arXiv subjects

Dong Li

Publications and source records attributed to Dong Li.

At least 253 records · Page 14Linked to original sources

arXiv2024

Automating Exploratory Proteomics Research via Language Models

With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advancement requires both specialized general models grounded in real-world scientific data and iterative, exploratory frameworks that mirror human scientific methodologies. In this paper, we present PROTEUS, a fully automated system for scientific discovery from raw proteomics data. PROTEUS uses large language models (LLMs) to perform hierarchical planning, execute specialized bioinformatics tools, and iteratively refine analysis workflows to generate high-quality scientific hypotheses. The system takes proteomics datasets as input and produces a comprehensive set of research objectives, analysis results, and novel biological hypotheses without human intervention. We evaluated PROTEUS on 12 proteomics datasets collected from various biological samples (e.g. immune cells, tumors) and different sample types (single-cell and bulk), generating 191 scientific hypotheses. These were assessed using both automatic LLM-based scoring on 5 metrics and detailed reviews from human experts. Results demonstrate that PROTEUS consistently produces reliable, logically coherent results that align well with existing literature while also proposing novel, evaluable hypotheses. The system's flexible architecture facilitates seamless integration of diverse analysis tools and adaptation to different proteomics data types. By automating complex proteomics analysis workflows and hypothesis generation, PROTEUS has the potential to considerably accelerate the pace of scientific discovery in proteomics research, enabling researchers to efficiently explore large-scale datasets and uncover biological insights.

cs.AI↗

arXiv2024

(Debiased) Contrastive Learning Loss for Recommendation (Technical Report)

In this paper, we perform a systemic examination of the recommendation losses, including listwise (softmax), pairwise(BPR), and pointwise (mean-squared error, MSE, and Cosine Contrastive Loss, CCL) losses through the lens of contrastive learning. We introduce and study both debiased InfoNCE and mutual information neural estimator (MINE), for the first time, under the recommendation setting. We also relate and differentiate these two losses with the BPR loss through the lower bound analysis. Furthermore, we present the debiased pointwise loss (for both MSE and CCL) and theoretically certify both iALS and EASE, two of the most popular linear models, are inherently debiased. The empirical experimental results demonstrate the effectiveness of the debiased losses and newly introduced mutual-information losses outperform the existing (biased) ones.

cs.AI↗

arXiv2024

Revisiting Recommendation Loss Functions through Contrastive Learning (Technical Report)

Inspired by the success of contrastive learning, we systematically examine recommendation losses, including listwise (softmax), pairwise (BPR), and pointwise (MSE and CCL) losses. In this endeavor, we introduce InfoNCE+, an optimized generalization of InfoNCE with balance coefficients, and highlight its performance advantages, particularly when aligned with our new decoupled contrastive loss, MINE+. We also leverage debiased InfoNCE to debias pointwise recommendation loss (CCL) as Debiased CCL. Interestingly, our analysis reveals that linear models like iALS and EASE are inherently debiased. Empirical results demonstrates the effectiveness of MINE+ and Debiased-CCL.

cs.AI↗

arXiv2024

Dissertation: On the Theoretical Foundation of Model Comparison and Evaluation for Recommender System

Recommender systems have become increasingly important with the rise of the web as a medium for electronic and business transactions. One of the key drivers of this technology is the ease with which users can provide feedback about their likes and dislikes through simple clicks of a mouse. This feedback is commonly collected in the form of ratings, but can also be inferred from a user's browsing and purchasing history. Recommender systems utilize users' historical data to infer customer interests and provide personalized recommendations. The basic principle of recommendations is that significant dependencies exist between user- and item-centric activity, which can be learned in a data-driven manner to make accurate predictions. Collaborative filtering is one family of recommendation algorithms that uses ratings from multiple users to predict missing ratings or uses binary click information to predict potential clicks. However, recommender systems can be more complex and incorporate auxiliary data such as content-based attributes, user interactions, and contextual information.

