Interpretable High-order Knowledge Graph Neural Network for Predicting Synthetic Lethality in Human Cancers

Synthetic lethality (SL) is a promising gene interaction for cancer therapy. Recent SL prediction methods integrate knowledge graphs (KGs) into graph neural networks (GNNs) and employ attention mechanisms to extract local subgraphs as explanations for target gene pairs. However, attention mechanisms often lack fidelity, typically generate a single explanation per gene pair, and fail to ensure trustworthy high-order structures in their explanations. To overcome these limitations, we propose Diverse Graph Information Bottleneck for Synthetic Lethality (DGIB4SL), a KG-based GNN that generates multiple faithful explanations for the same gene pair and effectively encodes high-order structures. Specifically, we introduce a novel DGIB objective, integrating a Determinant Point Process (DPP) constraint into the standard IB objective, and employ 13 motif-based adjacency matrices to capture high-order structures in gene representations. Experimental results show that DGIB4SL outperforms state-of-the-art baselines and provides multiple explanations for SL prediction, revealing diverse biological mechanisms underlying SL inference.

Causal Effect Estimation under Networked Interference without Networked Unconfoundedness Assumption

Estimating causal effects under networked interference is a crucial yet challenging problem. Existing methods based on observational data mainly rely on the networked unconfoundedness assumption, which guarantees the identification of networked effects. However, the networked unconfoundedness assumption is usually violated due to the latent confounders in observational data, hindering the identification of networked effects. Interestingly, in such networked settings, interactions between units provide valuable information for recovering latent confounders. In this paper, we identify three types of latent confounders in networked inference that hinder identification: those affecting only the individual, those affecting only neighbors, and those influencing both. Specifically, we devise a networked effect estimator based on identifiable representation learning techniques. Theoretically, we establish the identifiability of all latent confounders, and leveraging the identified latent confounders, we provide the networked effect identification result. Extensive experiments validate our theoretical results and demonstrate the effectiveness of the proposed method.

Long-term Causal Inference via Modeling Sequential Latent Confounding

Long-term causal inference is an important but challenging problem across various scientific domains. To solve the latent confounding problem in long-term observational studies, existing methods leverage short-term experimental data. Ghassami et al. propose an approach based on the Conditional Additive Equi-Confounding Bias (CAECB) assumption, which asserts that the confounding bias in the short-term outcome is equal to that in the long-term outcome, so that the long-term confounding bias and the causal effects can be identified. While effective in certain cases, this assumption is limited to scenarios with a one-dimensional short-term outcome. In this paper, we introduce a novel assumption that extends the CAECB assumption to accommodate temporal short-term outcomes. Our proposed assumption states a functional relationship between sequential confounding biases across temporal short-term outcomes, under which we theoretically establish the identification of long-term causal effects. Based on the identification result, we develop an estimator and conduct a theoretical analysis of its asymptotic properties. Extensive experiments validate our theoretical results and demonstrate the effectiveness of the proposed method.

Nonparametric Heterogeneous Long-term Causal Effect Estimation via Data Combination

Long-term causal inference has drawn increasing attention in many scientific domains. Existing methods mainly focus on estimating average long-term causal effects by combining long-term observational data and short-term experimental data. However, it is still understudied how to robustly and effectively estimate heterogeneous long-term causal effects, significantly limiting practical applications. In this paper, we propose several two-stage style nonparametric estimators for heterogeneous long-term causal effect estimation, including propensity-based, regression-based, and multiple robust estimators. We conduct a comprehensive theoretical analysis of their asymptotic properties under mild assumptions, with the ultimate goal of building a better understanding of the conditions under which some estimators can be expected to perform better. Extensive experiments across several semi-synthetic and real-world datasets validate the theoretical results and demonstrate the effectiveness of the proposed estimators.

Time Series Domain Adaptation via Latent Invariant Causal Mechanism

Time series domain adaptation aims to transfer the complex temporal dependence from the labeled source domain to the unlabeled target domain. Recent advances leverage the stable causal mechanism over observed variables to model the domain-invariant temporal dependence. However, modeling precise causal structures in high-dimensional data, such as videos, remains challenging. Additionally, direct causal edges may not exist among observed variables (e.g., pixels). These limitations hinder the applicability of existing approaches to real-world scenarios. To address these challenges, we find that the high-dimension time series data are generated from the low-dimension latent variables, which motivates us to model the causal mechanisms of the temporal latent process. Based on this intuition, we propose a latent causal mechanism identification framework that guarantees the uniqueness of the reconstructed latent causal structures. Specifically, we first identify latent variables by utilizing sufficient changes in historical information. Moreover, by enforcing the sparsity of the relationships of latent variables, we can achieve identifiable latent causal structures. Built on the theoretical results, we develop the Latent Causality Alignment (LCA) model that leverages variational inference, which incorporates an intra-domain latent sparsity constraint for latent structure reconstruction and an inter-domain latent sparsity constraint for domain-invariant structure reconstruction. Experiment results on eight benchmarks show a general improvement in the domain-adaptive time series classification and forecasting tasks, highlighting the effectiveness of our method in real-world scenarios. Codes are available at https://github.com/DMIRLAB-Group/LCA.

