OpenRaiser/Intern-Atlas huggingface dataset:
HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution
Venue: Conference NeurIPS 2023
Year: 2023

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers or fixed k-mers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyena's new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level - an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 18 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on 7 of 8 datasets on average by +10 accuracy points. Code at https://github.com/HazyResearch/hyena-dna.
Robust Concept Erasure via Kernelized Rate-Distortion Maximization
Venue: Conference NeurIPS 2023
Year: 2023

Distributed representations provide a vector space that captures meaningful relationships between data instances. The distributed nature of these representations, however, entangles together multiple attributes or concepts of data instances (e.g., the topic or sentiment of a text, characteristics of the author (age, gender, etc), etc). Recent work has proposed the task of concept erasure, in which rather than making a concept predictable, the goal is to remove an attribute from distributed representations while retaining other information from the original representation space as much as possible. In this paper, we propose a new distance metric learning-based objective, the Kernelized Rate-Distortion Maximizer (KRaM), for performing concept erasure. KRaM fits a transformation of representations to match a specified distance measure (defined by a labeled concept to erase) using a modified rate-distortion function. Specifically, KRaM's objective function aims to make instances with similar concept labels dissimilar in the learned representation space while retaining other information. We find that optimizing KRaM effectively erases various types of concepts: categorical, continuous, and vector-valued variables from data representations across diverse domains. We also provide a theoretical analysis of several properties of KRaM's objective. To assess the quality of the learned representations, we propose an alignment score to evaluate their similarity with the original representation space. Additionally, we conduct experiments to showcase KRaM's efficacy in various settings, from erasing binary gender variables in word embeddings to vector-valued variables in GPT-3 representations.
One Fits All: Power General Time Series Analysis by Pretrained LM
Venue: Conference NeurIPS 2023
Year: 2023

Although we have witnessed great success of pre-trained models in natural language processing (NLP) and computer vision (CV), limited progress has been made for general time series analysis. Unlike NLP and CV where a unified model can be used to perform different tasks, specially designed approach still dominates in each time series analysis task such as classification, anomaly detection, forecasting, and few-shot learning. The main challenge that blocks the development of pre-trained model for time series analysis is the lack of a large amount of data for training. In this work, we address this challenge by leveraging language or CV models, pre-trained from billions of tokens, for time series analysis. Specifically, we refrain from altering the self-attention and feedforward layers of the residual blocks in the pre-trained language or image model. This model, known as the Frozen Pretrained Transformer (FPT), is evaluated through fine-tuning on all major types of tasks involving time series. Our results demonstrate that pre-trained models on natural language or images can lead to a comparable or state-of-the-art performance in all main time series analysis tasks, as illustrated in Figure 1. We also found both theoretically and empirically that the self-attention module behaviors similarly to principle component analysis (PCA), an observation that helps explains how transformer bridges the domain gap and a crucial step towards understanding the universality of a pre-trained transformer.The code is publicly available at https://github.com/DAMO-DI-ML/One_Fits_All.
Near-Optimal Algorithms for Gaussians with Huber Contamination: Mean Estimation and Linear Regression
Venue: Conference NeurIPS 2023
Year: 2023

We study the fundamental problems of Gaussian mean estimation and linear regression with Gaussian covariates in the presence of Huber contamination. Our main contribution is the design of the first sample near-optimal and almost linear-time algorithms with optimal error guarantees for both of these problems. Specifically, for Gaussian robust mean estimation on $\mathbb{R}^d$ with contamination parameter $ε\in (0, ε_0)$ for a small absolute constant $ε_0$, we give an algorithm with sample complexity $n = \tilde{O}(d/ε^2)$ and almost linear runtime that approximates the target mean within $\ell_2$-error $O(ε)$. This improves on prior work that achieved this error guarantee with polynomially suboptimal sample and time complexity. For robust linear regression, we give the first algorithm with sample complexity $n = \tilde{O}(d/ε^2)$ and almost linear runtime that approximates the target regressor within $\ell_2$-error $O(ε)$. This is the first polynomial sample and time algorithm achieving the optimal error guarantee, answering an open question in the literature. At the technical level, we develop a methodology that yields almost-linear time algorithms for multi-directional filtering that may be of broader interest.
Causal Discovery from Subsampled Time Series with Proxy Variables
Venue: Conference NeurIPS 2023
Year: 2023

