Daily Papers

Complex systems are characterized by intricate interactions between entities that evolve dynamically over time. Accurate inference of these dynamic relationships is crucial for understanding and predicting system behavior. In this paper, we propose Regulatory Temporal Interaction Network Inference (RiTINI) for inferring time-varying interaction graphs in complex systems using a novel combination of space-and-time graph attentions and graph neural ordinary differential equations (ODEs). RiTINI leverages time-lapse signals on a graph prior, as well as perturbations of signals at various nodes in order to effectively capture the dynamics of the underlying system. This approach is distinct from traditional causal inference networks, which are limited to inferring acyclic and static graphs. In contrast, RiTINI can infer cyclic, directed, and time-varying graphs, providing a more comprehensive and accurate representation of complex systems. The graph attention mechanism in RiTINI allows the model to adaptively focus on the most relevant interactions in time and space, while the graph neural ODEs enable continuous-time modeling of the system's dynamics. We evaluate RiTINI's performance on various simulated and real-world datasets, demonstrating its state-of-the-art capability in inferring interaction graphs compared to previous methods.

Temporal graphs are widely used to model dynamic systems with time-varying interactions. In real-world scenarios, the underlying mechanisms of generating future interactions in dynamic systems are typically governed by a set of recurring substructures within the graph, known as temporal motifs. Despite the success and prevalence of current temporal graph neural networks (TGNN), it remains uncertain which temporal motifs are recognized as the significant indications that trigger a certain prediction from the model, which is a critical challenge for advancing the explainability and trustworthiness of current TGNNs. To address this challenge, we propose a novel approach, called Temporal Motifs Explainer (TempME), which uncovers the most pivotal temporal motifs guiding the prediction of TGNNs. Derived from the information bottleneck principle, TempME extracts the most interaction-related motifs while minimizing the amount of contained information to preserve the sparsity and succinctness of the explanation. Events in the explanations generated by TempME are verified to be more spatiotemporally correlated than those of existing approaches, providing more understandable insights. Extensive experiments validate the superiority of TempME, with up to 8.21% increase in terms of explanation accuracy across six real-world datasets and up to 22.96% increase in boosting the prediction Average Precision of current TGNNs.

We propose a novel machine learning approach for inferring causal variables of a target variable from observations. Our focus is on directly inferring a set of causal factors without requiring full causal graph reconstruction, which is computationally challenging in large-scale systems. The identified causal set consists of all potential regulators of the target variable under experimental settings, enabling efficient regulation when intervention costs and feasibility vary across variables. To achieve this, we train a neural network using supervised learning on simulated data to infer causality. By employing a local-inference strategy, our approach scales with linear complexity in the number of variables, efficiently scaling up to thousands of variables. Empirical results demonstrate superior performance in identifying causal relationships within large-scale gene regulatory networks, outperforming existing methods that emphasize full-graph discovery. We validate our model's generalization capability across out-of-distribution graph structures and generating mechanisms, including gene regulatory networks of E. coli and the human K562 cell line. Implementation codes are available at https://github.com/snu-mllab/Targeted-Cause-Discovery.

Many real-world systems exhibit temporal, dynamic behaviors, which are captured as time series of complex agent interactions. To perform temporal reasoning, current methods primarily encode temporal dynamics through simple sequence-based models. However, in general these models fail to efficiently capture the full spectrum of rich dynamics in the input, since the dynamics is not uniformly distributed. In particular, relevant information might be harder to extract and computing power is wasted for processing all individual timesteps, even if they contain no significant changes or no new information. Here we propose TimeGraphs, a novel approach that characterizes dynamic interactions as a hierarchical temporal graph, diverging from traditional sequential representations. Our approach models the interactions using a compact graph-based representation, enabling adaptive reasoning across diverse time scales. Adopting a self-supervised method, TimeGraphs constructs a multi-level event hierarchy from a temporal input, which is then used to efficiently reason about the unevenly distributed dynamics. This construction process is scalable and incremental to accommodate streaming data. We evaluate TimeGraphs on multiple datasets with complex, dynamic agent interactions, including a football simulator, the Resistance game, and the MOMA human activity dataset. The results demonstrate both robustness and efficiency of TimeGraphs on a range of temporal reasoning tasks. Our approach obtains state-of-the-art performance and leads to a performance increase of up to 12.2% on event prediction and recognition tasks over current approaches. Our experiments further demonstrate a wide array of capabilities including zero-shot generalization, robustness in case of data sparsity, and adaptability to streaming data flow.

Dynamic graph learning methods have recently emerged as powerful tools for modelling relational data evolving through time. However, despite extensive benchmarking efforts, it remains unclear whether current Temporal Graph Neural Networks (TGNNs) effectively capture core temporal patterns such as periodicity, cause-and-effect, and long-range dependencies. In this work, we introduce the Temporal Graph Reasoning Benchmark (T-GRAB), a comprehensive set of synthetic tasks designed to systematically probe the capabilities of TGNNs to reason across time. T-GRAB provides controlled, interpretable tasks that isolate key temporal skills: counting/memorizing periodic repetitions, inferring delayed causal effects, and capturing long-range dependencies over both spatial and temporal dimensions. We evaluate 11 temporal graph learning methods on these tasks, revealing fundamental shortcomings in their ability to generalize temporal patterns. Our findings offer actionable insights into the limitations of current models, highlight challenges hidden by traditional real-world benchmarks, and motivate the development of architectures with stronger temporal reasoning abilities. The code for T-GRAB can be found at: https://github.com/alirezadizaji/T-GRAB.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Gene regulatory network inference (GRNI) is a challenging problem, particularly owing to the presence of zeros in single-cell RNA sequencing data: some are biological zeros representing no gene expression, while some others are technical zeros arising from the sequencing procedure (aka dropouts), which may bias GRNI by distorting the joint distribution of the measured gene expressions. Existing approaches typically handle dropout error via imputation, which may introduce spurious relations as the true joint distribution is generally unidentifiable. To tackle this issue, we introduce a causal graphical model to characterize the dropout mechanism, namely, Causal Dropout Model. We provide a simple yet effective theoretical result: interestingly, the conditional independence (CI) relations in the data with dropouts, after deleting the samples with zero values (regardless if technical or not) for the conditioned variables, are asymptotically identical to the CI relations in the original data without dropouts. This particular test-wise deletion procedure, in which we perform CI tests on the samples without zeros for the conditioned variables, can be seamlessly integrated with existing structure learning approaches including constraint-based and greedy score-based methods, thus giving rise to a principled framework for GRNI in the presence of dropouts. We further show that the causal dropout model can be validated from data, and many existing statistical models to handle dropouts fit into our model as specific parametric instances. Empirical evaluation on synthetic, curated, and real-world experimental transcriptomic data comprehensively demonstrate the efficacy of our method.

Despite the successful application of Temporal Graph Networks (TGNs) for tasks such as dynamic node classification and link prediction, they still perform poorly on the task of dynamic node affinity prediction -- where the goal is to predict 'how much' two nodes will interact in the future. In fact, simple heuristic approaches such as persistent forecasts and moving averages over ground-truth labels significantly and consistently outperform TGNs. Building on this observation, we find that computing heuristics over messages is an equally competitive approach, outperforming TGN and all current temporal graph (TG) models on dynamic node affinity prediction. In this paper, we prove that no formulation of TGN can represent persistent forecasting or moving averages over messages, and propose to enhance the expressivity of TGNs by adding source-target identification to each interaction event message. We show that this modification is required to represent persistent forecasting, moving averages, and the broader class of autoregressive models over messages. Our proposed method, TGNv2, significantly outperforms TGN and all current TG models on all Temporal Graph Benchmark (TGB) dynamic node affinity prediction datasets.

Temporal knowledge graphs represent temporal facts (s,p,o,tau) relating a subject s and an object o via a relation label p at time tau, where tau could be a time point or time interval. Temporal knowledge graphs may exhibit static temporal patterns at distinct points in time and dynamic temporal patterns between different timestamps. In order to learn a rich set of static and dynamic temporal patterns and apply them for inference, several embedding approaches have been suggested in the literature. However, as most of them resort to single underlying embedding spaces, their capability to model all kinds of temporal patterns was severely limited by having to adhere to the geometric property of their one embedding space. We lift this limitation by an embedding approach that maps temporal facts into a product space of several heterogeneous geometric subspaces with distinct geometric properties, i.e.\ Complex, Dual, and Split-complex spaces. In addition, we propose a temporal-geometric attention mechanism to integrate information from different geometric subspaces conveniently according to the captured relational and temporal information. Experimental results on standard temporal benchmark datasets favorably evaluate our approach against state-of-the-art models.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

Real-world networks, with their evolving relations, are best captured as temporal graphs. However, existing software libraries are largely designed for static graphs where the dynamic nature of temporal graphs is ignored. Bridging this gap, we introduce TGX, a Python package specially designed for analysis of temporal networks that encompasses an automated pipeline for data loading, data processing, and analysis of evolving graphs. TGX provides access to eleven built-in datasets and eight external Temporal Graph Benchmark (TGB) datasets as well as any novel datasets in the .csv format. Beyond data loading, TGX facilitates data processing functionalities such as discretization of temporal graphs and node subsampling to accelerate working with larger datasets. For comprehensive investigation, TGX offers network analysis by providing a diverse set of measures, including average node degree and the evolving number of nodes and edges per timestamp. Additionally, the package consolidates meaningful visualization plots indicating the evolution of temporal patterns, such as Temporal Edge Appearance (TEA) and Temporal Edge Trafficc (TET) plots. The TGX package is a robust tool for examining the features of temporal graphs and can be used in various areas like studying social networks, citation networks, and tracking user interactions. We plan to continuously support and update TGX based on community feedback. TGX is publicly available on: https://github.com/ComplexData-MILA/TGX.

Interdisciplinary scientific breakthroughs mostly emerge unexpectedly, and forecasting the formation of novel research fields remains a major challenge. We introduce FOS (Future Of Science), a comprehensive time-aware graph-based benchmark that reconstructs annual co-occurrence graphs of 65,027 research sub-fields (spanning 19 general domains) over the period 1827-2024. In these graphs, edges denote the co-occurrence of two fields in a single publication and are timestamped with the corresponding publication year. Nodes are enriched with semantic embeddings, and edges are characterized by temporal and topological descriptors. We formulate the prediction of new field-pair linkages as a temporal link-prediction task, emphasizing the "first-time" connections that signify pioneering interdisciplinary directions. Through extensive experiments, we evaluate a suite of state-of-the-art temporal graph architectures under multiple negative-sampling regimes and show that (i) embedding long-form textual descriptions of fields significantly boosts prediction accuracy, and (ii) distinct model classes excel under different evaluation settings. Case analyses show that top-ranked link predictions on FOS align with field pairings that emerge in subsequent years of academic publications. We publicly release FOS, along with its temporal data splits and evaluation code, to establish a reproducible benchmark for advancing research in predicting scientific frontiers.

Temporal networks have been widely used to model real-world complex systems such as financial systems and e-commerce systems. In a temporal network, the joint neighborhood of a set of nodes often provides crucial structural information useful for predicting whether they may interact at a certain time. However, recent representation learning methods for temporal networks often fail to extract such information or depend on online construction of structural features, which is time-consuming. To address the issue, this work proposes Neighborhood-Aware Temporal network model (NAT). For each node in the network, NAT abandons the commonly-used one-single-vector-based representation while adopting a novel dictionary-type neighborhood representation. Such a dictionary representation records a downsampled set of the neighboring nodes as keys, and allows fast construction of structural features for a joint neighborhood of multiple nodes. We also design a dedicated data structure termed N-cache to support parallel access and update of those dictionary representations on GPUs. NAT gets evaluated over seven real-world large-scale temporal networks. NAT not only outperforms all cutting-edge baselines by averaged 1.2% and 4.2% in transductive and inductive link prediction accuracy, respectively, but also keeps scalable by achieving a speed-up of 4.1-76.7x against the baselines that adopt joint structural features and achieves a speed-up of 1.6-4.0x against the baselines that cannot adopt those features. The link to the code: https: //github.com/Graph-COM/Neighborhood-Aware-Temporal-Network.

We revisit the structure learning problem for dynamic Bayesian networks and propose a method that simultaneously estimates contemporaneous (intra-slice) and time-lagged (inter-slice) relationships between variables in a time-series. Our approach is score-based, and revolves around minimizing a penalized loss subject to an acyclicity constraint. To solve this problem, we leverage a recent algebraic result characterizing the acyclicity constraint as a smooth equality constraint. The resulting algorithm, which we call DYNOTEARS, outperforms other methods on simulated data, especially in high-dimensions as the number of variables increases. We also apply this algorithm on real datasets from two different domains, finance and molecular biology, and analyze the resulting output. Compared to state-of-the-art methods for learning dynamic Bayesian networks, our method is both scalable and accurate on real data. The simple formulation and competitive performance of our method make it suitable for a variety of problems where one seeks to learn connections between variables across time.

