OpenRaiser/Intern-Atlas huggingface dataset:
pTSE: A Multi-model Ensemble Method for Probabilistic Time Series Forecasting
Venue: Conference IJCAI 2023
Year: 2023

Various probabilistic time series forecasting models have sprung up and shown remarkably good performance. However, the choice of model highly relies on the characteristics of the input time series and the fixed distribution that the model is based on. Due to the fact that the probability distributions cannot be averaged over different models straightforwardly, the current time series model ensemble methods cannot be directly applied to improve the robustness and accuracy of forecasting. To address this issue, we propose pTSE, a multi-model distribution ensemble method for probabilistic forecasting based on Hidden Markov Model (HMM). pTSE only takes off-the-shelf outputs from member models without requiring further information about each model. Besides, we provide a complete theoretical analysis of pTSE to prove that the empirical distribution of time series subject to an HMM will converge to the stationary distribution almost surely. Experiments on benchmarks show the superiority of pTSE overall member models and competitive ensemble methods.
Hierarchical Transformer for Scalable Graph Learning
Venue: Conference IJCAI 2023
Year: 2023

Graph Transformer is gaining increasing attention in the field of machine learning and has demonstrated state-of-the-art performance on benchmarks for graph representation learning. However, as current implementations of Graph Transformer primarily focus on learning representations of small-scale graphs, the quadratic complexity of the global self-attention mechanism presents a challenge for full-batch training when applied to larger graphs. Additionally, conventional sampling-based methods fail to capture necessary high-level contextual information, resulting in a significant loss of performance. In this paper, we introduce the Hierarchical Scalable Graph Transformer (HSGT) as a solution to these challenges. HSGT successfully scales the Transformer architecture to node representation learning tasks on large-scale graphs, while maintaining high performance. By utilizing graph hierarchies constructed through coarsening techniques, HSGT efficiently updates and stores multi-scale information in node embeddings at different levels. Together with sampling-based training methods, HSGT effectively captures and aggregates multi-level information on the hierarchical graph using only Transformer blocks. Empirical evaluations demonstrate that HSGT achieves state-of-the-art performance on large-scale benchmarks with graphs containing millions of nodes with high efficiency.
Causal Deep Reinforcement Learning Using Observational Data
Venue: Conference IJCAI 2023
Year: 2023

Deep reinforcement learning (DRL) requires the collection of interventional data, which is sometimes expensive and even unethical in the real world, such as in the autonomous driving and the medical field. Offline reinforcement learning promises to alleviate this issue by exploiting the vast amount of observational data available in the real world. However, observational data may mislead the learning agent to undesirable outcomes if the behavior policy that generates the data depends on unobserved random variables (i.e., confounders). In this paper, we propose two deconfounding methods in DRL to address this problem. The methods first calculate the importance degree of different samples based on the causal inference technique, and then adjust the impact of different samples on the loss function by reweighting or resampling the offline dataset to ensure its unbiasedness. These deconfounding methods can be flexibly combined with existing model-free DRL algorithms such as soft actor-critic and deep Q-learning, provided that a weak condition can be satisfied by the loss functions of these algorithms. We prove the effectiveness of our deconfounding methods and validate them experimentally.
Prediction with Incomplete Data under Agnostic Mask Distribution Shift
Venue: Conference IJCAI 2023
Year: 2023

Data with missing values is ubiquitous in many applications. Recent years have witnessed increasing attention on prediction with only incomplete data consisting of observed features and a mask that indicates the missing pattern. Existing methods assume that the training and testing distributions are the same, which may be violated in real-world scenarios. In this paper, we consider prediction with incomplete data in the presence of distribution shift. We focus on the case where the underlying joint distribution of complete features and label is invariant, but the missing pattern, i.e., mask distribution may shift agnostically between training and testing. To achieve generalization, we leverage the observation that for each mask, there is an invariant optimal predictor. To avoid the exponential explosion when learning them separately, we approximate the optimal predictors jointly using a double parameterization technique. This has the undesirable side effect of allowing the learned predictors to rely on the intra-mask correlation and that between features and mask. We perform decorrelation to minimize this effect. Combining the techniques above, we propose a novel prediction method called StableMiss. Extensive experiments on both synthetic and real-world datasets show that StableMiss is robust and outperforms state-of-the-art methods under agnostic mask distribution shift.
Graph Sampling-based Meta-Learning for Molecular Property Prediction
Venue: Conference IJCAI 2023
Year: 2023