Inferring causal structures from time series data is the central interest of many scientific inquiries. A major barrier to such inference is the problem of subsampling, i.e., the frequency of measurement is much lower than that of causal influence. To overcome this problem, numerous methods have been proposed, yet either was limited to the linear case or failed to achieve identifiability. In this paper, we propose a constraint-based algorithm that can identify the entire causal structure from subsampled time series, without any parametric constraint. Our observation is that the challenge of subsampling arises mainly from hidden variables at the unobserved time steps. Meanwhile, every hidden variable has an observed proxy, which is essentially itself at some observable time in the future, benefiting from the temporal structure. Based on these, we can leverage the proxies to remove the bias induced by the hidden variables and hence achieve identifiability. Following this intuition, we propose a proxy-based causal discovery algorithm. Our algorithm is nonparametric and can achieve full causal identification. Theoretical advantages are reflected in synthetic and real-world experiments.
Chameleon: Plug-and-Play Compositional Reasoning with Large Language Models
Venue: Conference NeurIPS 2023
Year: 2023

Large language models (LLMs) have achieved remarkable progress in solving various natural language processing tasks due to emergent reasoning abilities. However, LLMs have inherent limitations as they are incapable of accessing up-to-date information (stored on the Web or in task-specific knowledge bases), using external tools, and performing precise mathematical and logical reasoning. In this paper, we present Chameleon, an AI system that mitigates these limitations by augmenting LLMs with plug-and-play modules for compositional reasoning. Chameleon synthesizes programs by composing various tools (e.g., LLMs, off-the-shelf vision models, web search engines, Python functions, and heuristic-based modules) for accomplishing complex reasoning tasks. At the heart of Chameleon is an LLM-based planner that assembles a sequence of tools to execute to generate the final response. We showcase the effectiveness of Chameleon on two multi-modal knowledge-intensive reasoning tasks: ScienceQA and TabMWP. Chameleon, powered by GPT-4, achieves an 86.54% overall accuracy on ScienceQA, improving the best published few-shot result by 11.37%. On TabMWP, GPT-4-powered Chameleon improves the accuracy by 17.0%, lifting the state of the art to 98.78%. Our analysis also shows that the GPT-4-powered planner exhibits more consistent and rational tool selection via inferring potential constraints from instructions, compared to a ChatGPT-powered planner. The project is available at https://chameleon-llm.github.io.
Diffusion Models and Semi-Supervised Learners Benefit Mutually with Few Labels
Venue: Conference NeurIPS 2023
Year: 2023

In an effort to further advance semi-supervised generative and classification tasks, we propose a simple yet effective training strategy called dual pseudo training (DPT), built upon strong semi-supervised learners and diffusion models. DPT operates in three stages: training a classifier on partially labeled data to predict pseudo-labels; training a conditional generative model using these pseudo-labels to generate pseudo images; and retraining the classifier with a mix of real and pseudo images. Empirically, DPT consistently achieves SOTA performance of semi-supervised generation and classification across various settings. In particular, with one or two labels per class, DPT achieves a Fréchet Inception Distance (FID) score of 3.08 or 2.52 on ImageNet 256x256. Besides, DPT outperforms competitive semi-supervised baselines substantially on ImageNet classification tasks, achieving top-1 accuracies of 59.0 (+2.8), 69.5 (+3.0), and 74.4 (+2.0) with one, two, or five labels per class, respectively. Notably, our results demonstrate that diffusion can generate realistic images with only a few labels (e.g., <0.1%) and generative augmentation remains viable for semi-supervised classification. Our code is available at https://github.com/ML-GSAI/DPT.
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction
Venue: Conference NeurIPS 2023
Year: 2023