Discovering the underlying relationships among variables from temporal observations has been a longstanding challenge in numerous scientific disciplines, including biology, finance, and climate science. The dynamics of such systems are often best described using continuous-time stochastic processes. Unfortunately, most existing structure learning approaches assume that the underlying process evolves in discrete-time and/or observations occur at regular time intervals. These mismatched assumptions can often lead to incorrect learned structures and models. In this work, we introduce a novel structure learning method, SCOTCH, which combines neural stochastic differential equations (SDE) with variational inference to infer a posterior distribution over possible structures. This continuous-time approach can naturally handle both learning from and predicting observations at arbitrary time points. Theoretically, we establish sufficient conditions for an SDE and SCOTCH to be structurally identifiable, and prove its consistency under infinite data limits. Empirically, we demonstrate that our approach leads to improved structure learning performance on both synthetic and real-world datasets compared to relevant baselines under regular and irregular sampling intervals.

Networks have become indispensable and ubiquitous structures in many fields to model the interactions among different entities, such as friendship in social networks or protein interactions in biological graphs. A major challenge is to understand the structure and dynamics of these systems. Although networks evolve through time, most existing graph representation learning methods target only static networks. Whereas approaches have been developed for the modeling of dynamic networks, there is a lack of efficient continuous time dynamic graph representation learning methods that can provide accurate network characterization and visualization in low dimensions while explicitly accounting for prominent network characteristics such as homophily and transitivity. In this paper, we propose the Piecewise-Velocity Model (PiVeM) for the representation of continuous-time dynamic networks. It learns dynamic embeddings in which the temporal evolution of nodes is approximated by piecewise linear interpolations based on a latent distance model with piecewise constant node-specific velocities. The model allows for analytically tractable expressions of the associated Poisson process likelihood with scalable inference invariant to the number of events. We further impose a scalable Kronecker structured Gaussian Process prior to the dynamics accounting for community structure, temporal smoothness, and disentangled (uncorrelated) latent embedding dimensions optimally learned to characterize the network dynamics. We show that PiVeM can successfully represent network structure and dynamics in ultra-low two-dimensional spaces. It outperforms relevant state-of-art methods in downstream tasks such as link prediction. In summary, PiVeM enables easily interpretable dynamic network visualizations and characterizations that can further improve our understanding of the intrinsic dynamics of time-evolving networks.

Node centralities play a pivotal role in network science, social network analysis, and recommender systems. In temporal data, static path-based centralities like closeness or betweenness can give misleading results about the true importance of nodes in a temporal graph. To address this issue, temporal generalizations of betweenness and closeness have been defined that are based on the shortest time-respecting paths between pairs of nodes. However, a major issue of those generalizations is that the calculation of such paths is computationally expensive. Addressing this issue, we study the application of De Bruijn Graph Neural Networks (DBGNN), a causality-aware graph neural network architecture, to predict temporal path-based centralities in time series data. We experimentally evaluate our approach in 13 temporal graphs from biological and social systems and show that it considerably improves the prediction of both betweenness and closeness centrality compared to a static Graph Convolutional Neural Network.

Temporal Point Processes (TPP) are probabilistic generative frameworks. They model discrete event sequences localized in continuous time. Generally, real-life events reveal descriptive information, known as marks. Marked TPPs model time and marks of the event together for practical relevance. Conditioned on past events, marked TPPs aim to learn the joint distribution of the time and the mark of the next event. For simplicity, conditionally independent TPP models assume time and marks are independent given event history. They factorize the conditional joint distribution of time and mark into the product of individual conditional distributions. This structural limitation in the design of TPP models hurt the predictive performance on entangled time and mark interactions. In this work, we model the conditional inter-dependence of time and mark to overcome the limitations of conditionally independent models. We construct a multivariate TPP conditioning the time distribution on the current event mark in addition to past events. Besides the conventional intensity-based models for conditional joint distribution, we also draw on flexible intensity-free TPP models from the literature. The proposed TPP models outperform conditionally independent and dependent models in standard prediction tasks. Our experimentation on various datasets with multiple evaluation metrics highlights the merit of the proposed approach.

Causal precedence between biochemical interactions is crucial in the biomedical domain, because it transforms collections of individual interactions, e.g., bindings and phosphorylations, into the causal mechanisms needed to inform meaningful search and inference. Here, we analyze causal precedence in the biomedical domain as distinct from open-domain, temporal precedence. First, we describe a novel, hand-annotated text corpus of causal precedence in the biomedical domain. Second, we use this corpus to investigate a battery of models of precedence, covering rule-based, feature-based, and latent representation models. The highest-performing individual model achieved a micro F1 of 43 points, approaching the best performers on the simpler temporal-only precedence tasks. Feature-based and latent representation models each outperform the rule-based models, but their performance is complementary to one another. We apply a sieve-based architecture to capitalize on this lack of overlap, achieving a micro F1 score of 46 points.

The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and trajectory inference. However, these methods consider cells as independent data points of population distributions. With spatial transcriptomics, we can represent cellular organization, along with dynamic cell-cell interactions that lead to changes in cell state. Still, key computational advances are necessary to enable the data-driven learning of such complex interactive cellular dynamics. While agent-based modeling (ABM) provides a powerful framework, traditional approaches rely on handcrafted rules derived from domain knowledge rather than data-driven approaches. To address this, we introduce Spatio Temporal Agent-Based Graph Evolution Dynamics(STAGED) integrating ABM with deep learning to model intercellular communication, and its effect on the intracellular gene regulatory network. Using graph ODE networks (GDEs) with shared weights per cell type, our approach represents genes as vertices and interactions as directed edges, dynamically learning their strengths through a designed attention mechanism. Trained to match continuous trajectories of simulated as well as inferred trajectories from spatial transcriptomics data, the model captures both intercellular and intracellular interactions, enabling a more adaptive and accurate representation of cellular dynamics.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

We introduce Bayesian Poisson Tucker decomposition (BPTD) for modeling country--country interaction event data. These data consist of interaction events of the form "country i took action a toward country j at time t." BPTD discovers overlapping country--community memberships, including the number of latent communities. In addition, it discovers directed community--community interaction networks that are specific to "topics" of action types and temporal "regimes." We show that BPTD yields an efficient MCMC inference algorithm and achieves better predictive performance than related models. We also demonstrate that it discovers interpretable latent structure that agrees with our knowledge of international relations.

Temporal hypergraphs provide a powerful paradigm for modeling time-dependent, higher-order interactions in complex systems. Representation learning for hypergraphs is essential for extracting patterns of the higher-order interactions that are critically important in real-world problems in social network analysis, neuroscience, finance, etc. However, existing methods are typically designed only for specific tasks or static hypergraphs. We present CAT-Walk, an inductive method that learns the underlying dynamic laws that govern the temporal and structural processes underlying a temporal hypergraph. CAT-Walk introduces a temporal, higher-order walk on hypergraphs, SetWalk, that extracts higher-order causal patterns. CAT-Walk uses a novel adaptive and permutation invariant pooling strategy, SetMixer, along with a set-based anonymization process that hides the identity of hyperedges. Finally, we present a simple yet effective neural network model to encode hyperedges. Our evaluation on 10 hypergraph benchmark datasets shows that CAT-Walk attains outstanding performance on temporal hyperedge prediction benchmarks in both inductive and transductive settings. It also shows competitive performance with state-of-the-art methods for node classification. (https://github.com/ubc-systopia/CATWalk)

We present a constraint-based algorithm for learning causal structures from observational time-series data, in the presence of latent confounders. We assume a discrete-time, stationary structural vector autoregressive process, with both temporal and contemporaneous causal relations. One may ask if temporal and contemporaneous relations should be treated differently. The presented algorithm gradually refines a causal graph by learning long-term temporal relations before short-term ones, where contemporaneous relations are learned last. This ordering of causal relations to be learnt leads to a reduction in the required number of statistical tests. We validate this reduction empirically and demonstrate that it leads to higher accuracy for synthetic data and more plausible causal graphs for real-world data compared to state-of-the-art algorithms.

We incorporate discrete and continuous time Markov processes as building blocks into probabilistic graphical models with latent and observed variables. We introduce the automatic Backward Filtering Forward Guiding (BFFG) paradigm (Mider et al., 2021) for programmable inference on latent states and model parameters. Our starting point is a generative model, a forward description of the probabilistic process dynamics. We backpropagate the information provided by observations through the model to transform the generative (forward) model into a pre-conditional model guided by the data. It approximates the actual conditional model with known likelihood-ratio between the two. The backward filter and the forward change of measure are suitable to be incorporated into a probabilistic programming context because they can be formulated as a set of transformation rules. The guided generative model can be incorporated in different approaches to efficiently sample latent states and parameters conditional on observations. We show applicability in a variety of settings, including Markov chains with discrete state space, interacting particle systems, state space models, branching diffusions and Gamma processes.

Can evolving networks be inferred and modeled without directly observing their nodes and edges? In many applications, the edges of a dynamic network might not be observed, but one can observe the dynamics of stochastic cascading processes (e.g., information diffusion, virus propagation) occurring over the unobserved network. While there have been efforts to infer networks based on such data, providing a generative probabilistic model that is able to identify the underlying time-varying network remains an open question. Here we consider the problem of inferring generative dynamic network models based on network cascade diffusion data. We propose a novel framework for providing a non-parametric dynamic network model--based on a mixture of coupled hierarchical Dirichlet processes-- based on data capturing cascade node infection times. Our approach allows us to infer the evolving community structure in networks and to obtain an explicit predictive distribution over the edges of the underlying network--including those that were not involved in transmission of any cascade, or are likely to appear in the future. We show the effectiveness of our approach using extensive experiments on synthetic as well as real-world networks.

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.

Future link prediction is a fundamental challenge in various real-world dynamic systems. To address this, numerous temporal graph neural networks (temporal GNNs) and benchmark datasets have been developed. However, these datasets often feature excessive repeated edges and lack complex sequential dynamics, a key characteristic inherent in many real-world applications such as recommender systems and ``Who-To-Follow'' on social networks. This oversight has led existing methods to inadvertently downplay the importance of learning sequential dynamics, focusing primarily on predicting repeated edges. In this study, we demonstrate that existing methods, such as GraphMixer and DyGFormer, are inherently incapable of learning simple sequential dynamics, such as ``a user who has followed OpenAI and Anthropic is more likely to follow AI at Meta next.'' Motivated by this issue, we introduce the Temporal Graph Benchmark with Sequential Dynamics (TGB-Seq), a new benchmark carefully curated to minimize repeated edges, challenging models to learn sequential dynamics and generalize to unseen edges. TGB-Seq comprises large real-world datasets spanning diverse domains, including e-commerce interactions, movie ratings, business reviews, social networks, citation networks and web link networks. Benchmarking experiments reveal that current methods usually suffer significant performance degradation and incur substantial training costs on TGB-Seq, posing new challenges and opportunities for future research. TGB-Seq datasets, leaderboards, and example codes are available at https://tgb-seq.github.io/.

Modeling dynamic graphs, such as those found in social networks, recommendation systems, and e-commerce platforms, is crucial for capturing evolving relationships and delivering relevant insights over time. Traditional approaches primarily rely on graph neural networks with temporal components or sequence generation models, which often focus narrowly on the historical context of target nodes. This limitation restricts the ability to adapt to new and emerging patterns in dynamic graphs. To address this challenge, we propose a novel framework, Retrieval-Augmented Generation for Dynamic Graph modeling (RAG4DyG), which enhances dynamic graph predictions by incorporating contextually and temporally relevant examples from broader graph structures. Our approach includes a time- and context-aware contrastive learning module to identify high-quality demonstrations and a graph fusion strategy to effectively integrate these examples with historical contexts. The proposed framework is designed to be effective in both transductive and inductive scenarios, ensuring adaptability to previously unseen nodes and evolving graph structures. Extensive experiments across multiple real-world datasets demonstrate the effectiveness of RAG4DyG in improving predictive accuracy and adaptability for dynamic graph modeling. The code and datasets are publicly available at https://github.com/YuxiaWu/RAG4DyG.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6% increase in drug response prediction correlation, 9.6% improvement in single-cell drug classification AUC, and 1.1% average gain in gene perturbation prediction accuracy.

Time-series forecasting is one of the most active research topics in artificial intelligence. Applications in real-world time series should consider two factors for achieving reliable predictions: modeling dynamic dependencies among multiple variables and adjusting the model's intrinsic hyperparameters. A still open gap in that literature is that statistical and ensemble learning approaches systematically present lower predictive performance than deep learning methods. They generally disregard the data sequence aspect entangled with multivariate data represented in more than one time series. Conversely, this work presents a novel neural network architecture for time-series forecasting that combines the power of graph evolution with deep recurrent learning on distinct data distributions; we named our method Recurrent Graph Evolution Neural Network (ReGENN). The idea is to infer multiple multivariate relationships between co-occurring time-series by assuming that the temporal data depends not only on inner variables and intra-temporal relationships (i.e., observations from itself) but also on outer variables and inter-temporal relationships (i.e., observations from other-selves). An extensive set of experiments was conducted comparing ReGENN with dozens of ensemble methods and classical statistical ones, showing sound improvement of up to 64.87% over the competing algorithms. Furthermore, we present an analysis of the intermediate weights arising from ReGENN, showing that by looking at inter and intra-temporal relationships simultaneously, time-series forecasting is majorly improved if paying attention to how multiple multivariate data synchronously evolve.