Molecular property is usually observed with a limited number of samples, and researchers have considered property prediction as a few-shot problem. One important fact that has been ignored by prior works is that each molecule can be recorded with several different properties simultaneously. To effectively utilize many-to-many correlations of molecules and properties, we propose a Graph Sampling-based Meta-learning (GS-Meta) framework for few-shot molecular property prediction. First, we construct a Molecule-Property relation Graph (MPG): molecule and properties are nodes, while property labels decide edges. Then, to utilize the topological information of MPG, we reformulate an episode in meta-learning as a subgraph of the MPG, containing a target property node, molecule nodes, and auxiliary property nodes. Third, as episodes in the form of subgraphs are no longer independent of each other, we propose to schedule the subgraph sampling process with a contrastive loss function, which considers the consistency and discrimination of subgraphs. Extensive experiments on 5 commonly-used benchmarks show GS-Meta consistently outperforms state-of-the-art methods by 5.71%-6.93% in ROC-AUC and verify the effectiveness of each proposed module. Our code is available at https://github.com/HICAI-ZJU/GS-Meta.
A Noisy-Label-Learning Formulation for Immune Repertoire Classification and Disease-Associated Immune Receptor Sequence Identification
Venue: Conference IJCAI 2023
Year: 2023

Immune repertoire classification, a typical multiple instance learning (MIL) problem, is a frontier research topic in computational biology that makes transformative contributions to new vaccines and immune therapies. However, the traditional instance-space MIL, directly assigning bag-level labels to instances, suffers from the massive amount of noisy labels and extremely low witness rate. In this work, we propose a noisy-label-learning formulation to solve the immune repertoire classification task. To remedy the inaccurate supervision of repertoire-level labels for a sequence-level classifier, we design a robust training strategy: The initial labels are smoothed to be asymmetric and are progressively corrected using the model's predictions throughout the training process. Furthermore, two models with the same architecture but different parameter initialization are co-trained simultaneously to remedy the known "confirmation bias" problem in the self-training-like schema. As a result, we obtain accurate sequence-level classification and, subsequently, repertoire-level classification. Experiments on the Cytomegalovirus (CMV) and Cancer datasets demonstrate our method's effectiveness and superior performance on sequence-level and repertoire-level tasks.
Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images
Venue: Conference IJCAI 2023
Year: 2023

Various strategies for label-scarce object detection have been explored by the computer vision research community. These strategies mainly rely on assumptions that are specific to natural images and not directly applicable to the biological and biomedical vision domains. For example, most semi-supervised learning strategies rely on a small set of labeled data as a confident source of ground truth. In many biological vision applications, however, the ground truth is unknown and indirect information might be available in the form of noisy estimations or orthogonal evidence. In this work, we frame a crucial problem in spatial transcriptomics - decoding barcodes from In-Situ-Sequencing (ISS) images - as a semi-supervised object detection (SSOD) problem. Our proposed framework incorporates additional available sources of information into a semi-supervised learning framework in the form of privileged information. The privileged information is incorporated into the teacher's pseudo-labeling in a teacher-student self-training iteration. Although the available privileged information could be data domain specific, we have introduced a general strategy of pseudo-labeling enhanced by privileged information (PLePI) and exemplified the concept using ISS images, as well on the COCO benchmark using extra evidence provided by CLIP.
Sequential Attention Source Identification Based on Feature Representation
Venue: Conference IJCAI 2023
Year: 2023

Snapshot observation based source localization has been widely studied due to its accessibility and low cost. However, the interaction of users in existing methods does not be addressed in time-varying infection scenarios. So these methods have a decreased accuracy in heterogeneous interaction scenarios. To solve this critical issue, this paper proposes a sequence-to-sequence based localization framework called Temporal-sequence based Graph Attention Source Identification (TGASI) based on an inductive learning idea. More specifically, the encoder focuses on generating multiple features by estimating the influence probability between two users, and the decoder distinguishes the importance of prediction sources in different timestamps by a designed temporal attention mechanism. It's worth mentioning that the inductive learning idea ensures that TGASI can detect the sources in new scenarios without knowing other prior knowledge, which proves the scalability of TGASI. Comprehensive experiments with the SOTA methods demonstrate the higher detection performance and scalability in different scenarios of TGASI.
Differentially Private Partial Set Cover with Applications to Facility Location
Venue: Conference IJCAI 2023
Year: 2023

