mtybilly/Instruct2DS huggingface dataset:
Once Read is Enough: Domain-specific Pretraining-free Language Models with Cluster-guided Sparse Experts for Long-tail Domain Knowledge
Authors: Fang Dong, Mengyi Chen, Jixian Zhou, Yubin Shi, Yixuan Chen, Mingzhi Dong, Yujiang Wang, Dongsheng Li, Xiaochen Yang, Rui Zhu, Robert Dick, Qin Lv, Fan Yang, Tun Lu, Ning Gu, Li Shang
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: Language models (LMs) only pretrained on a general and massive corpus usually cannot attain satisfying performance on domain-specific downstream tasks, and hence, applying domain-specific pretraining to LMs is a common and indispensable practice.However, domain-specific pretraining can be costly and time-consuming, hindering LMs' deployment in real-world applications.In this work, we consider the incapability to memorize domain-specific knowledge embedded in the general corpus with rare occurrences and long-tail distributions as the leading cause for pretrained LMs' inferior downstream performance. Analysis of Neural Tangent Kernels (NTKs) reveals that those long-tail data are commonly overlooked in the model's gradient updates and, consequently, are not effectively memorized, leading to poor domain-specific downstream performance.Based on the intuition that data with similar semantic meaning are closer in the embedding space, we devise a Cluster-guided Sparse Expert (CSE) layer to actively learn long-tail domain knowledge typically neglected in previous pretrained LMs.During pretraining, a CSE layer efficiently clusters domain knowledge together and assigns long-tail knowledge to designate extra experts. CSE is also a lightweight structure that only needs to be incorporated in several deep layers.With our training strategy, we found that during pretraining, data of long-tail knowledge gradually formulate isolated, outlier clusters in an LM's representation spaces, especially in deeper layers. Our experimental results show that only pretraining CSE-based LMs is enough to achieve superior performance than regularly pretrained-finetuned LMs on various downstream tasks, implying the prospects of domain-specific-pretraining-free language models.
Compressing Large Language Models using Low Rank and Low Precision Decomposition
Authors: Rajarshi Saha, Naomi Sagan, Varun Srivastava, Andrea J. Goldsmith, Mert Pilanci
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: The prohibitive sizes of Large Language Models (LLMs) today make it difficult to deploy them on memory-constrained edge devices. This work introduces $\rm CALDERA$ -- a new post-training LLM compression algorithm that harnesses the inherent low-rank structure of a weight matrix $\mathbf{W}$ by approximating it via a low-rank, low-precision decomposition as $\mathbf{W} \approx \mathbf{Q} + \mathbf{L}\mathbf{R}$. Here, $\mathbf{L}$ and $\mathbf{R}$ are low rank factors, and the entries of $\mathbf{Q}$, $\mathbf{L}$ and $\mathbf{R}$ are quantized. The model is compressed by substituting each layer with its $\mathbf{Q} + \mathbf{L}\mathbf{R}$ decomposition, and the zero-shot performance of the compressed model is evaluated. Additionally, $\mathbf{L}$ and $\mathbf{R}$ are readily amenable to low-rank adaptation, consequently enhancing the zero-shot performance. $\rm CALDERA$ obtains this decomposition by formulating it as an optimization problem $\min_{\mathbf{Q},\mathbf{L},\mathbf{R}}\lVert(\mathbf{Q} + \mathbf{L}\mathbf{R} - \mathbf{W})\mathbf{X}^\top\rVert_{\rm F}^2$, where $\mathbf{X}$ is the calibration data, and $\mathbf{Q}, \mathbf{L}, \mathbf{R}$ are constrained to be representable using low-precision formats. Theoretical upper bounds on the approximation error of $\rm CALDERA$ are established using a rank-constrained regression framework, and the tradeoff between compression ratio and model performance is studied by analyzing the impact of target rank and quantization bit budget. Results illustrate that compressing LlaMa-$2$ $7$B/$13$B/$70$B and LlaMa-$3$ $8$B models obtained using $\rm CALDERA$ outperforms existing post-training LLM compression techniques in the regime of less than $2.5$ bits per parameter.
Intervention and Conditioning in Causal Bayesian Networks
Authors: Sainyam Galhotra, Joseph Y. Halpern
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: Causal models are crucial for understanding complex systems andidentifying causal relationships among variables. Even though causalmodels are extremely popular, conditional probability calculation offormulas involving interventions pose significant challenges.In case of Causal Bayesian Networks (CBNs), Pearl assumes autonomy of mechanisms that determine interventions to calculate a range ofprobabilities. We show that by making simple yetoften realistic independence assumptions, it is possible to uniquely estimate the probability of an interventional formula (includingthe well-studied notions of probability of sufficiency and necessity). We discuss when these assumptions are appropriate.Importantly, in many cases of interest, when the assumptions are appropriate,these probability estimates can be evaluated usingobservational data, which carries immense significance in scenarioswhere conducting experiments is impractical or unfeasible.
