Daily Papers

The problem of community-level information pathway prediction (CLIPP) aims at predicting the transmission trajectory of content across online communities. A successful solution to CLIPP holds significance as it facilitates the distribution of valuable information to a larger audience and prevents the proliferation of misinformation. Notably, solving CLIPP is non-trivial as inter-community relationships and influence are unknown, information spread is multi-modal, and new content and new communities appear over time. In this work, we address CLIPP by collecting large-scale, multi-modal datasets to examine the diffusion of online YouTube videos on Reddit. We analyze these datasets to construct community influence graphs (CIGs) and develop a novel dynamic graph framework, INPAC (Information Pathway Across Online Communities), which incorporates CIGs to capture the temporal variability and multi-modal nature of video propagation across communities. Experimental results in both warm-start and cold-start scenarios show that INPAC outperforms seven baselines in CLIPP.

Multimodal learning significantly benefits cancer survival prediction, especially the integration of pathological images and genomic data. Despite advantages of multimodal learning for cancer survival prediction, massive redundancy in multimodal data prevents it from extracting discriminative and compact information: (1) An extensive amount of intra-modal task-unrelated information blurs discriminability, especially for gigapixel whole slide images (WSIs) with many patches in pathology and thousands of pathways in genomic data, leading to an ``intra-modal redundancy" issue. (2) Duplicated information among modalities dominates the representation of multimodal data, which makes modality-specific information prone to being ignored, resulting in an ``inter-modal redundancy" issue. To address these, we propose a new framework, Prototypical Information Bottlenecking and Disentangling (PIBD), consisting of Prototypical Information Bottleneck (PIB) module for intra-modal redundancy and Prototypical Information Disentanglement (PID) module for inter-modal redundancy. Specifically, a variant of information bottleneck, PIB, is proposed to model prototypes approximating a bunch of instances for different risk levels, which can be used for selection of discriminative instances within modality. PID module decouples entangled multimodal data into compact distinct components: modality-common and modality-specific knowledge, under the guidance of the joint prototypical distribution. Extensive experiments on five cancer benchmark datasets demonstrated our superiority over other methods.

We present the task of modeling information propagation in literature, in which we seek to identify pieces of information passing from character A to character B to character C, only given a description of their activity in text. We describe a new pipeline for measuring information propagation in this domain and publish a new dataset for speaker attribution, enabling the evaluation of an important component of this pipeline on a wider range of literary texts than previously studied. Using this pipeline, we analyze the dynamics of information propagation in over 5,000 works of fiction, finding that information flows through characters that fill structural holes connecting different communities, and that characters who are women are depicted as filling this role much more frequently than characters who are men.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

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.

The recent rise of Large Reasoning Models (LRMs) has significantly improved multi-step reasoning performance, but often at the cost of generating excessively long reasoning chains. This paper revisits the efficiency of such reasoning processes through an information-theoretic lens, revealing a fundamental trade-off between reasoning length and semantic efficiency. We propose two metrics, InfoBias and InfoGain, to quantify divergence from ideal reasoning paths and stepwise information contribution, respectively. Empirical analyses show that longer reasoning chains tend to exhibit higher information bias and diminishing information gain, especially for incorrect answers. Motivated by these findings, we introduce an entropy-based Adaptive Think strategy that dynamically halts reasoning once confidence is sufficiently high, improving efficiency while maintaining competitive accuracy. Compared to the Vanilla Think approach (default mode), our strategy yields a 1.10% improvement in average accuracy and a 50.80% reduction in token usage on QwQ-32B across six benchmark tasks spanning diverse reasoning types and difficulty levels, demonstrating superior efficiency and reasoning performance. These results underscore the promise of entropy-based methods for enhancing both accuracy and cost-effiiciency in large language model deployment.

Knowledge graph (KG) link prediction aims to infer new facts based on existing facts in the KG. Recent studies have shown that using the graph neighborhood of a node via graph neural networks (GNNs) provides more useful information compared to just using the query information. Conventional GNNs for KG link prediction follow the standard message-passing paradigm on the entire KG, which leads to superfluous computation, over-smoothing of node representations, and also limits their expressive power. On a large scale, it becomes computationally expensive to aggregate useful information from the entire KG for inference. To address the limitations of existing KG link prediction frameworks, we propose a novel retrieve-and-read framework, which first retrieves a relevant subgraph context for the query and then jointly reasons over the context and the query with a high-capacity reader. As part of our exemplar instantiation for the new framework, we propose a novel Transformer-based GNN as the reader, which incorporates graph-based attention structure and cross-attention between query and context for deep fusion. This simple yet effective design enables the model to focus on salient context information relevant to the query. Empirical results on two standard KG link prediction datasets demonstrate the competitive performance of the proposed method. Furthermore, our analysis yields valuable insights for designing improved retrievers within the framework.