Self-supervised pre-training methods on proteins have recently gained attention, with most approaches focusing on either protein sequences or structures, neglecting the exploration of their joint distribution, which is crucial for a comprehensive understanding of protein functions by integrating co-evolutionary information and structural characteristics. In this work, inspired by the success of denoising diffusion models in generative tasks, we propose the DiffPreT approach to pre-train a protein encoder by sequence-structure joint diffusion modeling. DiffPreT guides the encoder to recover the native protein sequences and structures from the perturbed ones along the joint diffusion trajectory, which acquires the joint distribution of sequences and structures. Considering the essential protein conformational variations, we enhance DiffPreT by a method called Siamese Diffusion Trajectory Prediction (SiamDiff) to capture the correlation between different conformers of a protein. SiamDiff attains this goal by maximizing the mutual information between representations of diffusion trajectories of structurally-correlated conformers. We study the effectiveness of DiffPreT and SiamDiff on both atom- and residue-level structure-based protein understanding tasks. Experimental results show that the performance of DiffPreT is consistently competitive on all tasks, and SiamDiff achieves new state-of-the-art performance, considering the mean ranks on all tasks. Our implementation is available at https://github.com/DeepGraphLearning/SiamDiff.
Progressive Ensemble Distillation: Building Ensembles for Efficient Inference
Venue: Conference NeurIPS 2023
Year: 2023

We study the problem of progressive ensemble distillation: Given a large, pretrained teacher model $g$, we seek to decompose the model into smaller, low-inference cost student models $f_i$, such that progressively evaluating additional models in this ensemble leads to improved predictions. The resulting ensemble allows for flexibly tuning accuracy vs. inference cost at runtime, which is useful for a number of applications in on-device inference. The method we propose, B-DISTIL , relies on an algorithmic procedure that uses function composition over intermediate activations to construct expressive ensembles with similar performance as $g$ , but with smaller student models. We demonstrate the effectiveness of B-DISTIL by decomposing pretrained models across standard image, speech, and sensor datasets. We also provide theoretical guarantees in terms of convergence and generalization.
Reinforcement-Enhanced Autoregressive Feature Transformation: Gradient-steered Search in Continuous Space for Postfix Expressions
Venue: Conference NeurIPS 2023
Year: 2023

Feature transformation aims to generate new pattern-discriminative feature space from original features to improve downstream machine learning (ML) task performances. However, the discrete search space for the optimal feature explosively grows on the basis of combinations of features and operations from low-order forms to high-order forms. Existing methods, such as exhaustive search, expansion reduction, evolutionary algorithms, reinforcement learning, and iterative greedy, suffer from large search space. Overly emphasizing efficiency in algorithm design usually sacrifices stability or robustness. To fundamentally fill this gap, we reformulate discrete feature transformation as a continuous space optimization task and develop an embedding-optimization-reconstruction framework. This framework includes four steps: 1) reinforcement-enhanced data preparation, aiming to prepare high-quality transformation-accuracy training data; 2) feature transformation operation sequence embedding, intending to encapsulate the knowledge of prepared training data within a continuous space; 3) gradient-steered optimal embedding search, dedicating to uncover potentially superior embeddings within the learned space; 4) transformation operation sequence reconstruction, striving to reproduce the feature transformation solution to pinpoint the optimal feature space.
FD-Align: Feature Discrimination Alignment for Fine-tuning Pre-Trained Models in Few-Shot Learning
Venue: Conference NeurIPS 2023
Year: 2023

Due to the limited availability of data, existing few-shot learning methods trained from scratch fail to achieve satisfactory performance. In contrast, large-scale pre-trained models such as CLIP demonstrate remarkable few-shot and zero-shot capabilities. To enhance the performance of pre-trained models for downstream tasks, fine-tuning the model on downstream data is frequently necessary. However, fine-tuning the pre-trained model leads to a decrease in its generalizability in the presence of distribution shift, while the limited number of samples in few-shot learning makes the model highly susceptible to overfitting. Consequently, existing methods for fine-tuning few-shot learning primarily focus on fine-tuning the model's classification head or introducing additional structure. In this paper, we introduce a fine-tuning approach termed Feature Discrimination Alignment (FD-Align). Our method aims to bolster the model's generalizability by preserving the consistency of spurious features across the fine-tuning process. Extensive experimental results validate the efficacy of our approach for both ID and OOD tasks. Once fine-tuned, the model can seamlessly integrate with existing methods, leading to performance improvements. Our code can be found in https://github.com/skingorz/FD-Align.
A Step Towards Worldwide Biodiversity Assessment:  The BIOSCAN-1M Insect Dataset
Venue: Conference NeurIPS 2023
Year: 2023