It was observed in \citet{gupta2009differentially} that the Set Cover problem has strong impossibility results under differential privacy. In our work, we observe that these hardness results dissolve when we turn to the Partial Set Cover problem, where we only need to cover a $ρ$-fraction of the elements in the universe, for some $ρ\in(0,1)$. We show that this relaxation enables us to avoid the impossibility results: under loose conditions on the input set system, we give differentially private algorithms which output an explicit set cover with non-trivial approximation guarantees. In particular, this is the first differentially private algorithm which outputs an explicit set cover. Using our algorithm for Partial Set Cover as a subroutine, we give a differentially private (bicriteria) approximation algorithm for a facility location problem which generalizes $k$-center/$k$-supplier with outliers. Like with the Set Cover problem, no algorithm has been able to give non-trivial guarantees for $k$-center/$k$-supplier-type facility location problems due to the high sensitivity and impossibility results. Our algorithm shows that relaxing the covering requirement to serving only a $ρ$-fraction of the population, for $ρ\in(0,1)$, enables us to circumvent the inherent hardness. Overall, our work is an important step in tackling and understanding impossibility results in private combinatorial optimization.
Choosing Well Your Opponents: How to Guide the Synthesis of Programmatic Strategies
Venue: Conference IJCAI 2023
Year: 2023

This paper introduces Local Learner (2L), an algorithm for providing a set of reference strategies to guide the search for programmatic strategies in two-player zero-sum games. Previous learning algorithms, such as Iterated Best Response (IBR), Fictitious Play (FP), and Double-Oracle (DO), can be computationally expensive or miss important information for guiding search algorithms. 2L actively selects a set of reference strategies to improve the search signal. We empirically demonstrate the advantages of our approach while guiding a local search algorithm for synthesizing strategies in three games, including MicroRTS, a challenging real-time strategy game. Results show that 2L learns reference strategies that provide a stronger search signal than IBR, FP, and DO. We also simulate a tournament of MicroRTS, where a synthesizer using 2L outperformed the winners of the two latest MicroRTS competitions, which were programmatic strategies written by human programmers.
Transferable Curricula through Difficulty Conditioned Generators
Venue: Conference IJCAI 2023
Year: 2023

Advancements in reinforcement learning (RL) have demonstrated superhuman performance in complex tasks such as Starcraft, Go, Chess etc. However, knowledge transfer from Artificial "Experts" to humans remain a significant challenge. A promising avenue for such transfer would be the use of curricula. Recent methods in curricula generation focuses on training RL agents efficiently, yet such methods rely on surrogate measures to track student progress, and are not suited for training robots in the real world (or more ambitiously humans). In this paper, we introduce a method named Parameterized Environment Response Model (PERM) that shows promising results in training RL agents in parameterized environments. Inspired by Item Response Theory, PERM seeks to model difficulty of environments and ability of RL agents directly. Given that RL agents and humans are trained more efficiently under the "zone of proximal development", our method generates a curriculum by matching the difficulty of an environment to the current ability of the student. In addition, PERM can be trained offline and does not employ non-stationary measures of student ability, making it suitable for transfer between students. We demonstrate PERM's ability to represent the environment parameter space, and training with RL agents with PERM produces a strong performance in deterministic environments. Lastly, we show that our method is transferable between students, without any sacrifice in training quality.
JEPOO: Highly Accurate Joint Estimation of Pitch, Onset and Offset for Music Information Retrieval
Venue: Conference IJCAI 2023
Year: 2023

Melody extraction is a core task in music information retrieval, and the estimation of pitch, onset and offset are key sub-tasks in melody extraction. Existing methods have limited accuracy, and work for only one type of data, either single-pitch or multipitch. In this paper, we propose a highly accurate method for joint estimation of pitch, onset and offset, named JEPOO. We address the challenges of joint learning optimization and handling both single-pitch and multi-pitch data through novel model design and a new optimization technique named Pareto modulated loss with loss weight regularization. This is the first method that can accurately handle both single-pitch and multi-pitch music data, and even a mix of them. A comprehensive experimental study on a wide range of real datasets shows that JEPOO outperforms state-ofthe-art methods by up to 10.6%, 8.3% and 10.3% for the prediction of Pitch, Onset and Offset, respectively, and JEPOO is robust for various types of data and instruments. The ablation study shows the effectiveness of each component of JEPOO.
HireVAE: An Online and Adaptive Factor Model Based on Hierarchical and Regime-Switch VAE
Venue: Conference IJCAI 2023
Year: 2023

Factor model is a fundamental investment tool in quantitative investment, which can be empowered by deep learning to become more flexible and efficient in practical complicated investing situations. However, it is still an open question to build a factor model that can conduct stock prediction in an online and adaptive setting, where the model can adapt itself to match the current market regime identified based on only point-in-time market information. To tackle this problem, we propose the first deep learning based online and adaptive factor model, HireVAE, at the core of which is a hierarchical latent space that embeds the underlying relationship between the market situation and stock-wise latent factors, so that HireVAE can effectively estimate useful latent factors given only historical market information and subsequently predict accurate stock returns. Across four commonly used real stock market benchmarks, the proposed HireVAE demonstrate superior performance in terms of active returns over previous methods, verifying the potential of such online and adaptive factor model.
MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation
Venue: Conference IJCAI 2023
Year: 2023