Link prediction is a very fundamental task on graphs. Inspired by traditional path-based methods, in this paper we propose a general and flexible representation learning framework based on paths for link prediction. Specifically, we define the representation of a pair of nodes as the generalized sum of all path representations, with each path representation as the generalized product of the edge representations in the path. Motivated by the Bellman-Ford algorithm for solving the shortest path problem, we show that the proposed path formulation can be efficiently solved by the generalized Bellman-Ford algorithm. To further improve the capacity of the path formulation, we propose the Neural Bellman-Ford Network (NBFNet), a general graph neural network framework that solves the path formulation with learned operators in the generalized Bellman-Ford algorithm. The NBFNet parameterizes the generalized Bellman-Ford algorithm with 3 neural components, namely INDICATOR, MESSAGE and AGGREGATE functions, which corresponds to the boundary condition, multiplication operator, and summation operator respectively. The NBFNet is very general, covers many traditional path-based methods, and can be applied to both homogeneous graphs and multi-relational graphs (e.g., knowledge graphs) in both transductive and inductive settings. Experiments on both homogeneous graphs and knowledge graphs show that the proposed NBFNet outperforms existing methods by a large margin in both transductive and inductive settings, achieving new state-of-the-art results.

We present a foundation model-derived method to identify highly informative tokens and events in electronic health records. Our approach considers incoming data in the entire context of a patient's hospitalization and so can flag anomalous events that rule-based approaches would consider within a normal range. We demonstrate that the events our model flags are significant for predicting downstream patient outcomes and that a fraction of events identified as carrying little information can safely be dropped. Additionally, we show how informativeness can help interpret the predictions of prognostic models trained on foundation model-derived representations.

Information-seeking is a core capability for AI agents, requiring them to gather and reason over tool-generated information across long trajectories. However, such multi-step information-seeking tasks remain challenging for agents backed by language models. While process reward models (PRMs) can guide agents by ranking candidate steps at test-time, existing PRMs, designed for short reasoning with binary judgment, cannot capture richer dimensions of information-seeking steps, such as tool interactions and reasoning over tool outputs, nor handle the rapidly growing context in long-horizon tasks. To address these limitations, we introduce PRInTS, a generative PRM trained with dual capabilities: (1) dense scoring based on the PRM's reasoning across multiple step quality dimensions (e.g., interpretation of tool outputs, tool call informativeness) and (2) trajectory summarization that compresses the growing context while preserving essential information for step evaluation. Extensive evaluations across FRAMES, GAIA (levels 1-3), and WebWalkerQA (easy-hard) benchmarks on multiple models, along with ablations, reveal that best-of-n sampling with PRInTS enhances information-seeking abilities of open-source models as well as specialized agents, matching or surpassing the performance of frontier models with a much smaller backbone agent and outperforming other strong reward modeling baselines.

Transformers use the dense self-attention mechanism which gives a lot of flexibility for long-range connectivity. Over multiple layers of a deep transformer, the number of possible connectivity patterns increases exponentially. However, very few of these contribute to the performance of the network, and even fewer are essential. We hypothesize that there are sparsely connected sub-networks within a transformer, called information pathways which can be trained independently. However, the dynamic (i.e., input-dependent) nature of these pathways makes it difficult to prune dense self-attention during training. But the overall distribution of these pathways is often predictable. We take advantage of this fact to propose Stochastically Subsampled self-Attention (SSA) - a general-purpose training strategy for transformers that can reduce both the memory and computational cost of self-attention by 4 to 8 times during training while also serving as a regularization method - improving generalization over dense training. We show that an ensemble of sub-models can be formed from the subsampled pathways within a network, which can achieve better performance than its densely attended counterpart. We perform experiments on a variety of NLP, computer vision and graph learning tasks in both generative and discriminative settings to provide empirical evidence for our claims and show the effectiveness of the proposed method.