Markov processes are widely used mathematical models for describing dynamic systems in various fields. However, accurately simulating large-scale systems at long time scales is computationally expensive due to the short time steps required for accurate integration. In this paper, we introduce an inference process that maps complex systems into a simplified representational space and models large jumps in time. To achieve this, we propose Time-lagged Information Bottleneck (T-IB), a principled objective rooted in information theory, which aims to capture relevant temporal features while discarding high-frequency information to simplify the simulation task and minimize the inference error. Our experiments demonstrate that T-IB learns information-optimal representations for accurately modeling the statistical properties and dynamics of the original process at a selected time lag, outperforming existing time-lagged dimensionality reduction methods.

Deep graph clustering has recently received significant attention due to its ability to enhance the representation learning capabilities of models in unsupervised scenarios. Nevertheless, deep clustering for temporal graphs, which could capture crucial dynamic interaction information, has not been fully explored. It means that in many clustering-oriented real-world scenarios, temporal graphs can only be processed as static graphs. This not only causes the loss of dynamic information but also triggers huge computational consumption. To solve the problem, we propose a general framework for deep Temporal Graph Clustering called TGC, which introduces deep clustering techniques to suit the interaction sequence-based batch-processing pattern of temporal graphs. In addition, we discuss differences between temporal graph clustering and static graph clustering from several levels. To verify the superiority of the proposed framework TGC, we conduct extensive experiments. The experimental results show that temporal graph clustering enables more flexibility in finding a balance between time and space requirements, and our framework can effectively improve the performance of existing temporal graph learning methods. The code is released: https://github.com/MGitHubL/Deep-Temporal-Graph-Clustering.

Temporal point processes are the dominant paradigm for modeling sequences of events happening at irregular intervals. The standard way of learning in such models is by estimating the conditional intensity function. However, parameterizing the intensity function usually incurs several trade-offs. We show how to overcome the limitations of intensity-based approaches by directly modeling the conditional distribution of inter-event times. We draw on the literature on normalizing flows to design models that are flexible and efficient. We additionally propose a simple mixture model that matches the flexibility of flow-based models, but also permits sampling and computing moments in closed form. The proposed models achieve state-of-the-art performance in standard prediction tasks and are suitable for novel applications, such as learning sequence embeddings and imputing missing data.

Finding multiple temporal relationships among locations can benefit a bunch of urban applications, such as dynamic offline advertising and smart public transport planning. While some efforts have been made on finding static relationships among locations, little attention is focused on studying time-aware location relationships. Indeed, abundant location-based human activities are time-varying and the availability of these data enables a new paradigm for understanding the dynamic relationships in a period among connective locations. To this end, we propose to study a new problem, namely multi-Temporal relationship inference among locations (Trial for short), where the major challenge is how to integrate dynamic and geographical influence under the relationship sparsity constraint. Specifically, we propose a solution to Trial with a graph learning scheme, which includes a spatially evolving graph neural network (SEENet) with two collaborative components: spatially evolving graph convolution module (SEConv) and spatially evolving self-supervised learning strategy (SE-SSL). SEConv performs the intra-time aggregation and inter-time propagation to capture the multifaceted spatially evolving contexts from the view of location message passing. In addition, SE-SSL designs time-aware self-supervised learning tasks in a global-local manner with additional evolving constraint to enhance the location representation learning and further handle the relationship sparsity. Finally, experiments on four real-world datasets demonstrate the superiority of our method over several state-of-the-art approaches.

Autoregressive models, despite their commendable performance in a myriad of generative tasks, face challenges stemming from their inherently sequential structure. Inference on these models, by design, harnesses a temporal dependency, where the current token's probability distribution is conditioned on preceding tokens. This inherent characteristic severely impedes computational efficiency during inference as a typical inference request can require more than thousands of tokens, where generating each token requires a load of entire model weights, making the inference more memory-bound. The large overhead becomes profound in real deployment where requests arrive randomly, necessitating various generation lengths. Existing solutions, such as dynamic batching and concurrent instances, introduce significant response delays and bandwidth contention, falling short of achieving optimal latency and throughput. To address these shortcomings, we propose Flover -- a temporal fusion framework for efficiently inferring multiple requests in parallel. We deconstruct the general generation pipeline into pre-processing and token generation, and equip the framework with a dedicated work scheduler for fusing the generation process temporally across all requests. By orchestrating the token-level parallelism, Flover exhibits optimal hardware efficiency and significantly spares the system resources. By further employing a fast buffer reordering algorithm that allows memory eviction of finished tasks, it brings over 11x inference speedup on GPT and 16x on LLAMA compared to the cutting-edge solutions provided by NVIDIA FasterTransformer. Crucially, by leveraging the advanced tensor parallel technique, Flover proves efficacious across diverse computational landscapes, from single-GPU setups to distributed scenarios, thereby offering robust performance optimization that adapts to variable use cases.

Stream networks, a unique class of spatiotemporal graphs, exhibit complex directional flow constraints and evolving dependencies, making uncertainty quantification a critical yet challenging task. Traditional conformal prediction methods struggle in this setting due to the need for joint predictions across multiple interdependent locations and the intricate spatio-temporal dependencies inherent in stream networks. Existing approaches either neglect dependencies, leading to overly conservative predictions, or rely solely on data-driven estimations, failing to capture the rich topological structure of the network. To address these challenges, we propose Spatio-Temporal Adaptive Conformal Inference (STACI), a novel framework that integrates network topology and temporal dynamics into the conformal prediction framework. STACI introduces a topology-aware nonconformity score that respects directional flow constraints and dynamically adjusts prediction sets to account for temporal distributional shifts. We provide theoretical guarantees on the validity of our approach and demonstrate its superior performance on both synthetic and real-world datasets. Our results show that STACI effectively balances prediction efficiency and coverage, outperforming existing conformal prediction methods for stream networks.

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

We address causal reasoning in multivariate time series data generated by stochastic processes. Existing approaches are largely restricted to static settings, ignoring the continuity and emission of variations across time. In contrast, we propose a learning paradigm that directly establishes causation between events in the course of time. We present two key lemmas to compute causal contributions and frame them as reinforcement learning problems. Our approach offers formal and computational tools for uncovering and quantifying causal relationships in diffusion processes, subsuming various important settings such as discrete-time Markov decision processes. Finally, in fairly intricate experiments and through sheer learning, our framework reveals and quantifies causal links, which otherwise seem inexplicable.

Multivariate time series data typically comprises two distinct modalities: variable semantics and sampled numerical observations. Traditional time series models treat variables as anonymous statistical signals, overlooking the rich semantic information embedded in variable names and data descriptions. However, these textual descriptors often encode critical domain knowledge that is essential for robust and interpretable modeling. Here we present TimeMKG, a multimodal causal reasoning framework that elevates time series modeling from low-level signal processing to knowledge informed inference. TimeMKG employs large language models to interpret variable semantics and constructs structured Multivariate Knowledge Graphs that capture inter-variable relationships. A dual-modality encoder separately models the semantic prompts, generated from knowledge graph triplets, and the statistical patterns from historical time series. Cross-modality attention aligns and fuses these representations at the variable level, injecting causal priors into downstream tasks such as forecasting and classification, providing explicit and interpretable priors to guide model reasoning. The experiment in diverse datasets demonstrates that incorporating variable-level knowledge significantly improves both predictive performance and generalization.

With the overwhelming amount of data available both on and offline today, recommender systems have become much needed to help users find items tailored to their interests. When social network information exists there are methods that utilize this information to make better recommendations, however the methods are often clunky with complex architectures and training procedures. Furthermore many of the existing methods utilize graph neural networks which are notoriously difficult to train. To address this, we propose Socially-aware Temporally caUsal Decoder recommender sYstems (STUDY). STUDY does joint inference over groups of users who are adjacent in the social network graph using a single forward pass of a modified transformer decoder network. We test our method in a school-based educational content setting, using classroom structure to define social networks. Our method outperforms both social and sequential methods while maintaining the design simplicity of a single homogeneous network that models all interactions in the data. We also carry out ablation studies to understand the drivers of our performance gains and find that our model depends on leveraging a social network structure that effectively models the similarities in user behavior.

We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and robust evaluation of machine learning models on temporal graphs. TGB datasets are of large scale, spanning years in duration, incorporate both node and edge-level prediction tasks and cover a diverse set of domains including social, trade, transaction, and transportation networks. For both tasks, we design evaluation protocols based on realistic use-cases. We extensively benchmark each dataset and find that the performance of common models can vary drastically across datasets. In addition, on dynamic node property prediction tasks, we show that simple methods often achieve superior performance compared to existing temporal graph models. We believe that these findings open up opportunities for future research on temporal graphs. Finally, TGB provides an automated machine learning pipeline for reproducible and accessible temporal graph research, including data loading, experiment setup and performance evaluation. TGB will be maintained and updated on a regular basis and welcomes community feedback. TGB datasets, data loaders, example codes, evaluation setup, and leaderboards are publicly available at https://tgb.complexdatalab.com/.

Modeling multivariate time series has long been a subject that has attracted researchers from a diverse range of fields including economics, finance, and traffic. A basic assumption behind multivariate time series forecasting is that its variables depend on one another but, upon looking closely, it is fair to say that existing methods fail to fully exploit latent spatial dependencies between pairs of variables. In recent years, meanwhile, graph neural networks (GNNs) have shown high capability in handling relational dependencies. GNNs require well-defined graph structures for information propagation which means they cannot be applied directly for multivariate time series where the dependencies are not known in advance. In this paper, we propose a general graph neural network framework designed specifically for multivariate time series data. Our approach automatically extracts the uni-directed relations among variables through a graph learning module, into which external knowledge like variable attributes can be easily integrated. A novel mix-hop propagation layer and a dilated inception layer are further proposed to capture the spatial and temporal dependencies within the time series. The graph learning, graph convolution, and temporal convolution modules are jointly learned in an end-to-end framework. Experimental results show that our proposed model outperforms the state-of-the-art baseline methods on 3 of 4 benchmark datasets and achieves on-par performance with other approaches on two traffic datasets which provide extra structural information.

Most graph neural network models learn embeddings of nodes in static attributed graphs for predictive analysis. Recent attempts have been made to learn temporal proximity of the nodes. We find that real dynamic attributed graphs exhibit complex co-evolution of node attributes and graph structure. Learning node embeddings for forecasting change of node attributes and birth and death of links over time remains an open problem. In this work, we present a novel framework called CoEvoGNN for modeling dynamic attributed graph sequence. It preserves the impact of earlier graphs on the current graph by embedding generation through the sequence. It has a temporal self-attention mechanism to model long-range dependencies in the evolution. Moreover, CoEvoGNN optimizes model parameters jointly on two dynamic tasks, attribute inference and link prediction over time. So the model can capture the co-evolutionary patterns of attribute change and link formation. This framework can adapt to any graph neural algorithms so we implemented and investigated three methods based on it: CoEvoGCN, CoEvoGAT, and CoEvoSAGE. Experiments demonstrate the framework (and its methods) outperform strong baselines on predicting an entire unseen graph snapshot of personal attributes and interpersonal links in dynamic social graphs and financial graphs.

Estimating single-cell responses across various perturbations facilitates the identification of key genes and enhances drug screening, significantly boosting experimental efficiency. However, single-cell sequencing is a destructive process, making it impossible to capture the same cell's phenotype before and after perturbation. Consequently, data collected under perturbed and unperturbed conditions are inherently unpaired. Existing methods either attempt to forcibly pair unpaired data using random sampling, or neglect the inherent relationship between unperturbed and perturbed cells during the modeling. In this work, we propose a framework based on Dual Diffusion Implicit Bridges (DDIB) to learn the mapping between different data distributions, effectively addressing the challenge of unpaired data. We further interpret this framework as a form of data augmentation. We integrate gene regulatory network (GRN) information to propagate perturbation signals in a biologically meaningful way, and further incorporate a masking mechanism to predict silent genes, improving the quality of generated profiles. Moreover, gene expression under the same perturbation often varies significantly across cells, frequently exhibiting a bimodal distribution that reflects intrinsic heterogeneity. To capture this, we introduce a more suitable evaluation metric. We propose Unlasting, dual conditional diffusion models that overcome the problem of unpaired single-cell perturbation data and strengthen the model's insight into perturbations under the guidance of the GRN, with a dedicated mask model designed to improve generation quality by predicting silent genes. In addition, we introduce a biologically grounded evaluation metric that better reflects the inherent heterogeneity in single-cell responses.