QUEST: Quality-Aware Metropolis-Hastings Sampling for Machine Translation
Authors: Gonçalo R. A. Faria, Sweta Agrawal, António Farinhas, Ricardo Rei, José G. C. de Souza, André F.T. Martins
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: An important challenge in machine translation (MT) is to generate high-quality and diverse translations. Prior work has shown that the estimated likelihood from the MT model correlates poorly with translation quality. In contrast, quality evaluation metrics (such as COMET or BLEURT) exhibit high correlations with human judgments, which has motivated their use as rerankers (such as quality-aware and minimum Bayes risk decoding). However, relying on a single translation with high estimated quality increases the chances of "gaming the metric''. In this paper, we address the problem of sampling a set of high-quality and diverse translations. We provide a simple and effective way to avoid over-reliance on noisy quality estimates by using them as the energy function of a Gibbs distribution. Instead of looking for a mode in the distribution, we generate multiple samples from high-density areas through the Metropolis-Hastings algorithm, a simple Markov chain Monte Carlo approach.  The results show that our proposed method leads to high-quality and diverse outputs across multiple language pairs (English$\leftrightarrow$\{German, Russian\}) with two strong decoder-only LLMs (Alma-7b, Tower-7b).
Molecule Design by Latent Prompt Transformer
Authors: Deqian Kong, Yuhao Huang, Jianwen Xie, Edouardo Honig, Ming Xu, Shuanghong Xue, Pei Lin, Sanping Zhou, Sheng Zhong, Nanning Zheng, Ying Nian Wu
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: This work explores the challenging problem of molecule design by framing it as a conditional generative modeling task, where target biological properties or desired chemical constraints serve as conditioning variables.We propose the Latent Prompt Transformer (LPT), a novel generative model comprising three components: (1) a latent vector with a learnable prior distribution modeled by a neural transformation of Gaussian white noise; (2) a molecule generation model based on a causal Transformer, which uses the latent vector as a prompt; and (3) a property prediction model that predicts a molecule's target properties and/or constraint values using the latent prompt. LPT can be learned by maximum likelihood estimation on molecule-property pairs. During property optimization, the latent prompt is inferred from target properties and constraints through posterior sampling and then used to guide the autoregressive molecule generation.After initial training on existing molecules and their properties, we adopt an online learning algorithm to progressively shift the model distribution towards regions that support desired target properties. Experiments demonstrate that LPT not only effectively discovers useful molecules across single-objective, multi-objective, and structure-constrained optimization tasks, but also exhibits strong sample efficiency.
MMBench-Video: A Long-Form Multi-Shot Benchmark for Holistic Video Understanding
Authors: Xinyu Fang, Kangrui Mao, Haodong Duan, Xiangyu Zhao, Yining Li, Dahua Lin, Kai Chen
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Datasets and Benchmarks Track), 2024

Abstract: The advent of large vision-language models (LVLMs) has spurred research into their applications in multi-modal contexts, particularly in video understanding. Traditional VideoQA benchmarks, despite providing quantitative metrics, often fail to encompass the full spectrum of video content and inadequately assess models' temporal comprehension. To address these limitations, we introduce MMBench-Video, a quantitative benchmark designed to rigorously evaluate LVLMs' proficiency in video understanding. MMBench-Video incorporates lengthy videos from YouTube and employs free-form questions, mirroring practical use cases. The benchmark is meticulously crafted to probe the models' temporal reasoning skills, with all questions human-annotated according to a carefully constructed ability taxonomy.We employ GPT-4 for automated assessment, demonstrating superior accuracy and robustness over earlier LLM-based evaluations. Utilizing MMBench-Video, we have conducted comprehensive evaluations that include both proprietary and open-source LVLMs for images and videos. MMBench-Video stands as a valuable resource for the research community, facilitating improved evaluation of LVLMs and catalyzing progress in the field of video understanding.
Improving Adversarial Robust Fairness via Anti-Bias Soft Label  Distillation
Authors: Shiji Zhao, Ranjie Duan, Xizhe Wang, Xingxing Wei
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: Adversarial Training (AT) has been widely proved to be an effective method to improve the adversarial robustness against adversarial examples for Deep Neural Networks (DNNs). As a variant of AT, Adversarial Robustness Distillation (ARD) has demonstrated its superior performance in improving the robustness of small student models with the guidance of large teacher models. However, both AT and ARD encounter the robust fairness problem: these models exhibit strong robustness when facing part of classes (easy class), but weak robustness when facing others (hard class). In this paper, we give an in-depth analysis of the potential factors and argue that the smoothness degree of samples' soft labels for different classes (i.e., hard class or easy class) will affect the robust fairness of DNNs from both empirical observation and theoretical analysis. Based on the above finding, we propose an Anti-Bias Soft Label Distillation (ABSLD) method to mitigate the adversarial robust fairness problem within the framework of Knowledge Distillation (KD). Specifically, ABSLD adaptively reduces the student's error risk gap between different classes to achieve fairness by adjusting the class-wise smoothness degree of samples' soft labels during the training process, and the smoothness degree of soft labels is controlled by assigning different temperatures in KD to different classes. Extensive experiments demonstrate that ABSLD outperforms state-of-the-art AT, ARD, and robust fairness methods in the comprehensive metric (Normalized Standard Deviation) of robustness and fairness.