cs.IR↗

arXiv2024

Reinforced In-Context Black-Box Optimization

Black-Box Optimization (BBO) has found successful applications in many fields of science and engineering. Recently, there has been a growing interest in meta-learning particular components of BBO algorithms to speed up optimization and get rid of tedious hand-crafted heuristics. As an extension, learning the entire algorithm from data requires the least labor from experts and can provide the most flexibility. In this paper, we propose RIBBO, a method to reinforce-learn a BBO algorithm from offline data in an end-to-end fashion. RIBBO employs expressive sequence models to learn the optimization histories produced by multiple behavior algorithms and tasks, leveraging the in-context learning ability of large models to extract task information and make decisions accordingly. Central to our method is to augment the optimization histories with \textit{regret-to-go} tokens, which are designed to represent the performance of an algorithm based on cumulative regret over the future part of the histories. The integration of regret-to-go tokens enables RIBBO to automatically generate sequences of query points that satisfy the user-desired regret, which is verified by its universally good empirical performance on diverse problems, including BBO benchmark functions, hyper-parameter optimization and robot control problems.

cs.LG↗

arXiv2024

iVideoGPT: Interactive VideoGPTs are Scalable World Models

World models empower model-based agents to interactively explore, reason, and plan within imagined environments for real-world decision-making. However, the high demand for interactivity poses challenges in harnessing recent advancements in video generative models for developing world models at scale. This work introduces Interactive VideoGPT (iVideoGPT), a scalable autoregressive transformer framework that integrates multimodal signals--visual observations, actions, and rewards--into a sequence of tokens, facilitating an interactive experience of agents via next-token prediction. iVideoGPT features a novel compressive tokenization technique that efficiently discretizes high-dimensional visual observations. Leveraging its scalable architecture, we are able to pre-train iVideoGPT on millions of human and robotic manipulation trajectories, establishing a versatile foundation that is adaptable to serve as interactive world models for a wide range of downstream tasks. These include action-conditioned video prediction, visual planning, and model-based reinforcement learning, where iVideoGPT achieves competitive performance compared with state-of-the-art methods. Our work advances the development of interactive general world models, bridging the gap between generative video models and practical model-based reinforcement learning applications. Code and pre-trained models are available at https://thuml.github.io/iVideoGPT.

cs.CV↗

arXiv2024

GDDA: Semantic OOD Detection on Graphs under Covariate Shift via Score-Based Diffusion Models

Out-of-distribution (OOD) detection poses a significant challenge for Graph Neural Networks (GNNs), particularly in open-world scenarios with varying distribution shifts. Most existing OOD detection methods on graphs primarily focus on identifying instances in test data domains caused by either semantic shifts (changes in data classes) or covariate shifts (changes in data features), while leaving the simultaneous occurrence of both distribution shifts under-explored. In this work, we address both types of shifts simultaneously and introduce a novel challenge for OOD detection on graphs: graph-level semantic OOD detection under covariate shift. In this scenario, variations between the training and test domains result from the concurrent presence of both covariate and semantic shifts, where only graphs associated with unknown classes are identified as OOD samples (OODs). To tackle this challenge, we propose a novel two-phase framework called Graph Disentangled Diffusion Augmentation (GDDA). The first phase focuses on disentangling graph representations into domain-invariant semantic factors and domain-specific style factors. In the second phase, we introduce a novel distribution-shift-controlled score-based generative diffusion model that generates latent factors outside the training semantic and style spaces. Additionally, auxiliary pseudo-in-distribution (InD) and pseudo-OOD graph representations are employed to enhance the effectiveness of the energy-based semantic OOD detector. Extensive empirical studies on three benchmark datasets demonstrate that our approach outperforms state-of-the-art baselines.

cs.LG↗

arXiv2024

DiP-GO: A Diffusion Pruner via Few-step Gradient Optimization

Diffusion models have achieved remarkable progress in the field of image generation due to their outstanding capabilities. However, these models require substantial computing resources because of the multi-step denoising process during inference. While traditional pruning methods have been employed to optimize these models, the retraining process necessitates large-scale training datasets and extensive computational costs to maintain generalization ability, making it neither convenient nor efficient. Recent studies attempt to utilize the similarity of features across adjacent denoising stages to reduce computational costs through simple and static strategies. However, these strategies cannot fully harness the potential of the similar feature patterns across adjacent timesteps. In this work, we propose a novel pruning method that derives an efficient diffusion model via a more intelligent and differentiable pruner. At the core of our approach is casting the model pruning process into a SubNet search process. Specifically, we first introduce a SuperNet based on standard diffusion via adding some backup connections built upon the similar features. We then construct a plugin pruner network and design optimization losses to identify redundant computation. Finally, our method can identify an optimal SubNet through few-step gradient optimization and a simple post-processing procedure. We conduct extensive experiments on various diffusion models including Stable Diffusion series and DiTs. Our DiP-GO approach achieves 4.4 x speedup for SD-1.5 without any loss of accuracy, significantly outperforming the previous state-of-the-art methods.