News articles are driven by the informational sources journalists use in reporting. Modeling when, how and why sources get used together in stories can help us better understand the information we consume and even help journalists with the task of producing it. In this work, we take steps toward this goal by constructing the largest and widest-ranging annotated dataset, to date, of informational sources used in news writing. We show that our dataset can be used to train high-performing models for information detection and source attribution. We further introduce a novel task, source prediction, to study the compositionality of sources in news articles. We show good performance on this task, which we argue is an important proof for narrative science exploring the internal structure of news articles and aiding in planning-based language generation, and an important step towards a source-recommendation system to aid journalists.

We automate deep step-by step reasoning in an LLM dialog thread by recursively exploring alternatives (OR-nodes) and expanding details (AND-nodes) up to a given depth. Starting from a single succinct task-specific initiator we steer the automated dialog thread to stay focussed on the task by synthesizing a prompt that summarizes the depth-first steps taken so far. Our algorithm is derived from a simple recursive descent implementation of a Horn Clause interpreter, except that we accommodate our logic engine to fit the natural language reasoning patterns LLMs have been trained on. Semantic similarity to ground-truth facts or oracle advice from another LLM instance is used to restrict the search space and validate the traces of justification steps returned as answers. At the end, the unique minimal model of a generated Horn Clause program collects the results of the reasoning process. As applications, we sketch implementations of consequence predictions, causal explanations, recommendation systems and topic-focussed exploration of scientific literature.

Given a node-attributed graph, and a graph task (link prediction or node classification), can we tell if a graph neural network (GNN) will perform well? More specifically, do the graph structure and the node features carry enough usable information for the task? Our goals are (1) to develop a fast tool to measure how much information is in the graph structure and in the node features, and (2) to exploit the information to solve the task, if there is enough. We propose NetInfoF, a framework including NetInfoF_Probe and NetInfoF_Act, for the measurement and the exploitation of network usable information (NUI), respectively. Given a graph data, NetInfoF_Probe measures NUI without any model training, and NetInfoF_Act solves link prediction and node classification, while two modules share the same backbone. In summary, NetInfoF has following notable advantages: (a) General, handling both link prediction and node classification; (b) Principled, with theoretical guarantee and closed-form solution; (c) Effective, thanks to the proposed adjustment to node similarity; (d) Scalable, scaling linearly with the input size. In our carefully designed synthetic datasets, NetInfoF correctly identifies the ground truth of NUI and is the only method being robust to all graph scenarios. Applied on real-world datasets, NetInfoF wins in 11 out of 12 times on link prediction compared to general GNN baselines.

Grokking, i.e., test performance keeps improving long after training loss converged, has been recently witnessed in neural network training, making the mechanism of generalization and other emerging capabilities such as reasoning mysterious. While prior studies usually train small models on a few toy or highly-specific tasks for thousands of epochs, we conduct the first study of grokking on checkpoints during one-pass pretraining of a 7B large language model (LLM), i.e., OLMoE. We compute the training loss and evaluate generalization on diverse benchmark tasks, including math reasoning, code generation, and commonsense/domain-specific knowledge retrieval tasks. Our study, for the first time, verifies that grokking still happens in the pretraining of large-scale foundation models, though different data may enter grokking stages asynchronously. We further demystify grokking's "emergence of generalization" by investigating LLM internal dynamics. Specifically, we find that training samples' pathways (i.e., expert choices across layers) evolve from random, instance-specific to more structured and shareable between samples during grokking. Also, the complexity of a sample's pathway reduces despite the converged loss. These indicate a memorization-to-generalization conversion, providing a mechanistic explanation of delayed generalization. In the study, we develop two novel metrics to quantify pathway distance and the complexity of a single pathway. We show their ability to predict the generalization improvement on diverse downstream tasks. They are efficient, simple to compute and solely dependent on training data. Hence, they have practical value for pretraining, enabling us to monitor the generalization performance without finetuning and test. Theoretically, we show that more structured pathways reduce model complexity and improve the generalization bound.