Spectral Learning of Shared Dynamics Between Generalized-Linear Processes
Authors: Lucine L. Oganesian, Omid G. Sani, Maryam M. Shanechi
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: Generalized-linear dynamical models (GLDMs) remain a widely-used framework within neuroscience for modeling time-series data, such as neural spiking activity or categorical decision outcomes. Whereas the standard usage of GLDMs is to model a single data source, certain applications require jointly modeling two generalized-linear time-series sources while also dissociating their shared and private dynamics. Most existing GLDM variants and their associated learning algorithms do not support this capability. Here we address this challenge by developing a multi-step analytical subspace identification algorithm for learning a GLDM that explicitly models shared vs. private dynamics within two generalized-linear time-series. In simulations, we demonstrate our algorithm's ability to dissociate and model the dynamics within two time-series sources while being agnostic to their respective observation distributions. In neural data, we consider two specific applications of our algorithm for modeling discrete population spiking activity with respect to a secondary time-series. In both synthetic and real data, GLDMs learned with our algorithm more accurately decoded one time-series from the other using lower-dimensional latent states, as compared to models identified using existing GLDM learning algorithms.
GaussianCut: Interactive segmentation via graph cut for 3D Gaussian Splatting
Authors: Umangi Jain, Ashkan Mirzaei, Igor Gilitschenski
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: We introduce GaussianCut, a new method for interactive multiview segmentation of scenes represented as 3D Gaussians. Our approach allows for selecting the objects to be segmented by interacting with a single view. It accepts intuitive user input, such as point clicks, coarse scribbles, or text. Using 3D Gaussian Splatting (3DGS) as the underlying scene representation simplifies the extraction of objects of interest which are considered to be a subset of the scene's Gaussians.  Our key idea is to represent the scene as a graph and use the graph-cut algorithm to minimize an energy function to effectively partition the Gaussians into foreground and background. To achieve this, we construct a graph based on scene Gaussians and devise a segmentation-aligned energy function on the graph to combine user inputs with scene properties. To obtain an initial coarse segmentation, we leverage 2D image/video segmentation models and further refine these coarse estimates using our graph construction. Our empirical evaluations show the adaptability of GaussianCut across a diverse set of scenes. GaussianCut achieves competitive performance with state-of-the-art approaches for 3D segmentation without requiring any additional segmentation-aware training
Class Distribution Shifts in Zero-Shot Learning: Learning Robust Representations
Authors: Yuli Slavutsky, Yuval Benjamini
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: Zero-shot learning methods typically assume that the new, unseen classes encountered during deployment come from the same distribution as the the classes in the training set. However, real-world scenarios often involve class distribution shifts (e.g., in age or gender for person identification), posing challenges for zero-shot classifiers that rely on learned representations from training classes. In this work, we propose and analyze a model that assumes that the attribute responsible for the shift is unknown in advance. We show that in this setting, standard training may lead to non-robust representations. To mitigate this, we develop an algorithm for learning robust representations in which (a) synthetic data environments are constructed via hierarchical sampling, and (b) environment balancing penalization, inspired by out-of-distribution problems, is applied. We show that our algorithm improves generalization to diverse class distributions in both simulations and experiments on real-world datasets.
Benchmarking Out-of-Distribution Generalization Capabilities of DNN-based Encoding Models for the Ventral Visual Cortex.
Authors: Spandan Madan, Will Xiao, Mingran Cao, Hanspeter Pfister, Margaret Livingstone, Gabriel Kreiman
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Datasets and Benchmarks Track), 2024

Abstract: We characterized the generalization capabilities of deep neural network encoding models when predicting neuronal responses from the visual cortex to flashed images. We collected MacaqueITBench, a large-scale dataset of neuronal population responses from the macaque inferior temporal (IT) cortex to over $300,000$ images, comprising $8,233$ unique natural images presented to seven monkeys over $109$ sessions. Using MacaqueITBench, we investigated the impact of distribution shifts on models predicting neuronal activity by dividing the images into Out-Of-Distribution (OOD) train and test splits. The OOD splits included variations in image contrast, hue, intensity, temperature, and saturation. Compared to the performance on in-distribution test images---the conventional way in which these models have been evaluated---models performed worse at predicting neuronal responses to out-of-distribution images, retaining as little as $20\\%$ of the performance on in-distribution test images. Additionally, the relative ranking of different models in terms of their ability to predict neuronal responses changed drastically across OOD shifts. The generalization performance under OOD shifts can be well accounted by a simple image similarity metric---the cosine distance between image representations extracted from a pre-trained object recognition model is a strong predictor of neuronal predictivity under different distribution shifts. The dataset of images, neuronal firing rate recordings, and computational benchmarks are hosted publicly at: https://github.com/Spandan-Madan/benchmarking_ood_generalization_visual_cortex.