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier.
D-Separation for Causal Self-Explanation
Venue: Conference NeurIPS 2023
Year: 2023

Rationalization is a self-explaining framework for NLP models. Conventional work typically uses the maximum mutual information (MMI) criterion to find the rationale that is most indicative of the target label. However, this criterion can be influenced by spurious features that correlate with the causal rationale or the target label. Instead of attempting to rectify the issues of the MMI criterion, we propose a novel criterion to uncover the causal rationale, termed the Minimum Conditional Dependence (MCD) criterion, which is grounded on our finding that the non-causal features and the target label are \emph{d-separated} by the causal rationale. By minimizing the dependence between the unselected parts of the input and the target label conditioned on the selected rationale candidate, all the causes of the label are compelled to be selected. In this study, we employ a simple and practical measure of dependence, specifically the KL-divergence, to validate our proposed MCD criterion. Empirically, we demonstrate that MCD improves the F1 score by up to $13.7\%$ compared to previous state-of-the-art MMI-based methods. Our code is available at: \url{https://github.com/jugechengzi/Rationalization-MCD}.
History Filtering in Imperfect Information Games: Algorithms and Complexity
Venue: Conference NeurIPS 2023
Year: 2023

Historically applied exclusively to perfect information games, depth-limited search with value functions has been key to recent advances in AI for imperfect information games. Most prominent approaches with strong theoretical guarantees require subgame decomposition - a process in which a subgame is computed from public information and player beliefs. However, subgame decomposition can itself require non-trivial computations, and its tractability depends on the existence of efficient algorithms for either full enumeration or generation of the histories that form the root of the subgame. Despite this, no formal analysis of the tractability of such computations has been established in prior work, and application domains have often consisted of games, such as poker, for which enumeration is trivial on modern hardware. Applying these ideas to more complex domains requires understanding their cost. In this work, we introduce and analyze the computational aspects and tractability of filtering histories for subgame decomposition. We show that constructing a single history from the root of the subgame is generally intractable, and then provide a necessary and sufficient condition for efficient enumeration. We also introduce a novel Markov Chain Monte Carlo-based generation algorithm for trick-taking card games - a domain where enumeration is often prohibitively expensive. Our experiments demonstrate its improved scalability in the trick-taking card game Oh Hell. These contributions clarify when and how depth-limited search via subgame decomposition can be an effective tool for sequential decision-making in imperfect information settings.
Constant Approximation for Individual Preference Stable Clustering
Venue: Conference NeurIPS 2023
Year: 2023

Individual preference (IP) stability, introduced by Ahmadi et al. (ICML 2022), is a natural clustering objective inspired by stability and fairness constraints. A clustering is $α$-IP stable if the average distance of every data point to its own cluster is at most $α$ times the average distance to any other cluster. Unfortunately, determining if a dataset admits a $1$-IP stable clustering is NP-Hard. Moreover, before this work, it was unknown if an $o(n)$-IP stable clustering always \emph{exists}, as the prior state of the art only guaranteed an $O(n)$-IP stable clustering. We close this gap in understanding and show that an $O(1)$-IP stable clustering always exists for general metrics, and we give an efficient algorithm which outputs such a clustering. We also introduce generalizations of IP stability beyond average distance and give efficient, near-optimal algorithms in the cases where we consider the maximum and minimum distances within and between clusters.
DeepACO: Neural-enhanced Ant Systems for Combinatorial Optimization
Venue: Conference NeurIPS 2023
Year: 2023

Ant Colony Optimization (ACO) is a meta-heuristic algorithm that has been successfully applied to various Combinatorial Optimization Problems (COPs). Traditionally, customizing ACO for a specific problem requires the expert design of knowledge-driven heuristics. In this paper, we propose DeepACO, a generic framework that leverages deep reinforcement learning to automate heuristic designs. DeepACO serves to strengthen the heuristic measures of existing ACO algorithms and dispense with laborious manual design in future ACO applications. As a neural-enhanced meta-heuristic, DeepACO consistently outperforms its ACO counterparts on eight COPs using a single neural architecture and a single set of hyperparameters. As a Neural Combinatorial Optimization method, DeepACO performs better than or on par with problem-specific methods on canonical routing problems. Our code is publicly available at https://github.com/henry-yeh/DeepACO.