Temporal reasoning is a crucial NLP task, providing a nuanced understanding of time-sensitive contexts within textual data. Although recent advancements in LLMs have demonstrated their potential in temporal reasoning, the predominant focus has been on tasks such as temporal expression and temporal relation extraction. These tasks are primarily designed for the extraction of direct and past temporal cues and to engage in simple reasoning processes. A significant gap remains when considering complex reasoning tasks such as event forecasting, which requires multi-step temporal reasoning on events and prediction on the future timestamp. Another notable limitation of existing methods is their incapability to provide an illustration of their reasoning process, hindering explainability. In this paper, we introduce the first task of explainable temporal reasoning, to predict an event's occurrence at a future timestamp based on context which requires multiple reasoning over multiple events, and subsequently provide a clear explanation for their prediction. Our task offers a comprehensive evaluation of both the LLMs' complex temporal reasoning ability, the future event prediction ability, and explainability-a critical attribute for AI applications. To support this task, we present the first multi-source instruction-tuning dataset of explainable temporal reasoning (ExpTime) with 26k derived from the temporal knowledge graph datasets and their temporal reasoning paths, using a novel knowledge-graph-instructed-generation strategy. Based on the dataset, we propose the first open-source LLM series TimeLlaMA based on the foundation LlaMA2, with the ability of instruction following for explainable temporal reasoning. We compare the performance of our method and a variety of LLMs, where our method achieves the state-of-the-art performance of temporal prediction and explanation.

Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support embodied, adaptable, and energy-efficient autonomous agents. A central theory in this domain is predictive coding, which posits that learning and behaviour are driven by hierarchical probabilistic inferences about the causes of sensory inputs. Biological realism constrains these networks to rely on simple local computations in the form of precision-weighted predictions and prediction errors. This can make this framework highly efficient, but its implementation comes with unique challenges on the software development side. Embedding such models in standard neural network libraries often becomes limiting, as these libraries' compilation and differentiation backends can force a conceptual separation between optimization algorithms and the systems being optimized. This critically departs from other biological principles such as self-monitoring, self-organisation, cellular growth and functional plasticity. In this paper, we introduce pyhgf: a Python package backed by JAX and Rust for creating, manipulating and sampling dynamic networks for predictive coding. We improve over other frameworks by enclosing the network components as transparent, modular and malleable variables in the message-passing steps. The resulting graphs can implement arbitrary computational complexities as beliefs propagation. But the transparency of core variables can also translate into inference processes that leverage self-organisation principles, and express structure learning, meta-learning or causal discovery as the consequence of network structural adaptation to surprising inputs. The code, tutorials and documentation are hosted at: https://github.com/ilabcode/pyhgf.

In this work, we introduce Boolformer, the first Transformer architecture trained to perform end-to-end symbolic regression of Boolean functions. First, we show that it can predict compact formulas for complex functions which were not seen during training, when provided a clean truth table. Then, we demonstrate its ability to find approximate expressions when provided incomplete and noisy observations. We evaluate the Boolformer on a broad set of real-world binary classification datasets, demonstrating its potential as an interpretable alternative to classic machine learning methods. Finally, we apply it to the widespread task of modelling the dynamics of gene regulatory networks. Using a recent benchmark, we show that Boolformer is competitive with state-of-the art genetic algorithms with a speedup of several orders of magnitude. Our code and models are available publicly.

Most knowledge graph completion (KGC) methods learn latent representations of entities and relations of a given graph by mapping them into a vector space. Although the majority of these methods focus on static knowledge graphs, a large number of publicly available KGs contain temporal information stating the time instant/period over which a certain fact has been true. Such graphs are often known as temporal knowledge graphs. Furthermore, knowledge graphs may also contain textual descriptions of entities and relations. Both temporal information and textual descriptions are not taken into account during representation learning by static KGC methods, and only structural information of the graph is leveraged. Recently, some studies have used temporal information to improve link prediction, yet they do not exploit textual descriptions and do not support inductive inference (prediction on entities that have not been seen in training). We propose a novel framework called TEMT that exploits the power of pre-trained language models (PLMs) for text-enhanced temporal knowledge graph completion. The knowledge stored in the parameters of a PLM allows TEMT to produce rich semantic representations of facts and to generalize on previously unseen entities. TEMT leverages textual and temporal information available in a KG, treats them separately, and fuses them to get plausibility scores of facts. Unlike previous approaches, TEMT effectively captures dependencies across different time points and enables predictions on unseen entities. To assess the performance of TEMT, we carried out several experiments including time interval prediction, both in transductive and inductive settings, and triple classification. The experimental results show that TEMT is competitive with the state-of-the-art.

Latent Graph Inference (LGI) relaxed the reliance of Graph Neural Networks (GNNs) on a given graph topology by dynamically learning it. However, most of LGI methods assume to have a (noisy, incomplete, improvable, ...) input graph to rewire and can solely learn regular graph topologies. In the wake of the success of Topological Deep Learning (TDL), we study Latent Topology Inference (LTI) for learning higher-order cell complexes (with sparse and not regular topology) describing multi-way interactions between data points. To this aim, we introduce the Differentiable Cell Complex Module (DCM), a novel learnable function that computes cell probabilities in the complex to improve the downstream task. We show how to integrate DCM with cell complex message passing networks layers and train it in a end-to-end fashion, thanks to a two-step inference procedure that avoids an exhaustive search across all possible cells in the input, thus maintaining scalability. Our model is tested on several homophilic and heterophilic graph datasets and it is shown to outperform other state-of-the-art techniques, offering significant improvements especially in cases where an input graph is not provided.

The R-Learner is a powerful, theoretically-grounded framework for estimating heterogeneous treatment effects, prized for its robustness to nuisance model errors. However, its application to network data, where causal heterogeneity is often graph-dependent, presents a critical challenge to its core assumption of a well-specified final-stage model. In this paper, we conduct a large-scale empirical study to systematically dissect the R-Learner framework on graphs. We provide the first rigorous evidence that the primary driver of performance is the inductive bias of the final-stage CATE estimator, an effect that dominates the choice of nuisance models. Our central finding is the quantification of a catastrophic "representation bottleneck": we prove with overwhelming statistical significance (p < 0.001) that R-Learners with a graph-blind final stage fail completely (MSE > 4.0), even when paired with powerful GNN nuisance models. Conversely, our proposed end-to-end Graph R-Learner succeeds and significantly outperforms a strong, non-DML GNN T-Learner baseline. Furthermore, we identify and provide a mechanistic explanation for a subtle, topology-dependent "nuisance bottleneck," linking it to GNN over-squashing via a targeted "Hub-Periphery Trade-off" analysis. Our findings are validated across diverse synthetic and semi-synthetic benchmarks. We release our code as a reproducible benchmark to facilitate future research on this critical "final-stage bottleneck."

Learning causal graphs from multivariate time series is a ubiquitous challenge in all application domains dealing with time-dependent systems, such as in Earth sciences, biology, or engineering, to name a few. Recent developments for this causal discovery learning task have shown considerable skill, notably the specific time-series adaptations of the popular conditional independence-based learning framework. However, uncertainty estimation is challenging for conditional independence-based methods. Here, we introduce a novel bootstrap approach designed for time series causal discovery that preserves the temporal dependencies and lag structure. It can be combined with a range of time series causal discovery methods and provides a measure of confidence for the links of the time series graphs. Furthermore, next to confidence estimation, an aggregation, also called bagging, of the bootstrapped graphs by majority voting results in bagged causal discovery methods. In this work, we combine this approach with the state-of-the-art conditional-independence-based algorithm PCMCI+. With extensive numerical experiments we empirically demonstrate that, in addition to providing confidence measures for links, Bagged-PCMCI+ improves in precision and recall as compared to its base algorithm PCMCI+, at the cost of higher computational demands. These statistical performance improvements are especially pronounced in the more challenging settings (short time sample size, large number of variables, high autocorrelation). Our bootstrap approach can also be combined with other time series causal discovery algorithms and can be of considerable use in many real-world applications.

Knowledge is inherently time-sensitive and continuously evolves over time. Although current Retrieval-Augmented Generation (RAG) systems enrich LLMs with external knowledge, they largely ignore this temporal nature. This raises two challenges for RAG. First, current RAG methods lack effective time-aware representations. Same facts of different time are difficult to distinguish with vector embeddings or conventional knowledge graphs. Second, most RAG evaluations assume a static corpus, leaving a blind spot regarding update costs and retrieval stability as knowledge evolves. To make RAG time-aware, we propose Temporal GraphRAG (TG-RAG), which models external corpora as a bi-level temporal graph consisting of a temporal knowledge graph with timestamped relations and a hierarchical time graph. Multi-granularity temporal summaries are generated for each time node to capture both key events and broader trends at that time. The design supports incremental updates by extracting new temporal facts from the incoming corpus and merging them into the existing graph. The temporal graph explicitly represents identical facts at different times as distinct edges to avoid ambiguity, and the time hierarchy graph allows only generating reports for new leaf time nodes and their ancestors, ensuring effective and efficient updates. During inference, TG-RAG dynamically retrieves a subgraph within the temporal and semantic scope of the query, enabling precise evidence gathering. Moreover, we introduce ECT-QA, a time-sensitive question-answering dataset featuring both specific and abstract queries, along with a comprehensive evaluation protocol designed to assess incremental update capabilities of RAG systems. Extensive experiments show that TG-RAG significantly outperforms existing baselines, demonstrating the effectiveness of our method in handling temporal knowledge and incremental updates.

Recent sequential recommendation models rely increasingly on consecutive short-term user-item interaction sequences to model user interests. These approaches have, however, raised concerns about both short- and long-term interests. (1) {\it short-term}: interaction sequences may not result from a monolithic interest, but rather from several intertwined interests, even within a short period of time, resulting in their failures to model skip behaviors; (2) {\it long-term}: interaction sequences are primarily observed sparsely at discrete intervals, other than consecutively over the long run. This renders difficulty in inferring long-term interests, since only discrete interest representations can be derived, without taking into account interest dynamics across sequences. In this study, we address these concerns by learning (1) multi-scale representations of short-term interests; and (2) dynamics-aware representations of long-term interests. To this end, we present an Interest Dynamics modeling framework using generative Neural Processes, coined IDNP, to model user interests from a functional perspective. IDNP learns a global interest function family to define each user's long-term interest as a function instantiation, manifesting interest dynamics through function continuity. Specifically, IDNP first encodes each user's short-term interactions into multi-scale representations, which are then summarized as user context. By combining latent global interest with user context, IDNP then reconstructs long-term user interest functions and predicts interactions at upcoming query timestep. Moreover, IDNP can model such interest functions even when interaction sequences are limited and non-consecutive. Extensive experiments on four real-world datasets demonstrate that our model outperforms state-of-the-arts on various evaluation metrics.

We propose TRACIE, a novel temporal reasoning dataset that evaluates the degree to which systems understand implicit events -- events that are not mentioned explicitly in natural language text but can be inferred from it. This introduces a new challenge in temporal reasoning research, where prior work has focused on explicitly mentioned events. Human readers can infer implicit events via commonsense reasoning, resulting in a more comprehensive understanding of the situation and, consequently, better reasoning about time. We find, however, that state-of-the-art models struggle when predicting temporal relationships between implicit and explicit events. To address this, we propose a neuro-symbolic temporal reasoning model, SYMTIME, which exploits distant supervision signals from large-scale text and uses temporal rules to combine start times and durations to infer end times. SYMTIME outperforms strong baseline systems on TRACIE by 5%, and by 11% in a zero prior knowledge training setting. Our approach also generalizes to other temporal reasoning tasks, as evidenced by a gain of 1%-9% on MATRES, an explicit event benchmark.

Temporal point processes (TPPs) are widely used to model the timing and occurrence of events in domains such as social networks, transportation systems, and e-commerce. In this paper, we introduce TPP-LLM, a novel framework that integrates large language models (LLMs) with TPPs to capture both the semantic and temporal aspects of event sequences. Unlike traditional methods that rely on categorical event type representations, TPP-LLM directly utilizes the textual descriptions of event types, enabling the model to capture rich semantic information embedded in the text. While LLMs excel at understanding event semantics, they are less adept at capturing temporal patterns. To address this, TPP-LLM incorporates temporal embeddings and employs parameter-efficient fine-tuning (PEFT) methods to effectively learn temporal dynamics without extensive retraining. This approach improves both predictive accuracy and computational efficiency. Experimental results across diverse real-world datasets demonstrate that TPP-LLM outperforms state-of-the-art baselines in sequence modeling and event prediction, highlighting the benefits of combining LLMs with TPPs.