Improved Guarantees for Fully Dynamic $k$-Center Clustering with Outliers in General Metric Spaces
Authors: Leyla Biabani, Annika Hennes, Denise La Gordt Dillie, Morteza Monemizadeh, Melanie Schmidt
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: The metric $k$-center clustering problem with $z$ outliers, also known as $(k,z)$-center clustering, involves clustering a given point set $P$ in a metric space $(M,d)$ using at most $k$ balls, minimizing the maximum ball radius while excluding up to $z$ points from the clustering. This problem holds fundamental significance in various domains such as machine learning, data mining, and database systems.This paper addresses the fully dynamic version of the problem, where the point set undergoes continuous updates (insertions and deletions) over time. The objective is to maintain an approximate $(k,z)$-center clustering with efficient update times. We propose a novel fully dynamic algorithm that maintains a $(4+\epsilon)$-approximate solution to the $(k,z)$-center clustering problem that covers all but at most $(1+\epsilon)z$ points at any time in the sequence with probability $1-k/e^{\Omega(\log k)}$. The algorithm achieves an expected amortized update time of $\mathcal{O}(\epsilon^{-2} k^6\log(k) \log(\Delta))$, and is applicable to general metric spaces. Our dynamic algorithm presents a significant improvement over the recent dynamic $(14+\epsilon)$-approximation algorithm by Chan, Lattanzi, Sozio, and Wang for this problem.
Constrained Synthesis with Projected Diffusion Models
Authors: Jacob K. Christopher, Stephen Baek, Ferdinando Fioretto
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: This paper introduces an approach to endow generative diffusion processes the ability to satisfy and certify compliance with constraints and physical principles. The proposed method recast the traditional sampling process of generative diffusion models as a constrained optimization problem, steering the generated data distribution to remain within a specified region to ensure adherence to the given constraints.These capabilities are validated on applications featuring both convex and challenging, non-convex, constraints as well as ordinary differential equations, in domains spanning from synthesizing new materials with precise morphometric properties, generating physics-informed motion, optimizing paths in planning scenarios, and human motion synthesis.
EHRCon: Dataset for Checking Consistency between Unstructured Notes and Structured Tables in Electronic Health Records
Authors: Yeonsu Kwon, Jiho Kim, Gyubok Lee, Seongsu Bae, Daeun Kyung, Wonchul Cha, Tom Pollard, Alistair Johnson, Edward Choi
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Datasets and Benchmarks Track), 2024

Abstract: Electronic Health Records (EHRs) are integral for storing comprehensive patient medical records, combining structured data (e.g., medications) with detailed clinical notes (e.g., physician notes). These elements are essential for straightforward data retrieval and provide deep, contextual insights into patient care. However, they often suffer from discrepancies due to unintuitive EHR system designs and human errors, posing serious risks to patient safety. To address this, we developed EHRCon, a new dataset and task specifically designed to ensure data consistency between structured tables and unstructured notes in EHRs.EHRCon was crafted in collaboration with healthcare professionals using the MIMIC-III EHR dataset, and includes manual annotations of 3,943 entities across 105 clinical notes checked against database entries for consistency.EHRCon has two versions, one using the original MIMIC-III schema, and another using the OMOP CDM schema, in order to increase its applicability and generalizability. Furthermore, leveraging the capabilities of large language models, we introduce CheckEHR, a novel framework for verifying the consistency between clinical notes and database tables. CheckEHR utilizes an eight-stage process and shows promising results in both few-shot and zero-shot settings. The code is available at \url{https://github.com/dustn1259/EHRCon}.
Revisiting motion information for RGB-Event tracking with MOT philosophy
Authors: Tianlu Zhang, Kurt Debattista, Qiang Zhang, Guiguang Ding, Jungong Han
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: RGB-Event single object tracking (SOT) aims to leverage the merits of RGB and event data to achieve higher performance. However, existing frameworks focus on exploring complementary appearance information within multi-modal data, and struggle to address the association problem of targets and distractors in the temporal domain using motion information from the event stream. In this paper, we introduce the Multi-Object Tracking (MOT) philosophy into RGB-E SOT to keep track of targets as well as distractors by using both RGB and event data, thereby improving the robustness of the tracker. Specifically, an appearance model is employed to predict the initial candidates. Subsequently, the initially predicted tracking results, in combination with the RGB-E features, are encoded into appearance and motion embeddings, respectively. Furthermore, a Spatial-Temporal Transformer Encoder is proposed to model the spatial-temporal relationships and learn discriminative features for each candidate through guidance of the appearance-motion embeddings. Simultaneously, a Dual-Branch Transformer Decoder is designed to adopt such motion and appearance information for candidate matching, thus distinguishing between targets and distractors. The proposed method is evaluated on multiple benchmark datasets and achieves state-of-the-art performance on all the datasets tested.
