papers huggingface dataset:
MorphGrower: A Synchronized Layer-by-layer Growing Approach for Plausible Neuronal Morphology Generation
Authors: Nianzu Yang, Kaipeng Zeng, Haotian Lu, Yexin Wu, Zexin Yuan, Danni Chen, Shengdian Jiang, Jiaxiang Wu, Yimin Wang, Junchi Yan

Neuronal morphology is essential for studying brain functioning and understanding neurodegenerative disorders. As acquiring real-world morphology data is expensive, computational approaches for morphology generation have been studied. Traditional methods heavily rely on expert-set rules and parameter tuning, making it difficult to generalize across different types of morphologies. Recently, MorphVAE was introduced as the sole learning-based method, but its generated morphologies lack plausibility, i.e., they do not appear realistic enough and most of the generated samples are topologically invalid. To fill this gap, this paper proposes MorphGrower, which mimicks the neuron natural growth mechanism for generation. Specifically, MorphGrower generates morphologies layer by layer, with each subsequent layer conditioned on the previously generated structure. During each layer generation, MorphGrower utilizes a pair of sibling branches as the basic generation block and generates branch pairs synchronously. This approach ensures topological validity and allows for fine-grained generation, thereby enhancing the realism of the final generated morphologies. Results on four real-world datasets demonstrate that MorphGrower outperforms MorphVAE by a notable margin. Importantly, the electrophysiological response simulation demonstrates the plausibility of our generated samples from a neuroscience perspective. Our code is available at https://github.com/Thinklab-SJTU/MorphGrower.
Mol-AE: Auto-Encoder Based Molecular Representation Learning With 3D Cloze Test Objective
Authors: Junwei Yang, Kangjie Zheng, Siyu Long, Zaiqing Nie, Ming Zhang, Xinyu Dai, Wei-Ying Ma, Hao Zhou

3D molecular representation learning has gained tremendous interest and achieved promising performance in various downstream tasks. A series of recent approaches follow a prevalent framework: an encoder-only model coupled with a coordinate denoising objective. However, through a series of analytical experiments, we prove that the encoder-only model with coordinate denoising objective exhibits inconsistency between pre-training and downstream objectives, as well as issues with disrupted atomic identifiers. To address these two issues, we propose Mol-AE for molecular representation learning, an auto-encoder model using positional encoding as atomic identifiers. We also propose a new training objective named 3D Cloze Test to make the model learn better atom spatial relationships from real molecular substructures. Empirical results demonstrate that Mol-AE achieves a large margin performance gain compared to the current state-of-the-art 3D molecular modeling approach.
What is Dataset Distillation Learning?
Authors: William Yang, Ye Zhu, Zhiwei Deng, Olga Russakovsky

Dataset distillation has emerged as a strategy to overcome the hurdles associated with large datasets by learning a compact set of synthetic data that retains essential information from the original dataset. While distilled data can be used to train high performing models, little is understood about how the information is stored. In this study, we posit and answer three questions about the behavior, representativeness, and point-wise information content of distilled data. We reveal distilled data cannot serve as a substitute for real data during training outside the standard evaluation setting for dataset distillation. Additionally, the distillation process retains high task performance by compressing information related to the early training dynamics of real models. Finally, we provide an framework for interpreting distilled data and reveal that individual distilled data points contain meaningful semantic information. This investigation sheds light on the intricate nature of distilled data, providing a better understanding on how they can be effectively utilized.
Protein Conformation Generation via Force-Guided SE(3) Diffusion Models
Authors: Yan Wang, Lihao Wang, Yuning Shen, Yiqun Wang, Huizhuo Yuan, Yue Wu, Quanquan Gu