Large language model (LLM) routers improve the efficiency of multi-model systems by directing each query to the most appropriate model while leveraging the diverse strengths of heterogeneous LLMs. Most existing approaches frame routing as a classification problem based solely on the input query. While this reduces overhead by avoiding inference across all models, it overlooks valuable information that could be gleaned from potential outputs and fails to capture implicit intent or contextual nuances that often emerge only during response generation. These limitations can result in suboptimal routing decisions, particularly for complex or ambiguous queries that require deeper semantic understanding. To address this challenge, we propose Lookahead, a routing framework that "foresees" potential model outputs by predicting their latent representations and uses these predictions to guide model selection, thus enabling more informed routing without full inference. Within this framework, we implement two approaches based on causal and masked language models. Empirical evaluations across seven public benchmarks - spanning instruction following, mathematical reasoning, and code generation - show that Lookahead consistently outperforms existing routing baselines, achieving an average performance gain of 7.7% over the state-of-the-art. Our code is available at https://github.com/huangcb01/lookahead-routing.

Large language models are limited by challenges in factuality and hallucinations to be directly employed off-the-shelf for judging the veracity of news articles, where factual accuracy is paramount. In this work, we propose DELL that identifies three key stages in misinformation detection where LLMs could be incorporated as part of the pipeline: 1) LLMs could generate news reactions to represent diverse perspectives and simulate user-news interaction networks; 2) LLMs could generate explanations for proxy tasks (e.g., sentiment, stance) to enrich the contexts of news articles and produce experts specializing in various aspects of news understanding; 3) LLMs could merge task-specific experts and provide an overall prediction by incorporating the predictions and confidence scores of varying experts. Extensive experiments on seven datasets with three LLMs demonstrate that DELL outperforms state-of-the-art baselines by up to 16.8\% in macro f1-score. Further analysis reveals that the generated reactions and explanations are greatly helpful in misinformation detection, while our proposed LLM-guided expert merging helps produce better-calibrated predictions.

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.

Large reasoning models (LRMs) have demonstrated impressive capabilities in complex problem-solving, yet their internal reasoning mechanisms remain poorly understood. In this paper, we investigate the reasoning trajectories of LRMs from an information-theoretic perspective. By tracking how mutual information (MI) between intermediate representations and the correct answer evolves during LRM reasoning, we observe an interesting MI peaks phenomenon: the MI at specific generative steps exhibits a sudden and significant increase during LRM's reasoning process. We theoretically analyze such phenomenon and show that as MI increases, the probability of model's prediction error decreases. Furthermore, these MI peaks often correspond to tokens expressing reflection or transition, such as ``Hmm'', ``Wait'' and ``Therefore,'' which we term as the thinking tokens. We then demonstrate that these thinking tokens are crucial for LRM's reasoning performance, while other tokens has minimal impacts. Building on these analyses, we propose two simple yet effective methods to improve LRM's reasoning performance, by delicately leveraging these thinking tokens. Overall, our work provides novel insights into the reasoning mechanisms of LRMs and offers practical ways to improve their reasoning capabilities. The code is available at https://github.com/ChnQ/MI-Peaks.

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.

Large language models (LLMs) have demonstrated remarkable capabilities in various complex tasks, yet they still suffer from hallucinations. Introducing external knowledge, such as knowledge graph, can enhance the LLMs' ability to provide factual answers. LLMs have the ability to interactively explore knowledge graphs. However, most approaches have been affected by insufficient internal knowledge excavation in LLMs, limited generation of trustworthy knowledge reasoning paths, and a vague integration between internal and external knowledge. Therefore, we propose KnowPath, a knowledge-enhanced large model framework driven by the collaboration of internal and external knowledge. It relies on the internal knowledge of the LLM to guide the exploration of interpretable directed subgraphs in external knowledge graphs, better integrating the two knowledge sources for more accurate reasoning. Extensive experiments on multiple real-world datasets confirm the superiority of KnowPath.

Large Language Models (LLMs) have shown impressive performance in complex reasoning tasks through Chain-of-Thought (CoT) reasoning, allowing models to break down problems into manageable sub-tasks. However, existing CoT evaluation techniques either require annotated CoT data or fall short in accurately assessing intermediate reasoning steps, leading to high rates of false positives. In this paper, we formalize CoT reasoning in LLMs through an information-theoretic lens. Specifically, our framework quantifies the `information gain' at each reasoning step, enabling the identification of failure modes in LLMs without the need for expensive annotated datasets. We demonstrate the efficacy of our approach through extensive experiments on toy and GSM-8K data, where it significantly outperforms existing outcome-based methods by providing more accurate insights into model performance on individual tasks.