PrivacyLens: Evaluating Privacy Norm Awareness of Language Models in Action
Authors: Yijia Shao, Tianshi Li, Weiyan Shi, Yanchen Liu, Diyi Yang
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Datasets and Benchmarks Track), 2024

Abstract: As language models (LMs) are widely utilized in personalized communication scenarios (e.g., sending emails, writing social media posts) and endowed with a certain level of agency, ensuring they act in accordance with the contextual privacy norms becomes increasingly critical. However, quantifying the privacy norm awareness of LMs and the emerging privacy risk in LM-mediated communication is challenging due to (1) the contextual and long-tailed nature of privacy-sensitive cases, and (2) the lack of evaluation approaches that capture realistic application scenarios. To address these challenges, we propose PrivacyLens, a novel framework designed to extend privacy-sensitive seeds into expressive vignettes and further into agent trajectories, enabling multi-level evaluation of privacy leakage in LM agents' actions. We instantiate PrivacyLens with a collection of privacy norms grounded in privacy literature and crowdsourced seeds. Using this dataset, we reveal a discrepancy between LM performance in answering probing questions and their actual behavior when executing user instructions in an agent setup. State-of-the-art LMs, like GPT-4 and Llama-3-70B, leak sensitive information in 25.68% and 38.69% of cases, even when prompted with privacy-enhancing instructions. We also demonstrate the dynamic nature of PrivacyLens by extending each seed into multiple trajectories to red-team LM privacy leakage risk. Dataset and code are available at https://github.com/SALT-NLP/PrivacyLens.
Revisiting, Benchmarking and Understanding Unsupervised Graph Domain Adaptation
Authors: Meihan Liu, Zhen Zhang, Jiachen Tang, Jiajun Bu, Bingsheng He, Sheng Zhou
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Datasets and Benchmarks Track), 2024

Abstract: Unsupervised Graph Domain Adaptation (UGDA) involves the transfer of knowledge from a label-rich source graph to an unlabeled target graph under domain discrepancies. Despite the proliferation of methods designed for this emerging task, the lack of standard experimental settings and fair performance comparisons makes it challenging to understand which and when models perform well across different scenarios. To fill this gap, we present the first comprehensive benchmark for unsupervised graph domain adaptation named GDABench, which encompasses 16 algorithms across diverse adaptation tasks. Through extensive experiments, we observe that the performance of current UGDA models varies significantly across different datasets and adaptation scenarios. Specifically, we recognize that when the source and target graphs face significant distribution shifts, it is imperative to formulate strategies to effectively address and mitigate graph structural shifts. We also find that with appropriate neighbourhood aggregation mechanisms, simple GNN variants can even surpass state-of-the-art UGDA baselines. To facilitate reproducibility, we have developed an easy-to-use library PyGDA for training and evaluating existing UGDA methods, providing a standardized platform in this community. Our source codes and datasets can be found at https://github.com/pygda-team/pygda.
Thompson Sampling For Combinatorial Bandits: Polynomial Regret and Mismatched Sampling Paradox
Authors: Raymond Zhang, Richard Combes
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: We consider Thompson Sampling (TS) for linear combinatorial semi-bandits and subgaussian rewards. We propose the first known TS whose finite-time regret does not scale exponentially with the dimension of the problem. We further show the mismatched sampling paradox: A learner who knows the rewards distributions and samples from the correct posterior distribution can perform exponentially worse than a learner who does not know the rewards and simply samples from a well-chosen Gaussian posterior. The code used to generate the experiments is available at https://github.com/RaymZhang/CTS-Mismatched-Paradox
CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM
Authors: Minkyu Jeon, Rishwanth Raghu, Miro Astore, Geoffrey Woollard, Ryan Feathers, Alkin Kaz, Sonya M. Hanson, Pilar Cossio, Ellen D. Zhong
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Datasets and Benchmarks Track), 2024

Abstract: Cryo-electron microscopy (cryo-EM)  is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. Its unique ability to capture structural variability has spurred the development of heterogeneous reconstruction algorithms that can infer distributions of 3D structures from noisy, unlabeled imaging data. Despite the growing number of advanced methods, progress in the field is hindered by the lack of standardized benchmarks with ground truth information and reliable validation metrics. Here, we introduce CryoBench, a suite of datasets, metrics, and benchmarks for heterogeneous reconstruction in cryo-EM. CryoBench includes five datasets representing different sources of heterogeneity and degrees of difficulty. These include conformational heterogeneity generated from designed motions of antibody complexes or sampled from a molecular dynamics simulation, as well as {compositional heterogeneity from mixtures of ribosome assembly states or 100 common complexes present in cells. We then analyze state-of-the-art heterogeneous reconstruction tools, including neural and non-neural methods, assess their sensitivity to noise, and propose new metrics for quantitative evaluation. We hope that CryoBench will be a foundational resource for accelerating algorithmic development and evaluation in the cryo-EM and machine learning communities. Project page: https://cryobench.cs.princeton.edu.