The conformational landscape of proteins is crucial to understanding their functionality in complex biological processes. Traditional physics-based computational methods, such as molecular dynamics (MD) simulations, suffer from rare event sampling and long equilibration time problems, hindering their applications in general protein systems. Recently, deep generative modeling techniques, especially diffusion models, have been employed to generate novel protein conformations. However, existing score-based diffusion methods cannot properly incorporate important physical prior knowledge to guide the generation process, causing large deviations in the sampled protein conformations from the equilibrium distribution. In this paper, to overcome these limitations, we propose a force-guided $\mathrm{SE}(3)$ diffusion model, ConfDiff, for protein conformation generation. By incorporating a force-guided network with a mixture of data-based score models, ConfDiff can generate protein conformations with rich diversity while preserving high fidelity. Experiments on a variety of protein conformation prediction tasks, including 12 fast-folding proteins and the Bovine Pancreatic Trypsin Inhibitor (BPTI), demonstrate that our method surpasses the state-of-the-art method.
Empowering Graph Invariance Learning with Deep Spurious Infomax
Authors: Tianjun Yao, Yongqiang Chen, Zhenhao Chen, Kai Hu, Zhiqiang Shen, Kun Zhang

Recently, there has been a surge of interest in developing graph neural networks that utilize the invariance principle on graphs to generalize the out-of-distribution (OOD) data. Due to the limited knowledge about OOD data, existing approaches often pose assumptions about the correlation strengths of the underlying spurious features and the target labels. However, this prior is often unavailable and will change arbitrarily in the real-world scenarios, which may lead to severe failures of the existing graph invariance learning methods. To bridge this gap, we introduce a novel graph invariance learning paradigm, which induces a robust and general inductive bias, which is built upon the observation that the infomax principle encourages learning spurious features regardless of spurious correlation strengths. We further propose the EQuAD framework that realizes this learning paradigm and employs tailored learning objectives that provably elicit invariant features by disentangling them from the spurious features learned through infomax. Notably, EQuAD shows stable and enhanced performance across different degrees of bias in synthetic datasets and challenging real-world datasets up to 31.76%.
Human vs. Generative AI in Content Creation Competition: Symbiosis or Conflict?
Authors: Fan Yao, Chuanhao Li, Denis Nekipelov, Hongning Wang, Haifeng Xu

The advent of generative AI (GenAI) technology produces a transformative impact on the content creation landscape, offering alternative approaches to produce diverse, good-quality content across media, thereby reshaping online ecosystems but also raising concerns about market over-saturation and the potential marginalization of human creativity. Our work introduces a competition model generalized from the Tullock contest to analyze the tension between human creators and GenAI. Our theory and simulations suggest that despite challenges, a stable equilibrium between human and AI-generated content is possible. Our work contributes to understanding the competitive dynamics in the content creation industry, offering insights into the future interplay between human creativity and technological advancements in GenAI.
Mobile Attention: Mobile-Friendly Linear-Attention for Vision Transformers
Authors: Zhiyu Yao, Jian Wang, Haixu Wu, Jingdong Wang, Mingsheng Long

Vision Transformers (ViTs) excel in computer vision tasks due to their ability to capture global context among tokens. However, their quadratic complexity $\mathcal{O}(N^2D)$ in terms of token number $N$ and feature dimension $D$ limits practical use on mobile devices, necessitating more mobile-friendly ViTs with reduced latency. Multi-head linear-attention is emerging as a promising alternative with linear complexity $\mathcal{O}(NDd)$, where $d$ is the per-head dimension. Still, more compute is needed as $d$ gets large for model accuracy. Reducing $d$ improves mobile friendliness at the expense of excessive small heads weak at learning valuable subspaces, ultimately impeding model capability. To overcome this efficiency-capability dilemma, we propose a novel Mobile-Attention design with a head-competition mechanism empowered by information flow, which prevents overemphasis on less important subspaces upon trivial heads while preserving essential subspaces to ensure Transformer’s capability. It enables linear-time complexity on mobile devices by supporting a small per-head dimension $d$ for mobile efficiency. By replacing the standard attention of ViTs with Mobile-Attention, our optimized ViTs achieved enhanced model capacity and competitive performance in a range of computer vision tasks. Specifically, we have achieved remarkable reductions in latency on the iPhone 12. Code is available at https://github.com/thuml/MobileAttention.
Socialized Learning: Making Each Other Better Through Multi-Agent Collaboration
Authors: Xinjie Yao, Yu Wang, Pengfei Zhu, Wanyu Lin, Jialu Li, Weihao Li, Qinghua Hu