cs.CV↗

arXiv2024

Amphista: Bi-directional Multi-head Decoding for Accelerating LLM Inference

Large Language Models (LLMs) inherently use autoregressive decoding, which lacks parallelism in inference and results in significantly slow inference speed. While methods such as Medusa constructs parallelized heads, they lack adequate information interaction across different prediction positions. To overcome this limitation, we introduce Amphista, an enhanced speculative decoding framework that builds upon Medusa. Specifically, Amphista models an Auto-embedding Block capable of parallel inference, incorporating bi-directional attention to enable interaction between different drafting heads. Additionally, Amphista integrates Staged Adaptation Layers, which ensure a seamless transition of semantic information from the target model's autoregressive inference to the drafting heads' non-autoregressive inference, effectively achieving paradigm shift and feature fusion. Experimental results on Vicuna models using MT-Bench and Spec-Bench demonstrate that Amphista achieves substantial acceleration while maintaining generation quality. On MT-Bench, Amphista delivers up to 2.75$\times$ speedup over vanilla autoregressive decoding and 1.40$\times$ over Medusa on Vicuna 33B in wall-clock time.

cs.AI↗

arXiv2024

Tuning Fast Memory Size based on Modeling of Page Migration for Tiered Memory

Tiered memory, built upon a combination of fast memory and slow memory, provides a cost-effective solution to meet ever-increasing requirements from emerging applications for large memory capacity. Reducing the size of fast memory is valuable to improve memory utilization in production and reduce production costs because fast memory tends to be expensive. However, deciding the fast memory size is challenging because there is a complex interplay between application characterization and the overhead of page migration used to mitigate the impact of limited fast memory capacity. In this paper, we introduce a system, Tuna, to decide fast memory size based on modeling of page migration. Tuna uses micro-benchmarking to model the impact of page migration on application performance using three metrics. Tuna decides the fast memory size based on offline modeling results and limited information on workload telemetry. Evaluating with common big-memory applications and using 5% as the performance loss target, we show that Tuna in combination with a page management system (TPP) saves fast memory by 8.5% on average (up to 16%). This is in contrast to the 5% saving in fast memory reported by Microsoft Pond for the same workloads (BFS and SSSP) and the same performance loss target.

cs.PF↗

arXiv2024

Summit Vitals: Multi-Camera and Multi-Signal Biosensing at High Altitudes

Video photoplethysmography (vPPG) is an emerging method for non-invasive and convenient measurement of physiological signals, utilizing two primary approaches: remote video PPG (rPPG) and contact video PPG (cPPG). Monitoring vitals in high-altitude environments, where heart rates tend to increase and blood oxygen levels often decrease, presents significant challenges. To address these issues, we introduce the SUMS dataset comprising 80 synchronized non-contact facial and contact finger videos from 10 subjects during exercise and oxygen recovery scenarios, capturing PPG, respiration rate (RR), and SpO2. This dataset is designed to validate video vitals estimation algorithms and compare facial rPPG with finger cPPG. Additionally, fusing videos from different positions (i.e., face and finger) reduces the mean absolute error (MAE) of SpO2 predictions by 7.6\% and 10.6\% compared to only face and only finger, respectively. In cross-subject evaluation, we achieve an MAE of less than 0.5 BPM for HR estimation and 2.5\% for SpO2 estimation, demonstrating the precision of our multi-camera fusion techniques. Our findings suggest that simultaneous training on multiple indicators, such as PPG and blood oxygen, can reduce MAE in SpO2 estimation by 17.8\%.