What Makes Partial-Label Learning Algorithms Effective?
Authors: Jiaqi Lv, Yangfan Liu, Shiyu Xia, Ning Xu, Miao Xu, Gang Niu, Min-Ling Zhang, Masashi Sugiyama, Xin Geng
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: A partial label (PL) specifies a set of candidate labels for an instance and partial-label learning (PLL) trains multi-class classifiers with PLs.Recently, many methods that incorporate techniques from other domains have shown strong potential.The expectation that stronger techniques would enhance performance has resulted in prominent PLL methods becoming not only highly complicated but also quite different from one another, making it challenging to choose the best direction for future algorithm design.While it is exciting to see higher performance, this leaves open a fundamental question: what makes a PLL method effective?We present a comprehensive empirical analysis of this question and summarize the success of PLL so far into some minimal algorithm design principles.Our findings reveal that high accuracy on benchmark-simulated datasets with PLs can misleadingly amplify the perceived effectiveness of some general techniques, which may improve representation learning but have limited impact on addressing the inherent challenges of PLs. We further identify the common behavior among successful PLL methods as a progressive transition from uniform to one-hot pseudo-labels, highlighting the critical role of mini-batch PL purification in achieving top performance.Based on our findings, we introduce a minimal working algorithm that is surprisingly simple yet effective, and propose an improved strategy to implement the design principles, suggesting a promising direction for improvements in PLL.
DiffHammer: Rethinking the Robustness of Diffusion-Based Adversarial Purification
Authors: Kaibo Wang, Xiaowen Fu, Yuxuan Han, Yang Xiang
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: Diffusion-based purification has demonstrated impressive robustness as an adversarial defense. However, concerns exist about whether this robustness arises from insufficient evaluation. Our research shows that EOT-based attacks face gradient dilemmas due to global gradient averaging, resulting in ineffective evaluations. Additionally, 1-evaluation underestimates resubmit risks in stochastic defenses. To address these issues, we propose an effective and efficient attack named DiffHammer. This method bypasses the gradient dilemma through selective attacks on vulnerable purifications, incorporating $N$-evaluation into loops and using gradient grafting for comprehensive and efficient evaluations. Our experiments validate that DiffHammer achieves effective results within 10-30 iterations, outperforming other methods. This calls into question the reliability of diffusion-based purification after mitigating the gradient dilemma and scrutinizing its resubmit risk.
Multidimensional Fractional Programming for Normalized Cuts
Authors: Yannan Chen, Beichen Huang, Licheng Zhao, Kaiming Shen
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: The Normalized cut (NCut) problem is a fundamental and yet notoriously difficult one in the unsupervised clustering field. Because the NCut problem is fractionally structured, the fractional programming (FP) based approach has worked its way into a new frontier. However, the conventional FP techniques are insufficient: the classic Dinkelbach's transform can only deal with a single ratio and hence is limited to the two-class clustering, while the state-of-the-art quadratic transform accounts for multiple ratios but fails to convert the NCut problem to a tractable form. This work advocates a novel extension of the quadratic transform to the multidimensional ratio case, thereby recasting the fractional 0-1 NCut problem into a bipartite matching problem---which can be readily solved in an iterative manner. Furthermore, we explore the connection between the proposed multidimensional FP method and the minorization-maximization theory to verify the convergence.
DiffusionBlend: Learning 3D Image Prior through Position-aware Diffusion Score Blending for 3D Computed Tomography Reconstruction
Authors: Bowen Song, Jason Hu, Zhaoxu Luo, Jeffrey A. Fessler, Liyue Shen
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: Diffusion models face significant challenges when employed for large-scale medical image reconstruction in real practice such as 3D Computed Tomography (CT).Due to the demanding memory, time, and data requirements, it is difficult to train a diffusion model directly on the entire volume of high-dimensional data to obtain an efficient 3D diffusion prior. Existing works utilizing diffusion priors on single 2D image slice with hand-crafted cross-slice regularization would sacrifice the z-axis consistency, which results in severe artifacts along the z-axis. In this work, we propose a novel framework that enables learning the 3D image prior through position-aware 3D-patch diffusion score blending for reconstructing large-scale 3D medical images. To the best of our knowledge, we are the first to utilize a 3D-patch diffusion prior for 3D medical image reconstruction. Extensive experiments on sparse view and limited angle CT reconstructionshow that our DiffusionBlend method significantly outperforms previous methodsand achieves state-of-the-art performance on real-world CT reconstruction problems with high-dimensional 3D image (i.e., $256 \times 256 \times 500$). Our algorithm also comes with better or comparable computational efficiency than previous state-of-the-art methods. Code is available at https://github.com/efzero/DiffusionBlend.