Large language models (LLMs) have significantly impacted many aspects of our lives. However, assessing and ensuring their chronological knowledge remains challenging. Existing approaches fall short in addressing the accumulative nature of knowledge, often relying on a single time stamp. To overcome this, we introduce ChroKnowBench, a benchmark dataset designed to evaluate chronologically accumulated knowledge across three key aspects: multiple domains, time dependency, temporal state. Our benchmark distinguishes between knowledge that evolves (e.g., scientific discoveries, amended laws) and knowledge that remain constant (e.g., mathematical truths, commonsense facts). Building on this benchmark, we present ChroKnowledge (Chronological Categorization of Knowledge), a novel sampling-based framework for evaluating and updating LLMs' non-parametric chronological knowledge. Our evaluation shows: (1) The ability of eliciting temporal knowledge varies depending on the data format that model was trained on. (2) LLMs partially recall knowledge or show a cut-off at temporal boundaries rather than recalling all aspects of knowledge correctly. Thus, we apply our ChroKnowPrompt, an in-depth prompting to elicit chronological knowledge by traversing step-by-step through the surrounding time spans. We observe that our framework successfully updates the overall knowledge across the entire timeline in both the biomedical domain (+11.9%) and the general domain (+2.8%), demonstrating its effectiveness in refining temporal knowledge. This non-parametric approach also enables knowledge updates not only in open-source models but also in proprietary LLMs, ensuring comprehensive applicability across model types. We perform a comprehensive analysis based on temporal characteristics of ChroKnowPrompt and validate the potential of various models to elicit intrinsic temporal knowledge through our method.

Team modeling remains a fundamental challenge at the intersection of Artificial Intelligence and the Social Sciences. Social Science research emphasizes the need to jointly model dynamics and relations, while practical applications demand unified models capable of inferring multiple team constructs simultaneously, providing interpretable insights and actionable recommendations to enhance team performance. However, existing works do not meet these practical demands. To bridge this gap, we present TRENN, a novel tempo-relational architecture that integrates: (i) an automatic temporal graph extractor, (ii) a tempo-relational encoder, (iii) a decoder for team construct prediction, and (iv) two complementary explainability modules. TRENN jointly captures relational and temporal team dynamics, providing a solid foundation for MT-TRENN, which extends TReNN by replacing the decoder with a multi-task head, enabling the model to learn shared Social Embeddings and simultaneously predict multiple team constructs, including Emergent Leadership, Leadership Style, and Teamwork components. Experimental results demonstrate that our approach significantly outperforms approaches that rely exclusively on temporal or relational information. Additionally, experimental evaluation has shown that the explainability modules integrated in MT-TRENN yield interpretable insights and actionable suggestions to support team improvement. These capabilities make our approach particularly well-suited for Human-Centered AI applications, such as intelligent decision-support systems in high-stakes collaborative environments.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

We propose DyGFormer, a new Transformer-based architecture for dynamic graph learning. DyGFormer is conceptually simple and only needs to learn from nodes' historical first-hop interactions by: (1) a neighbor co-occurrence encoding scheme that explores the correlations of the source node and destination node based on their historical sequences; (2) a patching technique that divides each sequence into multiple patches and feeds them to Transformer, allowing the model to effectively and efficiently benefit from longer histories. We also introduce DyGLib, a unified library with standard training pipelines, extensible coding interfaces, and comprehensive evaluating protocols to promote reproducible, scalable, and credible dynamic graph learning research. By performing exhaustive experiments on thirteen datasets for dynamic link prediction and dynamic node classification tasks, we find that DyGFormer achieves state-of-the-art performance on most of the datasets, demonstrating its effectiveness in capturing nodes' correlations and long-term temporal dependencies. Moreover, some results of baselines are inconsistent with previous reports, which may be caused by their diverse but less rigorous implementations, showing the importance of DyGLib. All the used resources are publicly available at https://github.com/yule-BUAA/DyGLib.

Temporal causal representation learning methods assume that causal mechanisms switch instantaneously between discrete domains, yet real-world systems often exhibit continuous mechanism transitions. For example, a vehicle's dynamics evolve gradually through a turning maneuver, and human gait shifts smoothly from walking to running. We formalize this setting by modeling transitional mechanisms as convex combinations of finitely many atomic mechanisms, governed by time-varying mixing coefficients. Our theoretical contributions establish that both the latent causal variables and the continuous mixing trajectory are jointly identifiable. We further propose TRACE, a Mixture-of-Experts framework where each expert learns one atomic mechanism during training, enabling recovery of mechanism trajectories at test time. This formulation generalizes to intermediate mechanism states never observed during training. Experiments on synthetic and real-world data demonstrate that TRACE recovers mixing trajectories with up to 0.99 correlation, substantially outperforming discrete-switching baselines.

Generating new molecules is fundamental to advancing critical applications such as drug discovery and material synthesis. Flows can generate molecules effectively by inverting the encoding process, however, existing flow models either require artifactual dequantization or specific node/edge orderings, lack desiderata such as permutation invariance, or induce discrepancy between the encoding and the decoding steps that necessitates post hoc validity correction. We circumvent these issues with novel continuous normalizing E(3)-equivariant flows, based on a system of node ODEs coupled as a graph PDE, that repeatedly reconcile locally toward globally aligned densities. Our models can be cast as message-passing temporal networks, and result in superlative performance on the tasks of density estimation and molecular generation. In particular, our generated samples achieve state-of-the-art on both the standard QM9 and ZINC250K benchmarks.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

Learning the continuous dynamics of a system from snapshots of its temporal marginals is a problem which appears throughout natural sciences and machine learning, including in quantum systems, single-cell biological data, and generative modeling. In these settings, we assume access to cross-sectional samples that are uncorrelated over time, rather than full trajectories of samples. In order to better understand the systems under observation, we would like to learn a model of the underlying process that allows us to propagate samples in time and thereby simulate entire individual trajectories. In this work, we propose Action Matching, a method for learning a rich family of dynamics using only independent samples from its time evolution. We derive a tractable training objective, which does not rely on explicit assumptions about the underlying dynamics and does not require back-propagation through differential equations or optimal transport solvers. Inspired by connections with optimal transport, we derive extensions of Action Matching to learn stochastic differential equations and dynamics involving creation and destruction of probability mass. Finally, we showcase applications of Action Matching by achieving competitive performance in a diverse set of experiments from biology, physics, and generative modeling.

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for de novo cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to de novo cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for de novo cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

The rapid expansion of medical literature presents growing challenges for structuring and integrating domain knowledge at scale. Knowledge Graphs (KGs) offer a promising solution by enabling efficient retrieval, automated reasoning, and knowledge discovery. However, current KG construction methods often rely on supervised pipelines with limited generalizability or naively aggregate outputs from Large Language Models (LLMs), treating biomedical corpora as static and ignoring the temporal dynamics and contextual uncertainty of evolving knowledge. To address these limitations, we introduce MedKGent, a LLM agent framework for constructing temporally evolving medical KGs. Leveraging over 10 million PubMed abstracts published between 1975 and 2023, we simulate the emergence of biomedical knowledge via a fine-grained daily time series. MedKGent incrementally builds the KG in a day-by-day manner using two specialized agents powered by the Qwen2.5-32B-Instruct model. The Extractor Agent identifies knowledge triples and assigns confidence scores via sampling-based estimation, which are used to filter low-confidence extractions and inform downstream processing. The Constructor Agent incrementally integrates the retained triples into a temporally evolving graph, guided by confidence scores and timestamps to reinforce recurring knowledge and resolve conflicts. The resulting KG contains 156,275 entities and 2,971,384 relational triples. Quality assessments by two SOTA LLMs and three domain experts demonstrate an accuracy approaching 90%, with strong inter-rater agreement. To evaluate downstream utility, we conduct RAG across seven medical question answering benchmarks using five leading LLMs, consistently observing significant improvements over non-augmented baselines. Case studies further demonstrate the KG's value in literature-based drug repurposing via confidence-aware causal inference.

Clinical trials are crucial for drug development but are time consuming, expensive, and often burdensome on patients. More importantly, clinical trials face uncertain outcomes due to issues with efficacy, safety, or problems with patient recruitment. If we were better at predicting the results of clinical trials, we could avoid having to run trials that will inevitably fail more resources could be devoted to trials that are likely to succeed. In this paper, we propose Hierarchical INteraction Network (HINT) for more general, clinical trial outcome predictions for all diseases based on a comprehensive and diverse set of web data including molecule information of the drugs, target disease information, trial protocol and biomedical knowledge. HINT first encode these multi-modal data into latent embeddings, where an imputation module is designed to handle missing data. Next, these embeddings will be fed into the knowledge embedding module to generate knowledge embeddings that are pretrained using external knowledge on pharmaco-kinetic properties and trial risk from the web. Then the interaction graph module will connect all the embedding via domain knowledge to fully capture various trial components and their complex relations as well as their influences on trial outcomes. Finally, HINT learns a dynamic attentive graph neural network to predict trial outcome. Comprehensive experimental results show that HINT achieves strong predictive performance, obtaining 0.772, 0.607, 0.623, 0.703 on PR-AUC for Phase I, II, III, and indication outcome prediction, respectively. It also consistently outperforms the best baseline method by up to 12.4\% on PR-AUC.

Jointly identifying a mixture of discrete and continuous factors of variability without supervision is a key problem in unraveling complex phenomena. Variational inference has emerged as a promising method to learn interpretable mixture representations. However, posterior approximation in high-dimensional latent spaces, particularly for discrete factors remains challenging. Here, we propose an unsupervised variational framework using multiple interacting networks called cpl-mixVAE that scales well to high-dimensional discrete settings. In this framework, the mixture representation of each network is regularized by imposing a consensus constraint on the discrete factor. We justify the use of this framework by providing both theoretical and experimental results. Finally, we use the proposed method to jointly uncover discrete and continuous factors of variability describing gene expression in a single-cell transcriptomic dataset profiling more than a hundred cortical neuron types.

Spatio-temporal prediction is a pivotal task with broad applications in traffic management, climate monitoring, energy scheduling, etc. However, existing methodologies often struggle to balance model expressiveness and computational efficiency, especially when scaling to large real-world datasets. To tackle these challenges, we propose STH-SepNet (Spatio-Temporal Hypergraph Separation Networks), a novel framework that decouples temporal and spatial modeling to enhance both efficiency and precision. Therein, the temporal dimension is modeled using lightweight large language models, which effectively capture low-rank temporal dynamics. Concurrently, the spatial dimension is addressed through an adaptive hypergraph neural network, which dynamically constructs hyperedges to model intricate, higher-order interactions. A carefully designed gating mechanism is integrated to seamlessly fuse temporal and spatial representations. By leveraging the fundamental principles of low-rank temporal dynamics and spatial interactions, STH-SepNet offers a pragmatic and scalable solution for spatio-temporal prediction in real-world applications. Extensive experiments on large-scale real-world datasets across multiple benchmarks demonstrate the effectiveness of STH-SepNet in boosting predictive performance while maintaining computational efficiency. This work may provide a promising lightweight framework for spatio-temporal prediction, aiming to reduce computational demands and while enhancing predictive performance. Our code is avaliable at https://github.com/SEU-WENJIA/ST-SepNet-Lightweight-LLMs-Meet-Adaptive-Hypergraphs.

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

In this paper, we introduce TimeGPT, the first foundation model for time series, capable of generating accurate predictions for diverse datasets not seen during training. We evaluate our pre-trained model against established statistical, machine learning, and deep learning methods, demonstrating that TimeGPT zero-shot inference excels in performance, efficiency, and simplicity. Our study provides compelling evidence that insights from other domains of artificial intelligence can be effectively applied to time series analysis. We conclude that large-scale time series models offer an exciting opportunity to democratize access to precise predictions and reduce uncertainty by leveraging the capabilities of contemporary advancements in deep learning.

Forecasting future links is a central task in temporal graph (TG) reasoning, requiring models to leverage historical interactions to predict upcoming ones. Traditional neural approaches, such as temporal graph neural networks, achieve strong performance but lack explainability and cannot be applied to unseen graphs without retraining. Recent studies have begun to explore using large language models (LLMs) for graph reasoning, but most of them are constrained to static graphs or small synthetic TGs and lack the evaluation of the quality of reasoning traces generated by LLMs. In this work, we present Reasoning-Enhanced Learning for Temporal Graphs (ReaL-TG), a reinforcement learning framework that fine-tunes LLMs to perform explainable link forecasting on real-world TGs. ReaL-TG uses outcome-based reward to encourage models to self-explore reasoning strategies from graph structure and to produce explanations that directly justify their predictions. To enable evaluation on LLM-generated reasoning traces, we propose a new evaluation protocol combining ranking metrics with an LLM-as-a-Judge system that assesses both the quality of reasoning and the impact of hallucinations. Experiments with ReaL-TG-4B, obtained by fine-tuning Qwen3-4B under our framework, show that it outperforms much larger frontier LLMs, including GPT-5 mini, on ranking metrics, while producing high-quality explanations confirmed by both the LLM judge and human evaluation.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

Continuous-time event sequences play a vital role in real-world domains such as healthcare, finance, online shopping, social networks, and so on. To model such data, temporal point processes (TPPs) have emerged as the most natural and competitive models, making a significant impact in both academic and application communities. Despite the emergence of many powerful models in recent years, there hasn't been a central benchmark for these models and future research endeavors. This lack of standardization impedes researchers and practitioners from comparing methods and reproducing results, potentially slowing down progress in this field. In this paper, we present EasyTPP, the first central repository of research assets (e.g., data, models, evaluation programs, documentations) in the area of event sequence modeling. Our EasyTPP makes several unique contributions to this area: a unified interface of using existing datasets and adding new datasets; a wide range of evaluation programs that are easy to use and extend as well as facilitate reproducible research; implementations of popular neural TPPs, together with a rich library of modules by composing which one could quickly build complex models. All the data and implementation can be found at https://github.com/ant-research/EasyTemporalPointProcess. We will actively maintain this benchmark and welcome contributions from other researchers and practitioners. Our benchmark will help promote reproducible research in this field, thus accelerating research progress as well as making more significant real-world impacts.