A significant use case of instruction-finetuned Large Language Models (LLMs) is to solve question-answering tasks interactively. In this setting, an LLM agent is tasked with making a prediction by sequentially querying relevant information from the user, as opposed to a single-turn conversation. This paper explores sequential querying strategies that aim to minimize the expected number of queries. One such strategy is Information Pursuit (IP), a greedy algorithm that at each iteration selects the query that maximizes information gain or equivalently minimizes uncertainty. However, obtaining accurate estimates of mutual information or conditional entropy for LLMs is very difficult in practice due to over- or under-confident LLM probabilities, which leads to suboptimal query selection and predictive performance. To better estimate the uncertainty at each iteration, we propose Conformal Information Pursuit (C-IP), an alternative approach to sequential information gain based on conformal prediction sets. More specifically, C-IP leverages a relationship between prediction sets and conditional entropy at each iteration to estimate uncertainty based on the average size of conformal prediction sets. In contrast to conditional entropy, we find that conformal prediction sets are a distribution-free and robust method of measuring uncertainty. Experiments with 20 Questions show that C-IP obtains better predictive performance and shorter query-answer chains compared to previous approaches to IP and uncertainty-based chain-of-thought methods. Furthermore, extending to an interactive medical setting between a doctor and a patient on the MediQ dataset, C-IP achieves competitive performance with direct single-turn prediction while offering greater interpretability.

We introduce a pattern mining framework that operates on semi-structured datasets and exploits the dichotomy between outcomes. Our approach takes advantage of constraint reasoning to find sequential patterns that occur frequently and exhibit desired properties. This allows the creation of novel pattern embeddings that are useful for knowledge extraction and predictive modeling. Finally, we present an application on customer intent prediction from digital clickstream data. Overall, we show that pattern embeddings play an integrator role between semi-structured data and machine learning models, improve the performance of the downstream task and retain interpretability.

The impact of person-job fit on job satisfaction and performance is widely acknowledged, which highlights the importance of providing workers with next steps at the right time in their career. This task of predicting the next step in a career is known as career path prediction, and has diverse applications such as turnover prevention and internal job mobility. Existing methods to career path prediction rely on large amounts of private career history data to model the interactions between job titles and companies. We propose leveraging the unexplored textual descriptions that are part of work experience sections in resumes. We introduce a structured dataset of 2,164 anonymized career histories, annotated with ESCO occupation labels. Based on this dataset, we present a novel representation learning approach, CareerBERT, specifically designed for work history data. We develop a skill-based model and a text-based model for career path prediction, which achieve 35.24% and 39.61% recall@10 respectively on our dataset. Finally, we show that both approaches are complementary as a hybrid approach achieves the strongest result with 43.01% recall@10.

The GPT-4 technical report suggests that downstream performance can be predicted from pre-training signals, but offers little methodological detail on how to quantify this. This work address this gap by modeling knowledge retention, the capacity of a pre-trained language model to memorize factual information from its corpus, and introduce a principled method to estimate it prior to training. We propose Size-dependent Mutual Information (SMI), an information-theoretic predictor that integrates knowledge frequency, knowledge specificity, and model size to forecast closed-book question answering (QA) accuracy. SMI is validated through large-scale document retrieval over the disclosed pre-training corpora of 21 public and 3 custom models, combined with a robust multi-template QA evaluation. Experiments show that SMI significantly outperforms repetition-based baselines and achieves R^2 > 0.7 in predicting QA accuracy for models above 1B parameters, without additional training. The analysis further reveals diminishing returns from scaling data and model size and provides evidence for an intrinsic upper bound on knowledge retention achievable by pre-training alone, motivating retrieval and other augmentation strategies.