Learning new knowledge frequently occurs in our dynamically changing world, e.g., humans culturally evolve by continuously acquiring new abilities to sustain their survival, leveraging collective intelligence rather than a large number of individual attempts. The effective learning paradigm during cultural evolution is termed socialized learning (SL). Consequently, a straightforward question arises: Can multi-agent systems acquire more new abilities like humans? In contrast to most existing methods that address continual learning and multi-agent collaboration, our emphasis lies in a more challenging problem: we prioritize the knowledge in the original expert classes, and as we adeptly learn new ones, the accuracy in the original expert classes stays superior among all in a directional manner. Inspired by population genetics and cognitive science, leading to unique and complete development, we propose Multi-Agent Socialized Collaboration (MASC), which achieves SL through interactions among multiple agents. Specifically, we introduce collective collaboration and reciprocal altruism modules, organizing collaborative behaviors, promoting information sharing, and facilitating learning and knowledge interaction among individuals. We demonstrate the effectiveness of multi-agent collaboration in an extensive empirical study. Our code will be publicly available at https://github.com/yxjdarren/SL.
Compressible Dynamics in Deep Overparameterized Low-Rank Learning & Adaptation
Authors: Can Yaras, Peng Wang, Laura Balzano, Qing Qu

While overparameterization in machine learning models offers great benefits in terms of optimization and generalization, it also leads to increased computational requirements as model sizes grow. In this work, we show that by leveraging the inherent low-dimensional structures of data and compressible dynamics within the model parameters, we can reap the benefits of overparameterization without the computational burdens. In practice, we demonstrate the effectiveness of this approach for deep low-rank matrix completion as well as fine-tuning language models. Our approach is grounded in theoretical findings for deep overparameterized low-rank matrix recovery, where we show that the learning dynamics of each weight matrix are confined to an invariant low-dimensional subspace. Consequently, we can construct and train compact, highly compressed factorizations possessing the same benefits as their overparameterized counterparts. In the context of deep matrix completion, our technique substantially improves training efficiency while retaining the advantages of overparameterization. For language model fine-tuning, we propose a method called "Deep LoRA", which improves the existing low-rank adaptation (LoRA) technique, leading to reduced overfitting and a simplified hyperparameter setup, while maintaining comparable efficiency. We validate the effectiveness of Deep LoRA on natural language tasks, particularly when fine-tuning with limited data.
EMC$^2$: Efficient MCMC Negative Sampling for Contrastive Learning with Global Convergence
Authors: Chung-Yiu Yau, Hoi To Wai, Parameswaran Raman, Soumajyoti Sarkar, Mingyi Hong

A key challenge in contrastive learning is to generate negative samples from a large sample set to contrast with positive samples, for learning better encoding of the data. These negative samples often follow a softmax distribution which are dynamically updated during the training process. However, sampling from this distribution is non-trivial due to the high computational costs in computing the partition function. In this paper, we propose an $\underline{\text{E}}$fficient $\underline{\text{M}}$arkov $\underline{\text{C}}$hain Monte Carlo negative sampling method for $\underline{\text{C}}$ontrastive learning (EMC$^2$). We follow the global contrastive learning loss as introduced in SogCLR, and propose EMC$^2$ which utilizes an adaptive Metropolis-Hastings subroutine to generate hardness-aware negative samples in an online fashion during the optimization. We prove that EMC$^2$ finds an $\mathcal{O}(1/\sqrt{T})$-stationary point of the global contrastive loss in $T$ iterations. Compared to prior works, EMC$^2$ is the first algorithm that exhibits global convergence (to stationarity) regardless of the choice of batch size while exhibiting low computation and memory cost. Numerical experiments validate that EMC$^2$ is effective with small batch training and achieves comparable or better performance than baseline algorithms. We report the results for pre-training image encoders on STL-10 and Imagenet-100.
Towards Robust Model-Based Reinforcement Learning Against Adversarial Corruption
Authors: Chenlu Ye, Jiafan He, Quanquan Gu, Tong Zhang