Molecular de novo design is a critical yet challenging task in scientific fields, aiming to design novel molecular structures with desired property profiles. Significant progress has been made by resorting to generative models for graphs. However, limited attention is paid to hierarchical generative models, which can exploit the inherent hierarchical structure (with rich semantic information) of the molecular graphs and generate complex molecules of larger size that we shall demonstrate to be difficult for most existing models. The primary challenge to hierarchical generation is the non-differentiable issue caused by the generation of intermediate discrete coarsened graph structures. To sidestep this issue, we cast the tricky hierarchical generation problem over discrete spaces as the reverse process of hierarchical representation learning and propose MolHF, a new hierarchical flow-based model that generates molecular graphs in a coarse-to-fine manner. Specifically, MolHF first generates bonds through a multi-scale architecture, then generates atoms based on the coarsened graph structure at each scale. We demonstrate that MolHF achieves state-of-the-art performance in random generation and property optimization, implying its high capacity to model data distribution. Furthermore, MolHF is the first flow-based model that can be applied to model larger molecules (polymer) with more than 100 heavy atoms. The code and models are available at https://github.com/violet-sto/MolHF.
An Effective and Efficient Time-aware Entity Alignment Framework via Two-aspect Three-view Label Propagation
Venue: Conference IJCAI 2023
Year: 2023

Entity alignment (EA) aims to find the equivalent entity pairs between different knowledge graphs (KGs), which is crucial to promote knowledge fusion. With the wide use of temporal knowledge graphs (TKGs), time-aware EA (TEA) methods appear to enhance EA. Existing TEA models are based on Graph Neural Networks (GNN) and achieve state-of-the-art (SOTA) performance, but it is difficult to transfer them to large-scale TKGs due to the scalability issue of GNN. In this paper, we propose an effective and efficient non-neural EA framework between TKGs, namely LightTEA, which consists of four essential components: (1) Two-aspect Three-view Label Propagation, (2) Sparse Similarity with Temporal Constraints, (3) Sinkhorn Operator, and (4) Temporal Iterative Learning. All of these modules work together to improve the performance of EA while reducing the time consumption of the model. Extensive experiments on public datasets indicate that our proposed model significantly outperforms the SOTA methods for EA between TKGs, and the time consumed by LightTEA is only dozens of seconds at most, no more than 10% of the most efficient TEA method.
One Model for All Domains: Collaborative Domain-Prefix Tuning for Cross-Domain NER
Venue: Conference IJCAI 2023
Year: 2023

Cross-domain NER is a challenging task to address the low-resource problem in practical scenarios. Previous typical solutions mainly obtain a NER model by pre-trained language models (PLMs) with data from a rich-resource domain and adapt it to the target domain. Owing to the mismatch issue among entity types in different domains, previous approaches normally tune all parameters of PLMs, ending up with an entirely new NER model for each domain. Moreover, current models only focus on leveraging knowledge in one general source domain while failing to successfully transfer knowledge from multiple sources to the target. To address these issues, we introduce Collaborative Domain-Prefix Tuning for cross-domain NER (CP-NER) based on text-to-text generative PLMs. Specifically, we present text-to-text generation grounding domain-related instructors to transfer knowledge to new domain NER tasks without structural modifications. We utilize frozen PLMs and conduct collaborative domain-prefix tuning to stimulate the potential of PLMs to handle NER tasks across various domains. Experimental results on the Cross-NER benchmark show that the proposed approach has flexible transfer ability and performs better on both one-source and multiple-source cross-domain NER tasks. Codes are available in https://github.com/zjunlp/DeepKE/tree/main/example/ner/cross.
Less Learn Shortcut: Analyzing and Mitigating Learning of Spurious Feature-Label Correlation
Venue: Conference IJCAI 2023
Year: 2023

Recent research has revealed that deep neural networks often take dataset biases as a shortcut to make decisions rather than understand tasks, leading to failures in real-world applications. In this study, we focus on the spurious correlation between word features and labels that models learn from the biased data distribution of training data. In particular, we define the word highly co-occurring with a specific label as biased word, and the example containing biased word as biased example. Our analysis shows that biased examples are easier for models to learn, while at the time of prediction, biased words make a significantly higher contribution to the models' predictions, and models tend to assign predicted labels over-relying on the spurious correlation between words and labels. To mitigate models' over-reliance on the shortcut (i.e. spurious correlation), we propose a training strategy Less-Learn-Shortcut (LLS): our strategy quantifies the biased degree of the biased examples and down-weights them accordingly. Experimental results on Question Matching, Natural Language Inference and Sentiment Analysis tasks show that LLS is a task-agnostic strategy and can improve the model performance on adversarial data while maintaining good performance on in-domain data.