Interference is ubiquitous when conducting causal experiments over networks. Except for certain network structures, causal inference on the network in the presence of interference is difficult due to the entanglement between the treatment assignments and the interference levels. In this article, we conduct causal inference under interference on an observed, sparse but connected network, and we propose a novel design of experiments based on an independent set. Compared to conventional designs, the independent-set design focuses on an independent subset of data and controls their interference exposures through the assignments to the rest (auxiliary set). We provide a lower bound on the size of the independent set from a greedy algorithm , and justify the theoretical performance of estimators under the proposed design. Our approach is capable of estimating both spillover effects and treatment effects. We justify its superiority over conventional methods and illustrate the empirical performance through simulations.

Large language models (LLMs) learn temporal concepts from the co-occurrence of related tokens in a sequence. Compared with conventional text generation, temporal reasoning, which reaches a conclusion based on mathematical, logical and commonsense knowledge, is more challenging. In this paper, we propose TempGraph-LLM, a new paradigm towards text-based temporal reasoning. To be specific, we first teach LLMs to translate the context into a temporal graph. A synthetic dataset, which is fully controllable and requires minimal supervision, is constructed for pre-training on this task. We prove in experiments that LLMs benefit from the pre-training on other tasks. On top of that, we guide LLMs to perform symbolic reasoning with the strategies of Chain of Thoughts (CoTs) bootstrapping and special data augmentation. We observe that CoTs with symbolic reasoning bring more consistent and reliable results than those using free text.

Many natural dynamic processes -- such as in vivo cellular differentiation or disease progression -- can only be observed through the lens of static sample snapshots. While challenging, reconstructing their temporal evolution to decipher underlying dynamic properties is of major interest to scientific research. Existing approaches enable data transport along a temporal axis but are poorly scalable in high dimension and require restrictive assumptions to be met. To address these issues, we propose \textbf{Multi-Marginal temporal Schr\"odinger Bridge Matching} (MMtSBM) for video generation from unpaired data, extending the theoretical guarantees and empirical efficiency of Diffusion Schr\"odinger Bridge Matching (arXiv:archive/2303.16852) by deriving the Iterative Markovian Fitting algorithm to multiple marginals in a novel factorized fashion. Experiments show that MMtSBM retains theoretical properties on toy examples, achieves state-of-the-art performance on real world datasets such as transcriptomic trajectory inference in 100 dimensions, and for the first time recovers couplings and dynamics in very high dimensional image settings. Our work establishes multi-marginal Schr\"odinger bridges as a practical and principled approach for recovering hidden dynamics from static data.

It is unclear whether strong forecasting performance reflects genuine temporal understanding or the ability to reason under contextual and event-driven conditions. We introduce TemporalBench, a multi-domain benchmark designed to evaluate temporal reasoning behavior under progressively richer informational settings. TemporalBench adopts a four-tier task taxonomy that examines historical structure interpretation, context-free forecasting, contextual temporal reasoning, and event-conditioned prediction across four real-world domains: retail, healthcare, energy, and physical systems. By controlling access to future targets and contextual information, the benchmark enables a diagnostic analysis of whether models can correctly interpret temporal patterns, align them with external context, and adapt predictions when conditions change. Extensive baseline experiments show that strong numerical forecasting accuracy does not reliably translate into robust contextual or event-aware temporal reasoning; instead, existing agent frameworks exhibit fragmented strengths and systematic failure modes that remain largely hidden under forecasting-only benchmarks. The TemporalBench dataset is publicly available at https://huggingface.co/datasets/Melady/TemporalBench, and we additionally provide a public leaderboard at https://huggingface.co/spaces/Melady/TemporalBench_Leaderboard.

Recent work has shown promising results in causal discovery by leveraging interventional data with gradient-based methods, even when the intervened variables are unknown. However, previous work assumes that the correspondence between samples and interventions is known, which is often unrealistic. We envision a scenario with an extensive dataset sampled from multiple intervention distributions and one observation distribution, but where we do not know which distribution originated each sample and how the intervention affected the system, i.e., interventions are entirely latent. We propose a method based on neural networks and variational inference that addresses this scenario by framing it as learning a shared causal graph among an infinite mixture (under a Dirichlet process prior) of intervention structural causal models. Experiments with synthetic and real data show that our approach and its semi-supervised variant are able to discover causal relations in this challenging scenario.

User response prediction is essential in industrial recommendation systems, such as online display advertising. Among all the features in recommendation models, user behaviors are among the most critical. Many works have revealed that a user's behavior reflects her interest in the candidate item, owing to the semantic or temporal correlation between behaviors and the candidate. While the literature has individually examined each of these correlations, researchers have yet to analyze them in combination, that is, the semantic-temporal correlation. We empirically measure this correlation and observe intuitive yet robust patterns. We then examine several popular user interest models and find that, surprisingly, none of them learn such correlation well. To fill this gap, we propose a Temporal Interest Network (TIN) to capture the semantic-temporal correlation simultaneously between behaviors and the target. We achieve this by incorporating target-aware temporal encoding, in addition to semantic encoding, to represent behaviors and the target. Furthermore, we conduct explicit 4-way interaction by deploying target-aware attention and target-aware representation to capture both semantic and temporal correlation. We conduct comprehensive evaluations on two popular public datasets, and our proposed TIN outperforms the best-performing baselines by 0.43% and 0.29% on GAUC, respectively. During online A/B testing in Tencent's advertising platform, TIN achieves 1.65% cost lift and 1.93% GMV lift over the base model. It has been successfully deployed in production since October 2023, serving the WeChat Moments traffic. We have released our code at https://github.com/zhouxy1003/TIN.

Graph retrieval based on subgraph isomorphism has several real-world applications such as scene graph retrieval, molecular fingerprint detection and circuit design. Roy et al. [35] proposed IsoNet, a late interaction model for subgraph matching, which first computes the node and edge embeddings of each graph independently of paired graph and then computes a trainable alignment map. Here, we present IsoNet++, an early interaction graph neural network (GNN), based on several technical innovations. First, we compute embeddings of all nodes by passing messages within and across the two input graphs, guided by an injective alignment between their nodes. Second, we update this alignment in a lazy fashion over multiple rounds. Within each round, we run a layerwise GNN from scratch, based on the current state of the alignment. After the completion of one round of GNN, we use the last-layer embeddings to update the alignments, and proceed to the next round. Third, IsoNet++ incorporates a novel notion of node-pair partner interaction. Traditional early interaction computes attention between a node and its potential partners in the other graph, the attention then controlling messages passed across graphs. In contrast, we consider node pairs (not single nodes) as potential partners. Existence of an edge between the nodes in one graph and non-existence in the other provide vital signals for refining the alignment. Our experiments on several datasets show that the alignments get progressively refined with successive rounds, resulting in significantly better retrieval performance than existing methods. We demonstrate that all three innovations contribute to the enhanced accuracy. Our code and datasets are publicly available at https://github.com/structlearning/isonetpp.

Time-series causal discovery (TSCD) is a fundamental problem of machine learning. However, existing synthetic datasets cannot properly evaluate or predict the algorithms' performance on real data. This study introduces the CausalTime pipeline to generate time-series that highly resemble the real data and with ground truth causal graphs for quantitative performance evaluation. The pipeline starts from real observations in a specific scenario and produces a matching benchmark dataset. Firstly, we harness deep neural networks along with normalizing flow to accurately capture realistic dynamics. Secondly, we extract hypothesized causal graphs by performing importance analysis on the neural network or leveraging prior knowledge. Thirdly, we derive the ground truth causal graphs by splitting the causal model into causal term, residual term, and noise term. Lastly, using the fitted network and the derived causal graph, we generate corresponding versatile time-series proper for algorithm assessment. In the experiments, we validate the fidelity of the generated data through qualitative and quantitative experiments, followed by a benchmarking of existing TSCD algorithms using these generated datasets. CausalTime offers a feasible solution to evaluating TSCD algorithms in real applications and can be generalized to a wide range of fields. For easy use of the proposed approach, we also provide a user-friendly website, hosted on www.causaltime.cc.

Biomedical Knowledge Graphs (BKGs) integrate diverse datasets to elucidate complex relationships within the biomedical field. Effective link prediction on these graphs can uncover valuable connections, such as potential novel drug-disease relations. We introduce a novel multimodal approach that unifies embeddings from specialized Language Models (LMs) with Graph Contrastive Learning (GCL) to enhance intra-entity relationships while employing a Knowledge Graph Embedding (KGE) model to capture inter-entity relationships for effective link prediction. To address limitations in existing BKGs, we present PrimeKG++, an enriched knowledge graph incorporating multimodal data, including biological sequences and textual descriptions for each entity type. By combining semantic and relational information in a unified representation, our approach demonstrates strong generalizability, enabling accurate link predictions even for unseen nodes. Experimental results on PrimeKG++ and the DrugBank drug-target interaction dataset demonstrate the effectiveness and robustness of our method across diverse biomedical datasets. Our source code, pre-trained models, and data are publicly available at https://github.com/HySonLab/BioMedKG

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

Temporal distribution shift (TDS) erodes the long-term accuracy of recommender systems, yet industrial practice still relies on periodic incremental training, which struggles to capture both stable and transient patterns. Existing approaches such as invariant learning and self-supervised learning offer partial solutions but often suffer from unstable temporal generalization, representation collapse, or inefficient data utilization. To address these limitations, we propose ELBO_TDS, a probabilistic framework that integrates seamlessly into industry-scale incremental learning pipelines. First, we identify key shifting factors through statistical analysis of real-world production data and design a simple yet effective data augmentation strategy that resamples these time-varying factors to extend the training support. Second, to harness the benefits of this extended distribution while preventing representation collapse, we model the temporal recommendation scenario using a causal graph and derive a self-supervised variational objective, ELBO_TDS, grounded in the causal structure. Extensive experiments supported by both theoretical and empirical analysis demonstrate that our method achieves superior temporal generalization, yielding a 2.33\% uplift in GMV per user and has been successfully deployed in Shopee Product Search. Code is available at https://github.com/FuCongResearchSquad/ELBO4TDS.

Mediation analysis learns the causal effect transmitted via mediator variables between treatments and outcomes and receives increasing attention in various scientific domains to elucidate causal relations. Most existing works focus on point-exposure studies where each subject only receives one treatment at a single time point. However, there are a number of applications (e.g., mobile health) where the treatments are sequentially assigned over time and the dynamic mediation effects are of primary interest. Proposing a reinforcement learning (RL) framework, we are the first to evaluate dynamic mediation effects in settings with infinite horizons. We decompose the average treatment effect into an immediate direct effect, an immediate mediation effect, a delayed direct effect, and a delayed mediation effect. Upon the identification of each effect component, we further develop robust and semi-parametrically efficient estimators under the RL framework to infer these causal effects. The superior performance of the proposed method is demonstrated through extensive numerical studies, theoretical results, and an analysis of a mobile health dataset.

We present graph attention networks (GATs), novel neural network architectures that operate on graph-structured data, leveraging masked self-attentional layers to address the shortcomings of prior methods based on graph convolutions or their approximations. By stacking layers in which nodes are able to attend over their neighborhoods' features, we enable (implicitly) specifying different weights to different nodes in a neighborhood, without requiring any kind of costly matrix operation (such as inversion) or depending on knowing the graph structure upfront. In this way, we address several key challenges of spectral-based graph neural networks simultaneously, and make our model readily applicable to inductive as well as transductive problems. Our GAT models have achieved or matched state-of-the-art results across four established transductive and inductive graph benchmarks: the Cora, Citeseer and Pubmed citation network datasets, as well as a protein-protein interaction dataset (wherein test graphs remain unseen during training).

The facts and time in the document are intricately intertwined, making temporal reasoning over documents challenging. Previous work models time implicitly, making it difficult to handle such complex relationships. To address this issue, we propose MTGER, a novel Multi-view Temporal Graph Enhanced Temporal Reasoning framework for temporal reasoning over time-involved documents. Concretely, MTGER explicitly models the temporal relationships among facts by multi-view temporal graphs. On the one hand, the heterogeneous temporal graphs explicitly model the temporal and discourse relationships among facts; on the other hand, the multi-view mechanism captures both time-focused and fact-focused information, allowing the two views to complement each other through adaptive fusion. To further improve the implicit reasoning capability of the model, we design a self-supervised time-comparing objective. Extensive experimental results demonstrate the effectiveness of our method on the TimeQA and SituatedQA datasets. Furthermore, MTGER gives more consistent answers under question perturbations.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Causal discovery for dynamical systems poses a major challenge in fields where active interventions are infeasible. Most methods used to investigate these systems and their associated benchmarks are tailored to deterministic, low-dimensional and weakly nonlinear time-series data. To address these limitations, we present CausalDynamics, a large-scale benchmark and extensible data generation framework to advance the structural discovery of dynamical causal models. Our benchmark consists of true causal graphs derived from thousands of coupled ordinary and stochastic differential equations as well as two idealized climate models. We perform a comprehensive evaluation of state-of-the-art causal discovery algorithms for graph reconstruction on systems with noisy, confounded, and lagged dynamics. CausalDynamics consists of a plug-and-play, build-your-own coupling workflow that enables the construction of a hierarchy of physical systems. We anticipate that our framework will facilitate the development of robust causal discovery algorithms that are broadly applicable across domains while addressing their unique challenges. We provide a user-friendly implementation and documentation on https://kausable.github.io/CausalDynamics.