Disentangling Long-Short Term State Under Unknown Interventions for Online Time Series Forecasting

Current methods for time series forecasting struggle in the online scenario, since it is difficult to preserve long-term dependency while adapting short-term changes when data are arriving sequentially. Although some recent methods solve this problem by controlling the updates of latent states, they cannot disentangle the long/short-term states, leading to the inability to effectively adapt to nonstationary. To tackle this challenge, we propose a general framework to disentangle long/short-term states for online time series forecasting. Our idea is inspired by the observations where short-term changes can be led by unknown interventions like abrupt policies in the stock market. Based on this insight, we formalize a data generation process with unknown interventions on short-term states. Under mild assumptions, we further leverage the independence of short-term states led by unknown interventions to establish the identification theory to achieve the disentanglement of long/short-term states. Built on this theory, we develop a long short-term disentanglement model (LSTD) to extract the long/short-term states with long/short-term encoders, respectively. Furthermore, the LSTD model incorporates a smooth constraint to preserve the long-term dependencies and an interrupted dependency constraint to enforce the forgetting of short-term dependencies, together boosting the disentanglement of long/short-term states. Experimental results on several benchmark datasets show that our \textbf{LSTD} model outperforms existing methods for online time series forecasting, validating its efficacy in real-world applications.

TP-UNet: Temporal Prompt Guided UNet for Medical Image Segmentation

The advancement of medical image segmentation techniques has been propelled by the adoption of deep learning techniques, particularly UNet-based approaches, which exploit semantic information to improve the accuracy of segmentations. However, the order of organs in scanned images has been disregarded by current medical image segmentation approaches based on UNet. Furthermore, the inherent network structure of UNet does not provide direct capabilities for integrating temporal information. To efficiently integrate temporal information, we propose TP-UNet that utilizes temporal prompts, encompassing organ-construction relationships, to guide the segmentation UNet model. Specifically, our framework is featured with cross-attention and semantic alignment based on unsupervised contrastive learning to combine temporal prompts and image features effectively. Extensive evaluations on two medical image segmentation datasets demonstrate the state-of-the-art performance of TP-UNet. Our implementation will be open-sourced after acceptance.

Recent Trends of Multimodal Affective Computing: A Survey from NLP Perspective

Multimodal affective computing (MAC) has garnered increasing attention due to its broad applications in analyzing human behaviors and intentions, especially in text-dominated multimodal affective computing field. This survey presents the recent trends of multimodal affective computing from NLP perspective through four hot tasks: multimodal sentiment analysis, multimodal emotion recognition in conversation, multimodal aspect-based sentiment analysis and multimodal multi-label emotion recognition. The goal of this survey is to explore the current landscape of multimodal affective research, identify development trends, and highlight the similarities and differences across various tasks, offering a comprehensive report on the recent progress in multimodal affective computing from an NLP perspective. This survey covers the formalization of tasks, provides an overview of relevant works, describes benchmark datasets, and details the evaluation metrics for each task. Additionally, it briefly discusses research in multimodal affective computing involving facial expressions, acoustic signals, physiological signals, and emotion causes. Additionally, we discuss the technical approaches, challenges, and future directions in multimodal affective computing. To support further research, we released a repository that compiles related works in multimodal affective computing, providing detailed resources and references for the community.

Unifying Invariant and Variant Features for Graph Out-of-Distribution via Probability of Necessity and Sufficiency

Graph Out-of-Distribution (OOD), requiring that models trained on biased data generalize to the unseen test data, has considerable real-world applications. One of the most mainstream methods is to extract the invariant subgraph by aligning the original and augmented data with the help of environment augmentation. However, these solutions might lead to the loss or redundancy of semantic subgraphs and result in suboptimal generalization. To address this challenge, we propose exploiting Probability of Necessity and Sufficiency (PNS) to extract sufficient and necessary invariant substructures. Beyond that, we further leverage the domain variant subgraphs related to the labels to boost the generalization performance in an ensemble manner. Specifically, we first consider the data generation process for graph data. Under mild conditions, we show that the sufficient and necessary invariant subgraph can be extracted by minimizing an upper bound, built on the theoretical advance of the probability of necessity and sufficiency. To further bridge the theory and algorithm, we devise the model called Sufficiency and Necessity Inspired Graph Learning (SNIGL), which ensembles an invariant subgraph classifier on top of latent sufficient and necessary invariant subgraphs, and a domain variant subgraph classifier specific to the test domain for generalization enhancement. Experimental results demonstrate that our SNIGL model outperforms the state-of-the-art techniques on six public benchmarks, highlighting its effectiveness in real-world scenarios.

Estimating Long-term Heterogeneous Dose-response Curve: Generalization Bound Leveraging Optimal Transport Weights

Long-term causal effect estimation is a significant but challenging problem in many applications. Existing methods rely on ideal assumptions to estimate long-term average effects, e.g., no unobserved confounders or a binary treatment,while in numerous real-world applications, these assumptions could be violated and average effects are unable to provide individual-level suggestions.In this paper,we address a more general problem of estimating the long-term heterogeneous dose-response curve (HDRC) while accounting for unobserved confounders. Specifically, to remove unobserved confounding in observational data, we introduce an optimal transport weighting framework to align the observational data to the experimental data with theoretical guarantees. Furthermore,to accurately predict the heterogeneous effects of continuous treatment, we establish a generalization bound on counterfactual prediction error by leveraging the reweighted distribution induced by optimal transport. Finally, we develop an HDRC estimator building upon the above theoretical foundations. Extensive experimental studies conducted on multiple synthetic and semi-synthetic datasets demonstrate the effectiveness of our proposed method.