Adversarial Schrödinger Bridge Matching
Authors: Nikita Gushchin, Daniil Selikhanovych, Sergei Kholkin, Evgeny Burnaev, Alexander Korotin
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: The Schrödinger Bridge (SB) problem offers a powerful framework for combining optimal transport and diffusion models. A promising recent approach to solve the SB problem is the Iterative Markovian Fitting (IMF) procedure, which alternates between Markovian and reciprocal projections of continuous-time stochastic processes. However, the model built by the IMF procedure has a long inference time due to using many steps of numerical solvers for stochastic differential equations. To address this limitation, we propose a novel Discrete-time IMF (D-IMF) procedure in which learning of stochastic processes is replaced by learning just a few transition probabilities in discrete time. Its great advantage is that in practice it can be naturally implemented using the Denoising Diffusion GAN (DD-GAN), an already well-established adversarial generative modeling technique. We show that our D-IMF procedure can provide the same quality of unpaired domain translation as the IMF, using only several generation steps instead of hundreds.
Infusing Self-Consistency into Density Functional Theory Hamiltonian Prediction via Deep Equilibrium Models
Authors: Zun Wang, Chang Liu, Nianlong Zou, He Zhang, Xinran Wei, Lin Huang, Lijun Wu, Bin Shao
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: In this study, we introduce a unified neural network architecture, the Deep Equilibrium Density Functional Theory Hamiltonian (DEQH) model, which incorporates Deep Equilibrium Models (DEQs) for predicting Density Functional Theory (DFT) Hamiltonians. The DEQH model inherently captures the self-consistency nature of Hamiltonian, a critical aspect often overlooked by traditional machine learning approaches for Hamiltonian prediction. By employing DEQ within our model architecture, we circumvent the need for DFT calculations during the training phase to introduce the Hamiltonian's self-consistency, thus addressing computational bottlenecks associated with large or complex systems. We propose a versatile framework that combines DEQ with off-the-shelf machine learning models for predicting Hamiltonians. When benchmarked on the MD17 and QH9 datasets, DEQHNet, an instantiation of the DEQH framework, has demonstrated a significant improvement in prediction accuracy. Beyond a predictor, the DEQH model is a Hamiltonian solver, in the sense that it uses the fixed-point solving capability of the deep equilibrium model to iteratively solve for the Hamiltonian. Ablation studies of DEQHNet further elucidate the network's effectiveness, offering insights into the potential of DEQ-integrated networks for Hamiltonian learning. We open source our implementation at https://github.com/Zun-Wang/DEQHNet.
TransVIP: Speech to Speech Translation System with Voice and Isochrony Preservation
Authors: Chenyang Le, Yao Qian, Dongmei Wang, Long Zhou, Shujie Liu, Xiaofei Wang, Midia Yousefi, Yanmin Qian, Jinyu Li, Sheng Zhao, Michael Zeng
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: There is a rising interest and trend in research towards directly translating speech from one language to another, known as end-to-end speech-to-speech translation. However, most end-to-end models struggle to outperform cascade models, i.e., a pipeline framework by concatenating speech recognition, machine translation and text-to-speech models. The primary challenges stem from the inherent complexities involved in direct translation tasks and the scarcity of data.  In this study, we introduce a novel model framework TransVIP that leverages diverse datasets in a cascade fashion yet facilitates end-to-end inference through joint probability. Furthermore, we propose two separated encoders to preserve the speaker’s voice characteristics and isochrony from the source speech during the translation process, making it highly suitable for scenarios such as video dubbing. Our experiments on the French-English language pair demonstrate that our model outperforms the current state-of-the-art speech-to-speech translation model.
Towards Visual Text Design Transfer Across Languages
Authors: Yejin Choi, Jiwan Chung, Sumin Shim, Giyeong Oh, Youngjae Yu
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Datasets and Benchmarks Track), 2024

Abstract: Visual text design plays a critical role in conveying themes, emotions, and atmospheres in multimodal formats such as film posters and album covers. Translating these visual and textual elements across languages extends the concept of translation beyond mere text, requiring the adaptation of aesthetic and stylistic features. To address this, we introduce a novel task of Multimodal Style Translation (MuST-Bench), a benchmark designed to evaluate the ability of visual text generation models to perform translation across different writing systems while preserving design intent.Our initial experiments on MuST-Bench reveal that existing visual text generation models struggle with the proposed task due to the inadequacy of textual descriptions in conveying visual design.In response, we introduce SIGIL, a framework for multimodal style translation that eliminates the need for style descriptions.SIGIL enhances image generation models through three innovations: glyph latent for multilingual settings, pre-trained VAEs for stable style guidance, and an OCR model with reinforcement learning feedback for optimizing readable character generation. SIGIL outperforms existing baselines by achieving superior style consistency and legibility while maintaining visual fidelity, setting itself apart from traditional description-based approaches. We release MuST-Bench publicly for broader use and exploration https://huggingface.co/datasets/yejinc/MuST-Bench.