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

Signed networks allow us to model conflicting relationships and interactions, such as friend/enemy and support/oppose. These signed interactions happen in real-time. Modeling such dynamics of signed networks is crucial to understanding the evolution of polarization in the network and enabling effective prediction of the signed structure (i.e., link signs and signed weights) in the future. However, existing works have modeled either (static) signed networks or dynamic (unsigned) networks but not dynamic signed networks. Since both sign and dynamics inform the graph structure in different ways, it is non-trivial to model how to combine the two features. In this work, we propose a new Graph Neural Network (GNN)-based approach to model dynamic signed networks, named SEMBA: Signed link's Evolution using Memory modules and Balanced Aggregation. Here, the idea is to incorporate the signs of temporal interactions using separate modules guided by balance theory and to evolve the embeddings from a higher-order neighborhood. Experiments on 4 real-world datasets and 4 different tasks demonstrate that SEMBA consistently and significantly outperforms the baselines by up to 80% on the tasks of predicting signs of future links while matching the state-of-the-art performance on predicting the existence of these links in the future. We find that this improvement is due specifically to the superior performance of SEMBA on the minority negative class.

We formalize constraint-based structure learning of the "true" causal graph from observed data when unobserved variables are also existent. We provide conditions for a "natural" family of constraint-based structure-learning algorithms that output graphs that are Markov equivalent to the causal graph. Under the faithfulness assumption, this natural family contains all exact structure-learning algorithms. We also provide a set of assumptions, under which any natural structure-learning algorithm outputs Markov equivalent graphs to the causal graph. These assumptions can be thought of as a relaxation of faithfulness, and most of them can be directly tested from (the underlying distribution) of the data, particularly when one focuses on structural causal models. We specialize the definitions and results for structural causal models.

The reliability of deep time series models is often compromised by their tendency to rely on confounding factors, which may lead to misleading results. Our newly recorded, naturally confounded dataset named P2S from a real mechanical production line emphasizes this. To tackle the challenging problem of mitigating confounders in time series data, we introduce Right on Time (RioT). Our method enables interactions with model explanations across both the time and frequency domain. Feedback on explanations in both domains is then used to constrain the model, steering it away from the annotated confounding factors. The dual-domain interaction strategy is crucial for effectively addressing confounders in time series datasets. We empirically demonstrate that RioT can effectively guide models away from the wrong reasons in P2S as well as popular time series classification and forecasting datasets.

Multitask Gaussian process (MTGP) is powerful for joint learning of multiple tasks with complicated correlation patterns. However, due to the assembling of additive independent latent functions, all current MTGPs including the salient linear model of coregionalization (LMC) and convolution frameworks cannot effectively represent and learn the hierarchical latent interactions between its latent functions. In this paper, we further investigate the interactions in LMC of MTGP and then propose a novel kernel representation of the hierarchical interactions, which ameliorates both the expressiveness and the interpretability of MTGP. Specifically, we express the interaction as a product of function interaction and coefficient interaction. The function interaction is modeled by using cross convolution of latent functions. The coefficient interaction between the LMCs is described as a cross coregionalization term. We validate that considering the interactions can promote knowledge transferring in MTGP and compare our approach with some state-of-the-art MTGPs on both synthetic- and real-world datasets.

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present generating higher-order interactions. The important regulators of higher-order interactions are unstudied. To address this, we applied a new high-dimensional geometry approach that quantifies epistasis in a fitness landscape to ask how individual genes and species influence the interactions in the rest of the biological network. We then generated and also reanalyzed 5-dimensional datasets (two genetic, two microbiome). We identified key genes (e.g. the rbs locus and pykF) and species (e.g. Lactobacilli) that control the interactions of many other genes and species. These higher-order master regulators can induce or suppress evolutionary and ecological diversification by controlling the topography of the fitness landscape. Thus, we provide mathematical intuition and justification for exploration of biological networks in higher dimensions.

Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experimental or interventional conditions. BaCaDI is fully differentiable, which allows us to infer the complex joint posterior over the intervention targets and the causal structure via efficient gradient-based variational inference. In experiments on synthetic causal discovery tasks and simulated gene-expression data, BaCaDI outperforms related methods in identifying causal structures and intervention targets.

Knowledge about the hidden factors that determine particular system dynamics is crucial for both explaining them and pursuing goal-directed interventions. Inferring these factors from time series data without supervision remains an open challenge. Here, we focus on spatiotemporal processes, including wave propagation and weather dynamics, for which we assume that universal causes (e.g. physics) apply throughout space and time. A recently introduced DIstributed SpatioTemporal graph Artificial Neural network Architecture (DISTANA) is used and enhanced to learn such processes, requiring fewer parameters and achieving significantly more accurate predictions compared to temporal convolutional neural networks and other related approaches. We show that DISTANA, when combined with a retrospective latent state inference principle called active tuning, can reliably derive location-respective hidden causal factors. In a current weather prediction benchmark, DISTANA infers our planet's land-sea mask solely by observing temperature dynamics and, meanwhile, uses the self inferred information to improve its own future temperature predictions.

The capabilities and adoption of deep neural networks (DNNs) grow at an exhilarating pace: Vision models accurately classify human actions in videos and identify cancerous tissue in medical scans as precisely than human experts; large language models answer wide-ranging questions, generate code, and write prose, becoming the topic of everyday dinner-table conversations. Even though their uses are exhilarating, the continually increasing model sizes and computational complexities have a dark side. The economic cost and negative environmental externalities of training and serving models is in evident disharmony with financial viability and climate action goals. Instead of pursuing yet another increase in predictive performance, this dissertation is dedicated to the improvement of neural network efficiency. Specifically, a core contribution addresses the efficiency aspects during online inference. Here, the concept of Continual Inference Networks (CINs) is proposed and explored across four publications. CINs extend prior state-of-the-art methods developed for offline processing of spatio-temporal data and reuse their pre-trained weights, improving their online processing efficiency by an order of magnitude. These advances are attained through a bottom-up computational reorganization and judicious architectural modifications. The benefit to online inference is demonstrated by reformulating several widely used network architectures into CINs, including 3D CNNs, ST-GCNs, and Transformer Encoders. An orthogonal contribution tackles the concurrent adaptation and computational acceleration of a large source model into multiple lightweight derived models. Drawing on fusible adapter networks and structured pruning, Structured Pruning Adapters achieve superior predictive accuracy under aggressive pruning using significantly fewer learned weights compared to fine-tuning with pruning.

Normalizing flows are powerful non-parametric statistical models that function as a hybrid between density estimators and generative models. Current learning algorithms for normalizing flows assume that data points are sampled independently, an assumption that is frequently violated in practice, which may lead to erroneous density estimation and data generation. We propose a likelihood objective of normalizing flows incorporating dependencies between the data points, for which we derive a flexible and efficient learning algorithm suitable for different dependency structures. We show that respecting dependencies between observations can improve empirical results on both synthetic and real-world data, and leads to higher statistical power in a downstream application to genome-wide association studies.

Generating temporal data under conditions is crucial for forecasting, imputation, and generative tasks. Such data often has metadata and partially observed signals that jointly influence the generated values. However, existing methods face three key limitations: (1) they condition on either the metadata or observed values, but rarely both together; (2) they adopt either training-time approaches that fail to generalize to unseen scenarios, or inference-time approaches that ignore metadata; and (3) they suffer from trade-offs between generation speed and temporal coherence across time windows--choosing either slow but coherent autoregressive methods or fast but incoherent parallel ones. We propose WaveStitch, a novel diffusion-based method to overcome these hurdles through: (1) dual-sourced conditioning on both metadata and partially observed signals; (2) a hybrid training-inference architecture, incorporating metadata during training and observations at inference via gradient-based guidance; and (3) a novel pipeline-style paradigm that generates time windows in parallel while preserving coherence through an inference-time conditional loss and a stitching mechanism. Across diverse datasets, WaveStitch demonstrates adaptability to arbitrary patterns of observed signals, achieving 1.81x lower mean-squared-error compared to the state-of-the-art, and generates data up to 166.48x faster than autoregressive methods while maintaining coherence. Our code is available at: https://github.com/adis98/WaveStitch

Reasoning about time and temporal relations is an integral aspect of human cognition, essential for perceiving the world and navigating our experiences. Though large language models (LLMs) have demonstrated impressive performance in many reasoning tasks, temporal reasoning remains challenging due to its intrinsic complexity. In this work, we first study an essential task of temporal reasoning -- temporal graph generation, to unveil LLMs' inherent, global reasoning capabilities. We show that this task presents great challenges even for the most powerful LLMs, such as GPT-3.5/4. We also notice a significant performance gap by small models (<10B) that lag behind LLMs by 50%. Next, we study how to close this gap with a budget constraint, e.g., not using model finetuning. We propose a new prompting technique tailored for temporal reasoning, Narrative-of-Thought (NoT), that first converts the events set to a Python class, then prompts a small model to generate a temporally grounded narrative, guiding the final generation of a temporal graph. Extensive experiments showcase the efficacy of NoT in improving various metrics. Notably, NoT attains the highest F1 on the Schema-11 evaluation set, while securing an overall F1 on par with GPT-3.5. NoT also achieves the best structural similarity across the board, even compared with GPT-3.5/4. Our code is available at https://github.com/launchnlp/NoT.

Interpreting time series models is uniquely challenging because it requires identifying both the location of time series signals that drive model predictions and their matching to an interpretable temporal pattern. While explainers from other modalities can be applied to time series, their inductive biases do not transfer well to the inherently challenging interpretation of time series. We present TimeX, a time series consistency model for training explainers. TimeX trains an interpretable surrogate to mimic the behavior of a pretrained time series model. It addresses the issue of model faithfulness by introducing model behavior consistency, a novel formulation that preserves relations in the latent space induced by the pretrained model with relations in the latent space induced by TimeX. TimeX provides discrete attribution maps and, unlike existing interpretability methods, it learns a latent space of explanations that can be used in various ways, such as to provide landmarks to visually aggregate similar explanations and easily recognize temporal patterns. We evaluate TimeX on eight synthetic and real-world datasets and compare its performance against state-of-the-art interpretability methods. We also conduct case studies using physiological time series. Quantitative evaluations demonstrate that TimeX achieves the highest or second-highest performance in every metric compared to baselines across all datasets. Through case studies, we show that the novel components of TimeX show potential for training faithful, interpretable models that capture the behavior of pretrained time series models.

In causal inference, estimating heterogeneous treatment effects (HTE) is critical for identifying how different subgroups respond to interventions, with broad applications in fields such as precision medicine and personalized advertising. Although HTE estimation methods aim to improve accuracy, how to provide explicit subgroup descriptions remains unclear, hindering data interpretation and strategic intervention management. In this paper, we propose CURLS, a novel rule learning method leveraging HTE, which can effectively describe subgroups with significant treatment effects. Specifically, we frame causal rule learning as a discrete optimization problem, finely balancing treatment effect with variance and considering the rule interpretability. We design an iterative procedure based on the minorize-maximization algorithm and solve a submodular lower bound as an approximation for the original. Quantitative experiments and qualitative case studies verify that compared with state-of-the-art methods, CURLS can find subgroups where the estimated and true effects are 16.1% and 13.8% higher and the variance is 12.0% smaller, while maintaining similar or better estimation accuracy and rule interpretability. Code is available at https://osf.io/zwp2k/.

Understanding protein dynamics is critical for elucidating their biological functions. The increasing availability of molecular dynamics (MD) data enables the training of deep generative models to efficiently explore the conformational space of proteins. However, existing approaches either fail to explicitly capture the temporal dependencies between conformations or do not support direct generation of time-independent samples. To address these limitations, we introduce ConfRover, an autoregressive model that simultaneously learns protein conformation and dynamics from MD trajectories, supporting both time-dependent and time-independent sampling. At the core of our model is a modular architecture comprising: (i) an encoding layer, adapted from protein folding models, that embeds protein-specific information and conformation at each time frame into a latent space; (ii) a temporal module, a sequence model that captures conformational dynamics across frames; and (iii) an SE(3) diffusion model as the structure decoder, generating conformations in continuous space. Experiments on ATLAS, a large-scale protein MD dataset of diverse structures, demonstrate the effectiveness of our model in learning conformational dynamics and supporting a wide range of downstream tasks. ConfRover is the first model to sample both protein conformations and trajectories within a single framework, offering a novel and flexible approach for learning from protein MD data.