cs.CV↗

arXiv2024

Construction Methods Based on Minimum Weight Distribution for Polar Codes with Successive Cancellation List Decoding

Minimum weight distribution (MWD) is an important metric to calculate the first term of union bound called minimum weight union bound (MWUB). In this paper, we first prove the maximum likelihood (ML) performance approaches MWUB as signal-to-noise ratio (SNR) goes to infinity and provide the deviation when MWD and SNR are given. Then, we propose a nested reliability sequence, namely MWD sequence, to construct polar codes independently of channel information. In the sequence, synthetic channels are sorted by partial MWD which is used to evaluate the influence of information bit on MWD and we prove the MWD sequence is the optimum sequence evaluated by MWUB for polar codes obeying partial order. Finally, we introduce an entropy constraint to establish a relationship between list size and MWUB and propose a heuristic construction method named entropy constraint bit-swapping (ECBS) algorithm, where we initialize information set by the MWD sequence and gradually swap information bit and frozen bit to satisfy the entropy constraint. The simulation results show the MWD sequence is more suitable for constructing polar codes with short code length than the polar sequence in 5G and the ECBS algorithm can improve MWD to show better performance as list size increases.

cs.IT↗

arXiv2024

Resultant: Incremental Effectiveness on Likelihood for Unsupervised Out-of-Distribution Detection

Unsupervised out-of-distribution (U-OOD) detection is to identify OOD data samples with a detector trained solely on unlabeled in-distribution (ID) data. The likelihood function estimated by a deep generative model (DGM) could be a natural detector, but its performance is limited in some popular "hard" benchmarks, such as FashionMNIST (ID) vs. MNIST (OOD). Recent studies have developed various detectors based on DGMs to move beyond likelihood. However, despite their success on "hard" benchmarks, most of them struggle to consistently surpass or match the performance of likelihood on some "non-hard" cases, such as SVHN (ID) vs. CIFAR10 (OOD) where likelihood could be a nearly perfect detector. Therefore, we appeal for more attention to incremental effectiveness on likelihood, i.e., whether a method could always surpass or at least match the performance of likelihood in U-OOD detection. We first investigate the likelihood of variational DGMs and find its detection performance could be improved in two directions: i) alleviating latent distribution mismatch, and ii) calibrating the dataset entropy-mutual integration. Then, we apply two techniques for each direction, specifically post-hoc prior and dataset entropy-mutual calibration. The final method, named Resultant, combines these two directions for better incremental effectiveness compared to either technique alone. Experimental results demonstrate that the Resultant could be a new state-of-the-art U-OOD detector while maintaining incremental effectiveness on likelihood in a wide range of tasks.

stat.ML↗

arXiv2024

Very long-periodic pulsations detected simultaneously in a white-light flare and sunspot penumbra

We investigate the origin of very long-periodic pulsations (VLPs) in the white-light emission of an X6.4 flare on 2024 February 22 (SOL2024-02-22T22:08), which occurred at the edge of a sunspot group. The flare white-light fluxes reveal four successive and repetitive pulsations, which are simultaneously measured by the Helioseismic and Magnetic Imager and the White-light Solar Telescope. A quasi-period of 8.6$^{+1.5}_{-1.9}$ minutes, determined by the Morlet wavelet transform, is detected in the visible continuum channel. The modulation depth, which is defined as the ratio between the oscillatory amplitude and its long-term trend, is smaller than 0.1%, implying that the QPP feature is a weak wave process. Imaging observations show that the X6.4 flare occurs near a sunspot group. Moreover, the white-light brightening is located in sunspot penumbra, and a similar quasi-period of about 8.5$^{+1.6}_{-1.8}$ minutes is identified in one penumbral location of the nearest sunspot. The map of Fourier power distribution suggests that a similar periodicity is universally existing in most parts of the penumbra that is close to the penumbral-photospheric boundary. Our observations support the scenario of that the white-light QPP is probably modulated by the slow-mode magnetoacoustic gravity wave leaking from the sunspot penumbra.

