OpenRaiser/Intern-Atlas huggingface dataset:
Sourcerer: Sample-based Maximum Entropy Source Distribution Estimation
Venue: Conference NeurIPS 2024
Year: 2024

Scientific modeling applications often require estimating a distribution of parameters consistent with a dataset of observations - an inference task also known as source distribution estimation. This problem can be ill-posed, however, since many different source distributions might produce the same distribution of data-consistent simulations. To make a principled choice among many equally valid sources, we propose an approach which targets the maximum entropy distribution, i.e., prioritizes retaining as much uncertainty as possible. Our method is purely sample-based - leveraging the Sliced-Wasserstein distance to measure the discrepancy between the dataset and simulations - and thus suitable for simulators with intractable likelihoods. We benchmark our method on several tasks, and show that it can recover source distributions with substantially higher entropy than recent source estimation methods, without sacrificing the fidelity of the simulations. Finally, to demonstrate the utility of our approach, we infer source distributions for parameters of the Hodgkin-Huxley model from experimental datasets with thousands of single-neuron measurements. In summary, we propose a principled method for inferring source distributions of scientific simulator parameters while retaining as much uncertainty as possible.
On Socially Fair Low-Rank Approximation and Column Subset Selection
Venue: Conference NeurIPS 2024
Year: 2024

Low-rank approximation and column subset selection are two fundamental and related problems that are applied across a wealth of machine learning applications. In this paper, we study the question of socially fair low-rank approximation and socially fair column subset selection, where the goal is to minimize the loss over all sub-populations of the data. We show that surprisingly, even constant-factor approximation to fair low-rank approximation requires exponential time under certain standard complexity hypotheses. On the positive side, we give an algorithm for fair low-rank approximation that, for a constant number of groups and constant-factor accuracy, runs in $2^{\text{poly}(k)}$ time rather than the naïve $n^{\text{poly}(k)}$, which is a substantial improvement when the dataset has a large number $n$ of observations. We then show that there exist bicriteria approximation algorithms for fair low-rank approximation and fair column subset selection that run in polynomial time.
Perception of Knowledge Boundary for Large Language Models through Semi-open-ended Question Answering
Venue: Conference NeurIPS 2024
Year: 2024

Large Language Models (LLMs) are widely used for knowledge-seeking yet suffer from hallucinations. The knowledge boundary (KB) of an LLM limits its factual understanding, beyond which it may begin to hallucinate. Investigating the perception of LLMs' KB is crucial for detecting hallucinations and LLMs' reliable generation. Current studies perceive LLMs' KB on questions with a concrete answer (close-ended questions) while paying limited attention to semi-open-ended questions (SoeQ) that correspond to many potential answers. Some researchers achieve it by judging whether the question is answerable or not. However, this paradigm is unsuitable for SoeQ, which are usually partially answerable, containing both answerable and ambiguous (unanswerable) answers. Ambiguous answers are essential for knowledge-seeking, but they may go beyond the KB of LLMs. In this paper, we perceive the LLMs' KB with SoeQ by discovering more ambiguous answers. First, we apply an LLM-based approach to construct SoeQ and obtain answers from a target LLM. Unfortunately, the output probabilities of mainstream black-box LLMs are inaccessible to sample for low-probability ambiguous answers. Therefore, we apply an open-sourced auxiliary model to explore ambiguous answers for the target LLM. We calculate the nearest semantic representation for existing answers to estimate their probabilities, with which we reduce the generation probability of high-probability answers to achieve a more effective generation. Finally, we compare the results from the RAG-based evaluation and LLM self-evaluation to categorize four types of ambiguous answers that are beyond the KB of the target LLM. Following our method, we construct a dataset to perceive the KB for GPT-4. We find that GPT-4 performs poorly on SoeQ and is often unaware of its KB. Besides, our auxiliary model, LLaMA-2-13B, is effective in discovering more ambiguous answers.
Compressing Large Language Models using Low Rank and Low Precision Decomposition
Venue: Conference NeurIPS 2024
Year: 2024

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/$13B$/$70$B and LlaMa-$3$ $8$B models using $\rm CALDERA$ outperforms existing post-training LLM compression techniques in the regime of less than $2.5$ bits per parameter. The implementation is available at: https://github.com/pilancilab/caldera.
Intervention and Conditioning in Causal Bayesian Networks
Venue: Conference NeurIPS 2024
Year: 2024

Causal models are crucial for understanding complex systems and identifying causal relationships among variables. Even though causal models are extremely popular, conditional probability calculation of formulas involving interventions pose significant challenges. In case of Causal Bayesian Networks (CBNs), Pearl assumes autonomy of mechanisms that determine interventions to calculate a range of probabilities. We show that by making simple yet often realistic independence assumptions, it is possible to uniquely estimate the probability of an interventional formula (including the 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 using observational data, which carries immense significance in scenarios where conducting experiments is impractical or unfeasible.
QUEST: Quality-Aware Metropolis-Hastings Sampling for Machine Translation
Venue: Conference NeurIPS 2024
Year: 2024

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).
MMBench-Video: A Long-Form Multi-Shot Benchmark for Holistic Video Understanding
Venue: Conference NeurIPS 2024
Year: 2024

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. The evalutation code of MMBench-Video will be integrated into VLMEvalKit: https://github.com/open-compass/VLMEvalKit.
Improving Adversarial Robust Fairness via Anti-Bias Soft Label  Distillation
Venue: Conference NeurIPS 2024
Year: 2024

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.
GaussianCut: Interactive segmentation via graph cut for 3D Gaussian Splatting
Venue: Conference NeurIPS 2024
Year: 2024

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
Venue: Conference NeurIPS 2024
Year: 2024

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.
Constrained Synthesis with Projected Diffusion Models
Venue: Conference NeurIPS 2024
Year: 2024

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
Venue: Conference NeurIPS 2024
Year: 2024

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 4,101 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 https://github.com/dustn1259/EHRCon.
Revisiting, Benchmarking and Understanding Unsupervised Graph Domain Adaptation
Venue: Conference NeurIPS 2024
Year: 2024

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 5 datasets with 74 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.
DiffusionBlend: Learning 3D Image Prior through Position-aware Diffusion Score Blending for 3D Computed Tomography Reconstruction
Venue: Conference NeurIPS 2024
Year: 2024

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 reconstruction show that our DiffusionBlend method significantly outperforms previous methods and 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.
Adversarial Schrödinger Bridge Matching
Venue: Conference NeurIPS 2024
Year: 2024

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. We provide the code at https://github.com/Daniil-Selikhanovych/ASBM.
Infusing Self-Consistency into Density Functional Theory Hamiltonian Prediction via Deep Equilibrium Models
Venue: Conference NeurIPS 2024
Year: 2024

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
Venue: Conference NeurIPS 2024
Year: 2024

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.