This study tackles the challenges of adversarial corruption in model-based reinforcement learning (RL), where the transition dynamics can be corrupted by an adversary. Existing studies on corruption-robust RL mostly focus on the setting of model-free RL, where robust least-square regression is often employed for value function estimation. However, these techniques cannot be directly applied to model-based RL. In this paper, we focus on model-based RL and take the maximum likelihood estimation (MLE) approach to learn transition model. Our work encompasses both online and offline settings. In the online setting, we introduce an algorithm called corruption-robust optimistic MLE (CR-OMLE), which leverages total-variation (TV)-based information ratios as uncertainty weights for MLE. We prove that CR-OMLE achieves a regret of $\tilde{\mathcal{O}}(\sqrt{T} + C)$, where $C$ denotes the cumulative corruption level after $T$ episodes. We also prove a lower bound to show that the additive dependence on $C$ is optimal. We extend our weighting technique to the offline setting, and propose an algorithm named corruption-robust pessimistic MLE (CR-PMLE). Under a uniform coverage condition, CR-PMLE exhibits suboptimality worsened by $\mathcal{O}(C/n)$, nearly matching the lower bound. To the best of our knowledge, this is the first work on corruption-robust model-based RL algorithms with provable guarantees.
Adaptive Sampling of k-Space in Magnetic Resonance for Rapid Pathology Prediction
Authors: Chen-Yu Yen, Raghav Singhal, Umang Sharma, Rajesh Ranganath, Sumit Chopra, Lerrel Pinto

Magnetic Resonance (MR) imaging, despite its proven diagnostic utility, remains an inaccessible imaging modality for disease surveillance at the population level. A major factor rendering MR inaccessible is lengthy scan times. An MR scanner collects measurements associated with the underlying anatomy in the Fourier space, also known as the k-space. Creating a high-fidelity image requires collecting large quantities of such measurements, increasing the scan time. Traditionally to accelerate an MR scan, image reconstruction from under-sampled k-space data is the method of choice. However, recent works show the feasibility of bypassing image reconstruction and directly learning to detect disease directly from a sparser learned subset of the k-space measurements. In this work, we propose Adaptive Sampling for MR (ASMR), a sampling method that learns an adaptive policy to sequentially select k-space samples to optimize for target disease detection. On 6 out of 8 pathology classification tasks spanning the Knee, Brain, and Prostate MR scans, ASMR reaches within 2% of the performance of a fully sampled classifier while using only 8% of the k-space, as well as outperforming prior state-of-the-art work in k-space sampling such as EMRT, LOUPE, and DPS.
StableMask: Refining Causal Masking in Decoder-only Transformer
Authors: Qingyu Yin, Xuzheng He, Xiang Zhuang, Yu Zhao, Jianhua Yao, Xiaoyu Shen, Qiang Zhang

The decoder-only Transformer architecture with causal masking and relative position encoding (RPE) has become the de facto choice in language modeling. Despite its exceptional performance across various tasks, we have identified two limitations: First, it prevents all attended tokens from having zero weights during the softmax stage, even if the current embedding has sufficient self-contained information. This compels the model to assign disproportional excessive attention to specific tokens. Second, RPE-based Transformers are not universal approximators due to their limited capacity at encoding absolute positional information, which limits their application in position-critical tasks. In this work, we propose StableMask: a parameter-free method to address both limitations by refining the causal mask. It introduces pseudo-attention values to balance attention distributions and encodes absolute positional information via a progressively decreasing mask ratio. StableMask’s effectiveness is validated both theoretically and empirically, showing significant enhancements in language models with parameter sizes ranging from 71M to 1.4B across diverse datasets and encoding methods. We further show that it supports integration with existing optimization techniques, making it easily usable in practical applications.
Junk DNA Hypothesis: Pruning Small Pre-Trained Weights $\textitIrreversibly$ and $\textitMonotonically$ Impairs “Difficult" Downstream Tasks in LLMs
Authors: Lu Yin, Ajay Kumar Jaiswal, Shiwei Liu, Souvik Kundu, Zhangyang Wang