astro-ph.SR↗

arXiv2024

UMAD: University of Macau Anomaly Detection Benchmark Dataset

Anomaly detection is critical in surveillance systems and patrol robots by identifying anomalous regions in images for early warning. Depending on whether reference data are utilized, anomaly detection can be categorized into anomaly detection with reference and anomaly detection without reference. Currently, anomaly detection without reference, which is closely related to out-of-distribution (OoD) object detection, struggles with learning anomalous patterns due to the difficulty of collecting sufficiently large and diverse anomaly datasets with the inherent rarity and novelty of anomalies. Alternatively, anomaly detection with reference employs the scheme of change detection to identify anomalies by comparing semantic changes between a reference image and a query one. However, there are very few ADr works due to the scarcity of public datasets in this domain. In this paper, we aim to address this gap by introducing the UMAD Benchmark Dataset. To our best knowledge, this is the first benchmark dataset designed specifically for anomaly detection with reference in robotic patrolling scenarios, e.g., where an autonomous robot is employed to detect anomalous objects by comparing a reference and a query video sequences. The reference sequences can be taken by the robot along a specified route when there are no anomalous objects in the scene. The query sequences are captured online by the robot when it is patrolling in the same scene following the same route. Our benchmark dataset is elaborated such that each query image can find a corresponding reference based on accurate robot localization along the same route in the prebuilt 3D map, with which the reference and query images can be geometrically aligned using adaptive warping. Besides the proposed benchmark dataset, we evaluate the baseline models of ADr on this dataset.

cs.RO↗

arXiv2024

Enhancing One-shot Pruned Pre-trained Language Models through Sparse-Dense-Sparse Mechanism

Pre-trained language models (PLMs) are engineered to be robust in contextual understanding and exhibit outstanding performance in various natural language processing tasks. However, their considerable size incurs significant computational and storage costs. Modern pruning strategies employ one-shot techniques to compress PLMs without the need for retraining on task-specific or otherwise general data; however, these approaches often lead to an indispensable reduction in performance. In this paper, we propose SDS, a Sparse-Dense-Sparse pruning framework to enhance the performance of the pruned PLMs from a weight distribution optimization perspective. We outline the pruning process in three steps. Initially, we prune less critical connections in the model using conventional one-shot pruning methods. Next, we reconstruct a dense model featuring a pruning-friendly weight distribution by reactivating pruned connections with sparse regularization. Finally, we perform a second pruning round, yielding a superior pruned model compared to the initial pruning. Experimental results demonstrate that SDS outperforms the state-of-the-art pruning techniques SparseGPT and Wanda under an identical sparsity configuration. For instance, SDS reduces perplexity by 9.13 on Raw-Wikitext2 and improves accuracy by an average of 2.05% across multiple zero-shot benchmarks for OPT-125M with 2:4 sparsity.

cs.CL↗

arXiv2024

HGRN2: Gated Linear RNNs with State Expansion

Hierarchically gated linear RNN (HGRN, \citealt{HGRN}) has demonstrated competitive training speed and performance in language modeling while offering efficient inference. However, the recurrent state size of HGRN remains relatively small, limiting its expressiveness. To address this issue, we introduce a simple outer product-based state expansion mechanism, which significantly enlarges the recurrent state size without introducing any additional parameters. This enhancement also provides a linear attention interpretation for HGRN2, enabling hardware-efficient training. Our extensive experiments verify the advantage of HGRN2 over HGRN consistently across different settings and competitive with other recurrent models.

cs.CL↗

arXiv2024

Learning Fair Invariant Representations under Covariate and Correlation Shifts Simultaneously

Achieving the generalization of an invariant classifier from training domains to shifted test domains while simultaneously considering model fairness is a substantial and complex challenge in machine learning. Existing methods address the problem of fairness-aware domain generalization, focusing on either covariate shift or correlation shift, but rarely consider both at the same time. In this paper, we introduce a novel approach that focuses on learning a fairness-aware domain-invariant predictor within a framework addressing both covariate and correlation shifts simultaneously, ensuring its generalization to unknown test domains inaccessible during training. In our approach, data are first disentangled into content and style factors in latent spaces. Furthermore, fairness-aware domain-invariant content representations can be learned by mitigating sensitive information and retaining as much other information as possible. Extensive empirical studies on benchmark datasets demonstrate that our approach surpasses state-of-the-art methods with respect to model accuracy as well as both group and individual fairness.

cs.LG↗