Doubly Hierarchical Geometric Representations for Strand-based Human Hairstyle Generation
Authors: Yunlu Chen, Francisco Vicente Carrasco, Christian Häne, Giljoo Nam, Jean-Charles Bazin, Fernando De la Torre
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: We introduce a doubly hierarchical generative representation for strand-based 3D hairstyle geometry that progresses from coarse, low-pass filtered guide hair to densely populated hair strands rich in high-frequency details. We employ the Discrete Cosine Transform (DCT) to separate low-frequency structural curves from high-frequency curliness and noise, avoiding the Gibbs' oscillation issues associated with the standard Fourier transform in open curves. Unlike the guide hair sampled from the scalp UV map grids which may lose capturing details of the hairstyle in existing methods, our method samples optimal sparse guide strands by utilising $k$-medoids clustering centres from low-pass filtered dense strands, which more accurately retain the hairstyle's inherent characteristics. The proposed variational autoencoder-based generation network, with an architecture inspired by geometric deep learning and implicit neural representations, facilitates flexible, off-the-grid guide strand modelling and enables the completion of dense strands in any quantity and density, drawing on principles from implicit neural representations. Empirical evaluations confirm the capacity of the model to generate convincing guide hair and dense strands, complete with nuanced high-frequency details.
Untrained Neural Nets for Snapshot Compressive Imaging: Theory and Algorithms
Authors: Mengyu Zhao, Xi Chen, Xin Yuan, Shirin Jalali
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: Snapshot compressive imaging (SCI) recovers high-dimensional (3D) data cubes from a single 2D measurement, enabling diverse applications like video and hyperspectral imaging to go beyond standard techniques in terms of acquisition speed and efficiency. In this paper, we focus on SCI recovery algorithms that employ untrained neural networks (UNNs), such as deep image prior (DIP), to model source structure. Such UNN-based methods are appealing as they have the potential of avoiding the computationally intensive retraining required for different source models and different measurement scenarios. We first develop a theoretical framework for characterizing the performance of such UNN-based methods. The theoretical framework, on the one hand, enables us to optimize the parameters of data-modulating masks, and on the other hand, provides a fundamental connection between the number of data frames that can be recovered from a single measurement to the parameters of the untrained NN. We also employ the recently proposed bagged-deep-image-prior (bagged-DIP) idea to develop SCI Bagged Deep Video Prior (SCI-BDVP) algorithms that address the common challenges faced by standard UNN solutions. Our experimental results show that in video SCI our proposed solution achieves state-of-the-art among UNN methods, and in the case of noisy measurements, it even outperforms supervised solutions. Code is publicly available at https://github.com/Computational-Imaging-RU/SCI-BDVP.
Enhancing Feature Diversity Boosts Channel-Adaptive Vision Transformers
Authors: Chau Pham, Bryan A. Plummer
Published in: Advances in Neural Information Processing Systems 37  (NeurIPS 2024) (Main Conference Track), 2024

Abstract: Multi-Channel Imaging (MCI) contains an array of challenges for encoding useful feature representations not present in traditional images. For example, images from two different satellites may both contain RGB channels, but the remaining channels can be different for each imaging source. Thus, MCI models must support a variety of channel configurations at test time. Recent work has extended traditional visual encoders for MCI, such as Vision Transformers (ViT), by supplementing pixel information with an encoding representing the channel configuration. However, these methods treat each channel equally, i.e., they do not consider the unique properties of each channel type, which can result in needless and potentially harmful redundancies in the learned features. For example, if RGB channels are always present, the other channels can focus on extracting information that cannot be captured by the RGB channels. To this end, we propose DiChaViT, which aims to enhance the diversity in the learned features of MCI-ViT models. This is achieved through a novel channel sampling strategy that encourages the selection of more distinct channel sets for training. Additionally, we employ regularization and initialization techniques to increase the likelihood that new information is learned from each channel. Many of our improvements are architecture agnostic and can be incorporated into new architectures as they are developed. Experiments on both satellite and cell microscopy datasets, CHAMMI, JUMP-CP, and So2Sat, report DiChaViT yields a 1.5 - 5.0% gain over the state-of-the-art. Our code is publicly available at https://github.com/chaudatascience/diversechannelvit.