We present Junk DNA Hypothesis by adopting a novel task-centric angle for the pre-trained weights of large language models (LLMs). It has been believed that weights in LLMs contain significant redundancy, leading to the conception that a considerable chunk of the parameters can be removed by pruning without compromising performance. Contrary to this belief, this paper presents a counter-argument: small-magnitude weights of pre-trained model weights encode vital knowledge essential for tackling difficult downstream tasks - manifested as the monotonic relationship between the performance drop of downstream tasks across the difficulty spectrum, as we prune more pre-trained weights by magnitude. Moreover, we reveal that these seemingly inconsequential weights can result in irreparable loss of knowledge and performance degradation in difficult tasks, even when downstream continual training is allowed. Interestingly, our evaluations show that the other popular compression, namely quantization fail to exhibit similar “monotonic" effect and does not as convincingly disentangle this task-difficulty information. To study formally, we introduce several quantifiable metrics to gauge the downstream task difficulty: (a) within the same task category, and (b) across different task categories. Our extensive experiments substantiate the Junk DNA Hypothesis across a diverse range of model sizes, tasks, datasets, and even pruning methods. Codes are available at https://github.com/VITA-Group/Junk_DNA_Hypothesis.git.
Characterizing Truthfulness in Large Language Model Generations with Local Intrinsic Dimension
Authors: Fan Yin, Jayanth Srinivasa, Kai-Wei Chang

We study how to characterize and predict the truthfulness of texts generated from large language models (LLMs), which serves as a crucial step in building trust between humans and LLMs. Although several approaches based on entropy or verbalized uncertainty have been proposed to calibrate model predictions, these methods are often intractable, sensitive to hyperparameters, and less reliable when applied in generative tasks with LLMs. In this paper, we suggest investigating internal activations and quantifying LLM’s truthfulness using the local intrinsic dimension (LID) of model activations. Through experiments on four question answering (QA) datasets, we demonstrate the effectiveness of our proposed method. Additionally, we study intrinsic dimensions in LLMs and their relations with model layers, autoregressive language modeling, and the training of LLMs, revealing that intrinsic dimensions can be a powerful approach to understanding LLMs.
High-Dimensional Bayesian Optimization via Semi-Supervised Learning with Optimized Unlabeled Data Sampling
Authors: Yuxuan Yin, Yu Wang, Peng Li

We introduce a novel semi-supervised learning approach, named Teacher-Student Bayesian Optimization ($\texttt{TSBO}$), integrating the teacher-student paradigm into BO to minimize expensive labeled data queries for the first time. $\texttt{TSBO}$ incorporates a teacher model, an unlabeled data sampler, and a student model. The student is trained on unlabeled data locations generated by the sampler, with pseudo labels predicted by the teacher. The interplay between these three components implements a unique selective regularization to the teacher in the form of student feedback. This scheme enables the teacher to predict high-quality pseudo labels, enhancing the generalization of the GP surrogate model in the search space. To fully exploit $\texttt{TSBO}$, we propose two optimized unlabeled data samplers to construct effective student feedback that well aligns with the objective of Bayesian optimization. Furthermore, we quantify and leverage the uncertainty of the teacher-student model for the provision of reliable feedback to the teacher in the presence of risky pseudo-label predictions. $\texttt{TSBO}$ demonstrates significantly improved sample-efficiency in several global optimization tasks under tight labeled data budgets. The implementation is available at https://github.com/reminiscenty/TSBO-Official.