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

Temporal reasoning is pivotal for Large Language Models (LLMs) to comprehend the real world. However, existing works neglect the real-world challenges for temporal reasoning: (1) intensive temporal information, (2) fast-changing event dynamics, and (3) complex temporal dependencies in social interactions. To bridge this gap, we propose a multi-level benchmark TIME, designed for temporal reasoning in real-world scenarios. TIME consists of 38,522 QA pairs, covering 3 levels with 11 fine-grained sub-tasks. This benchmark encompasses 3 sub-datasets reflecting different real-world challenges: TIME-Wiki, TIME-News, and TIME-Dial. We conduct extensive experiments on reasoning models and non-reasoning models. And we conducted an in-depth analysis of temporal reasoning performance across diverse real-world scenarios and tasks, and summarized the impact of test-time scaling on temporal reasoning capabilities. Additionally, we release TIME-Lite, a human-annotated subset to foster future research and standardized evaluation in temporal reasoning. The code is available at https://github.com/sylvain-wei/TIME , and the dataset is available at https://huggingface.co/datasets/SylvainWei/TIME .

Demystifying the interactions among multiple agents from their past trajectories is fundamental to precise and interpretable trajectory prediction. However, previous works mainly consider static, pair-wise interactions with limited relational reasoning. To promote more comprehensive interaction modeling and relational reasoning, we propose DynGroupNet, a dynamic-group-aware network, which can i) model time-varying interactions in highly dynamic scenes; ii) capture both pair-wise and group-wise interactions; and iii) reason both interaction strength and category without direct supervision. Based on DynGroupNet, we further design a prediction system to forecast socially plausible trajectories with dynamic relational reasoning. The proposed prediction system leverages the Gaussian mixture model, multiple sampling and prediction refinement to promote prediction diversity, training stability and trajectory smoothness, respectively. Extensive experiments show that: 1)DynGroupNet can capture time-varying group behaviors, infer time-varying interaction category and interaction strength during trajectory prediction without any relation supervision on physical simulation datasets; 2)DynGroupNet outperforms the state-of-the-art trajectory prediction methods by a significant improvement of 22.6%/28.0%, 26.9%/34.9%, 5.1%/13.0% in ADE/FDE on the NBA, NFL Football and SDD datasets and achieve the state-of-the-art performance on the ETH-UCY dataset.

Most existing causal discovery methods rely on the assumption of no latent confounders, limiting their applicability in solving real-life problems. In this paper, we introduce a novel, versatile framework for causal discovery that accommodates the presence of causally-related hidden variables almost everywhere in the causal network (for instance, they can be effects of observed variables), based on rank information of covariance matrix over observed variables. We start by investigating the efficacy of rank in comparison to conditional independence and, theoretically, establish necessary and sufficient conditions for the identifiability of certain latent structural patterns. Furthermore, we develop a Rank-based Latent Causal Discovery algorithm, RLCD, that can efficiently locate hidden variables, determine their cardinalities, and discover the entire causal structure over both measured and hidden ones. We also show that, under certain graphical conditions, RLCD correctly identifies the Markov Equivalence Class of the whole latent causal graph asymptotically. Experimental results on both synthetic and real-world personality data sets demonstrate the efficacy of the proposed approach in finite-sample cases.

The growing popularity of neuro symbolic reasoning has led to the adoption of various forms of differentiable (i.e., fuzzy) first order logic. We introduce PyReason, a software framework based on generalized annotated logic that both captures the current cohort of differentiable logics and temporal extensions to support inference over finite periods of time with capabilities for open world reasoning. Further, PyReason is implemented to directly support reasoning over graphical structures (e.g., knowledge graphs, social networks, biological networks, etc.), produces fully explainable traces of inference, and includes various practical features such as type checking and a memory-efficient implementation. This paper reviews various extensions of generalized annotated logic integrated into our implementation, our modern, efficient Python-based implementation that conducts exact yet scalable deductive inference, and a suite of experiments. PyReason is available at: github.com/lab-v2/pyreason.

While Mechanistic Interpretability has identified interpretable circuits in LLMs, their causal origins in training data remain elusive. We introduce Mechanistic Data Attribution (MDA), a scalable framework that employs Influence Functions to trace interpretable units back to specific training samples. Through extensive experiments on the Pythia family, we causally validate that targeted intervention--removing or augmenting a small fraction of high-influence samples--significantly modulates the emergence of interpretable heads, whereas random interventions show no effect. Our analysis reveals that repetitive structural data (e.g., LaTeX, XML) acts as a mechanistic catalyst. Furthermore, we observe that interventions targeting induction head formation induce a concurrent change in the model's in-context learning (ICL) capability. This provides direct causal evidence for the long-standing hypothesis regarding the functional link between induction heads and ICL. Finally, we propose a mechanistic data augmentation pipeline that consistently accelerates circuit convergence across model scales, providing a principled methodology for steering the developmental trajectories of LLMs.

Causal inference is a critical task across fields such as healthcare, economics, and the social sciences. While recent advances in machine learning, especially those based on the deep-learning architectures, have shown potential in estimating causal effects, existing approaches often fall short in handling complex causal structures and lack adaptability across various causal scenarios. In this paper, we present a novel transformer-based method for causal inference that overcomes these challenges. The core innovation of our model lies in its integration of causal Directed Acyclic Graphs (DAGs) directly into the attention mechanism, enabling it to accurately model the underlying causal structure. This allows for flexible estimation of both average treatment effects (ATE) and conditional average treatment effects (CATE). Extensive experiments on both synthetic and real-world datasets demonstrate that our approach surpasses existing methods in estimating causal effects across a wide range of scenarios. The flexibility and robustness of our model make it a valuable tool for researchers and practitioners tackling complex causal inference problems.

While large language models (LLMs) show great potential in temporal reasoning, most existing work focuses heavily on enhancing performance, often neglecting the explainable reasoning processes underlying the results. To address this gap, we introduce a comprehensive benchmark covering a wide range of temporal granularities, designed to systematically evaluate LLMs' capabilities in explainable temporal reasoning. Furthermore, our findings reveal that LLMs struggle to deliver convincing explanations when relying solely on textual information. To address challenge, we propose GETER, a novel structure-aware generative framework that integrates Graph structures with text for Explainable TEmporal Reasoning. Specifically, we first leverage temporal knowledge graphs to develop a temporal encoder that captures structural information for the query. Subsequently, we introduce a structure-text prefix adapter to map graph structure features into the text embedding space. Finally, LLMs generate explanation text by seamlessly integrating the soft graph token with instruction-tuning prompt tokens. Experimental results indicate that GETER achieves state-of-the-art performance while also demonstrating its effectiveness as well as strong generalization capabilities. Our dataset and code are available at https://github.com/carryTatum/GETER.

Neural Temporal Point Processes (TPPs) are the prevalent paradigm for modeling continuous-time event sequences, such as user activities on the web and financial transactions. In real-world applications, event data is typically received in a streaming manner, where the distribution of patterns may shift over time. Additionally, privacy and memory constraints are commonly observed in practical scenarios, further compounding the challenges. Therefore, the continuous monitoring of a TPP to learn the streaming event sequence is an important yet under-explored problem. Our work paper addresses this challenge by adopting Continual Learning (CL), which makes the model capable of continuously learning a sequence of tasks without catastrophic forgetting under realistic constraints. Correspondingly, we propose a simple yet effective framework, PromptTPPOur code is available at {\small \url{ https://github.com/yanyanSann/PromptTPP}}, by integrating the base TPP with a continuous-time retrieval prompt pool. The prompts, small learnable parameters, are stored in a memory space and jointly optimized with the base TPP, ensuring that the model learns event streams sequentially without buffering past examples or task-specific attributes. We present a novel and realistic experimental setup for modeling event streams, where PromptTPP consistently achieves state-of-the-art performance across three real user behavior datasets.

Reasoning about time is of fundamental importance. Many facts are time-dependent. For example, athletes change teams from time to time, and different government officials are elected periodically. Previous time-dependent question answering (QA) datasets tend to be biased in either their coverage of time spans or question types. In this paper, we introduce a comprehensive probing dataset \tempreason to evaluate the temporal reasoning capability of large language models. Our dataset includes questions of three temporal reasoning levels. In addition, we also propose a novel learning framework to improve the temporal reasoning capability of large language models, based on temporal span extraction and time-sensitive reinforcement learning. We conducted experiments in closed book QA, open book QA, and reasoning QA settings and demonstrated the effectiveness of our approach. Our code and data are released on https://github.com/DAMO-NLP-SG/TempReason.

Key graph-based problems play a central role in understanding network topology and uncovering patterns of similarity in homogeneous and temporal data. Such patterns can be revealed by analyzing communities formed by nodes, which in turn can be effectively modeled through temporal k-cores. This paper introduces a novel decentralized and incremental algorithm for computing the core decomposition of temporal networks. Decentralized solutions leverage the ability of network nodes to communicate and coordinate locally, addressing complex problems in a scalable, adaptive, and timely manner. By leveraging previously computed coreness values, our approach significantly reduces the activation of nodes and the volume of message exchanges when the network changes over time. This enables scalability with only a minimal trade-off in precision. Experimental evaluations on large real-world networks under varying levels of dynamism demonstrate the efficiency of our solution compared to a state-of-the-art approach, particularly in terms of active nodes, communication overhead, and convergence speed.

Complex cell signaling systems -- governed by varying protein abundances and interactions -- generate diverse cell types across organs. These systems evolve under influences such as age, sex, diet, environmental exposures, and diseases, making them challenging to decode given the involvement of tens of thousands of genes and proteins. Recently, hundreds of millions of single-cell omics data have provided a robust foundation for understanding these signaling networks within various cell subpopulations and conditions. Inspired by the success of large foundation models (for example, large language models and large vision models) pre-trained on massive datasets, we introduce OmniCellTOSG, the first dataset of cell text-omic signaling graphs (TOSGs). Each TOSG represents the signaling network of an individual or meta-cell and is labeled with information such as organ, disease, sex, age, and cell subtype. OmniCellTOSG offers two key contributions. First, it introduces a novel graph model that integrates human-readable annotations -- such as biological functions, cellular locations, signaling pathways, related diseases, and drugs -- with quantitative gene and protein abundance data, enabling graph reasoning to decode cell signaling. This approach calls for new joint models combining large language models and graph neural networks. Second, the dataset is built from single-cell RNA sequencing data of approximately 120 million cells from diverse tissues and conditions (healthy and diseased) and is fully compatible with PyTorch. This facilitates the development of innovative cell signaling models that could transform research in life sciences, healthcare, and precision medicine. The OmniCellTOSG dataset is continuously expanding and will be updated regularly. The dataset and code are available at https://github.com/FuhaiLiAiLab/OmniCellTOSG.

Mechanistic Interpretability aims to reverse engineer the algorithms implemented by neural networks by studying their weights and activations. An obstacle to reverse engineering neural networks is that many of the parameters inside a network are not involved in the computation being implemented by the network. These degenerate parameters may obfuscate internal structure. Singular learning theory teaches us that neural network parameterizations are biased towards being more degenerate, and parameterizations with more degeneracy are likely to generalize further. We identify 3 ways that network parameters can be degenerate: linear dependence between activations in a layer; linear dependence between gradients passed back to a layer; ReLUs which fire on the same subset of datapoints. We also present a heuristic argument that modular networks are likely to be more degenerate, and we develop a metric for identifying modules in a network that is based on this argument. We propose that if we can represent a neural network in a way that is invariant to reparameterizations that exploit the degeneracies, then this representation is likely to be more interpretable, and we provide some evidence that such a representation is likely to have sparser interactions. We introduce the Interaction Basis, a tractable technique to obtain a representation that is invariant to degeneracies from linear dependence of activations or Jacobians.

Large language models (LLMs) are typically trained on fixed snapshots of the web, which means that their knowledge becomes stale and their predictions risk temporal leakage: relying on information that lies in the future relative to a query. We tackle this problem by pre-training from scratch a set of GPT-style experts on disjoint two-year slices of a 2013-2024 corpus and combining them through TiMoE, a Time-aware Mixture of Language Experts. At inference time, TiMoE masks all experts whose training window ends after the query timestamp and merges the remaining log-probabilities in a shared space, guaranteeing strict causal validity while retaining the breadth of multi-period knowledge. We also release TSQA, a 10k-question benchmark whose alternatives are explicitly labelled as past, future or irrelevant, allowing fine-grained measurement of temporal hallucinations. Experiments on eight standard NLP tasks plus TSQA show that a co-adapted TiMoE variant matches or exceeds the best single-period expert and cuts future-knowledge errors by up to 15%. Our results demonstrate that modular, time-segmented pre-training paired with causal routing is a simple yet effective path toward LLMs that stay chronologically grounded without sacrificing general performance much. We open source our code at TiMoE (Github): https://github.com/epfml/TiMoE