Large language models (LLMs) have made remarkable strides in various natural language processing tasks, but their performance on complex reasoning problems remains hindered by a lack of explainability and trustworthiness. This issue, often manifesting as hallucinations or unattributable reasoning processes, limits their applicability in complex reasoning scenarios. To address this, we propose Knowledge Graph-constrained Trajectory Reasoning Attribution and Chain Explanation Supervision (KG-TRACES), a novel framework that enhances the reasoning ability of LLMs through explicit supervision over reasoning paths and processes. KG-TRACES jointly supervises the model to: (1) predict symbolic relation paths, (2) predict full triple-level reasoning paths, and (3) generate attribution-aware reasoning processes grounded in the reasoning paths. At inference phase, the model adapts to both KG-available and KG-unavailable scenarios, retrieving reasoning paths from a KG when possible or predicting plausible reasoning paths with only intrinsic knowledge when not. This design enables the model to reason in an explainable and source-attributable pattern. Through extensive experiments on complex reasoning tasks, we demonstrate that KG-TRACES significantly outperforms existing SOTA: it improves Hits@1 by 1.6% and F1 by 4.7% on WebQSP, and achieves improvements of 4.8% in Hits@1 and 2.1% in F1 on CWQ. Moreover, we show its transferability to specialized domains such as medicine. By visualizing the intermediate steps of reasoning processes, we further show that the explicit supervision introduced by KG-TRACES leads to more stable and goal-directed reasoning processes, aligning closely with correct answers. Code is available at https://github.com/Edaizi/KG-TRACES.

Background: Electronic Health Records hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Existing approaches focus mostly on structured data and a subset of single-domain outcomes. We explore how temporal modelling of patients from free text and structured data, using deep generative transformers can be used to forecast a wide range of future disorders, substances, procedures or findings. Methods: We present Foresight, a novel transformer-based pipeline that uses named entity recognition and linking tools to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, substances, procedures and findings. We processed the entire free-text portion from three different hospital datasets totalling 811336 patients covering both physical and mental health. Findings: On tests in two UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 0.68, 0.76 and 0.88 was achieved for forecasting the next disorder in a patient timeline, while precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by five clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. As a generative model, it can forecast follow-on biomedical concepts for as many steps as required. Interpretation: Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials and clinical research to study the progression of disorders, simulate interventions and counterfactuals, and educational purposes.

Predicting highly-cited papers is a long-standing challenge due to the complex interactions of research content, scholarly communities, and temporal dynamics. Recent advances in large language models (LLMs) raise the question of whether early-stage textual information can provide useful signals of long-term scientific impact. Focusing on statistical publications, we propose a flexible, text-centered framework that leverages LLMs and structured prompt design to predict highly cited papers. Specifically, we utilize information available at the time of publication, including titles, abstracts, keywords, and limited bibliographic metadata. Using a large corpus of statistical papers, we evaluate predictive performance across multiple publication periods and alternative definitions of highly cited papers. The proposed approach achieves stable and competitive performance relative to existing methods and demonstrates strong generalization over time. Textual analysis further reveals that papers predicted as highly cited concentrate on recurring topics such as causal inference and deep learning. To facilitate practical use of the proposed approach, we further develop a WeChat mini program, Stat Highly Cited Papers, which provides an accessible interface for early-stage citation impact assessment. Overall, our results provide empirical evidence that LLMs can capture meaningful early signals of long-term citation impact, while also highlighting their limitations as tools for research impact assessment.

This paper studies the problem of embedding very large information networks into low-dimensional vector spaces, which is useful in many tasks such as visualization, node classification, and link prediction. Most existing graph embedding methods do not scale for real world information networks which usually contain millions of nodes. In this paper, we propose a novel network embedding method called the "LINE," which is suitable for arbitrary types of information networks: undirected, directed, and/or weighted. The method optimizes a carefully designed objective function that preserves both the local and global network structures. An edge-sampling algorithm is proposed that addresses the limitation of the classical stochastic gradient descent and improves both the effectiveness and the efficiency of the inference. Empirical experiments prove the effectiveness of the LINE on a variety of real-world information networks, including language networks, social networks, and citation networks. The algorithm is very efficient, which is able to learn the embedding of a network with millions of vertices and billions of edges in a few hours on a typical single machine. The source code of the LINE is available online.

Target-guided open-domain conversation aims to proactively and naturally guide a dialogue agent or human to achieve specific goals, topics or keywords during open-ended conversations. Existing methods mainly rely on single-turn datadriven learning and simple target-guided strategy without considering semantic or factual knowledge relations among candidate topics/keywords. This results in poor transition smoothness and low success rate. In this work, we adopt a structured approach that controls the intended content of system responses by introducing coarse-grained keywords, attains smooth conversation transition through turn-level supervised learning and knowledge relations between candidate keywords, and drives an conversation towards an specified target with discourse-level guiding strategy. Specially, we propose a novel dynamic knowledge routing network (DKRN) which considers semantic knowledge relations among candidate keywords for accurate next topic prediction of next discourse. With the help of more accurate keyword prediction, our keyword-augmented response retrieval module can achieve better retrieval performance and more meaningful conversations. Besides, we also propose a novel dual discourse-level target-guided strategy to guide conversations to reach their goals smoothly with higher success rate. Furthermore, to push the research boundary of target-guided open-domain conversation to match real-world scenarios better, we introduce a new large-scale Chinese target-guided open-domain conversation dataset (more than 900K conversations) crawled from Sina Weibo. Quantitative and human evaluations show our method can produce meaningful and effective target-guided conversations, significantly improving over other state-of-the-art methods by more than 20% in success rate and more than 0.6 in average smoothness score.

Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.

Knowledge graphs enable a wide variety of applications, including question answering and information retrieval. Despite the great effort invested in their creation and maintenance, even the largest (e.g., Yago, DBPedia or Wikidata) remain incomplete. We introduce Relational Graph Convolutional Networks (R-GCNs) and apply them to two standard knowledge base completion tasks: Link prediction (recovery of missing facts, i.e. subject-predicate-object triples) and entity classification (recovery of missing entity attributes). R-GCNs are related to a recent class of neural networks operating on graphs, and are developed specifically to deal with the highly multi-relational data characteristic of realistic knowledge bases. We demonstrate the effectiveness of R-GCNs as a stand-alone model for entity classification. We further show that factorization models for link prediction such as DistMult can be significantly improved by enriching them with an encoder model to accumulate evidence over multiple inference steps in the relational graph, demonstrating a large improvement of 29.8% on FB15k-237 over a decoder-only baseline.

Graph neural networks achieve high accuracy in link prediction by jointly leveraging graph topology and node attributes. Topology, however, is represented indirectly; state-of-the-art methods based on subgraph classification label nodes with distance to the target link, so that, although topological information is present, it is tempered by pooling. This makes it challenging to leverage features like loops and motifs associated with network formation mechanisms. We propose a link prediction algorithm based on a new pooling scheme called WalkPool. WalkPool combines the expressivity of topological heuristics with the feature-learning ability of neural networks. It summarizes a putative link by random walk probabilities of adjacent paths. Instead of extracting transition probabilities from the original graph, it computes the transition matrix of a "predictive" latent graph by applying attention to learned features; this may be interpreted as feature-sensitive topology fingerprinting. WalkPool can leverage unsupervised node features or be combined with GNNs and trained end-to-end. It outperforms state-of-the-art methods on all common link prediction benchmarks, both homophilic and heterophilic, with and without node attributes. Applying WalkPool to a set of unsupervised GNNs significantly improves prediction accuracy, suggesting that it may be used as a general-purpose graph pooling scheme.

Knowledge Graph (KG) reasoning, which aims to infer new facts from structured knowledge repositories, plays a vital role in Natural Language Processing (NLP) systems. Its effectiveness critically depends on constructing informative and contextually relevant reasoning paths. However, existing graph neural networks (GNNs) often adopt rigid, query-agnostic path-exploration strategies, limiting their ability to adapt to diverse linguistic contexts and semantic nuances. To address these limitations, we propose MoKGR, a mixture-of-experts framework that personalizes path exploration through two complementary components: (1) a mixture of length experts that adaptively selects and weights candidate path lengths according to query complexity, providing query-specific reasoning depth; and (2) a mixture of pruning experts that evaluates candidate paths from a complementary perspective, retaining the most informative paths for each query. Through comprehensive experiments on diverse benchmark, MoKGR demonstrates superior performance in both transductive and inductive settings, validating the effectiveness of personalized path exploration in KGs reasoning.

Misinformation is a complex societal issue, and mitigating solutions are difficult to create due to data deficiencies. To address this problem, we have curated the largest collection of (mis)information datasets in the literature, totaling 75. From these, we evaluated the quality of all of the 36 datasets that consist of statements or claims. We assess these datasets to identify those with solid foundations for empirical work and those with flaws that could result in misleading and non-generalizable results, such as insufficient label quality, spurious correlations, or political bias. We further provide state-of-the-art baselines on all these datasets, but show that regardless of label quality, categorical labels may no longer give an accurate evaluation of detection model performance. We discuss alternatives to mitigate this problem. Overall, this guide aims to provide a roadmap for obtaining higher quality data and conducting more effective evaluations, ultimately improving research in misinformation detection. All datasets and other artifacts are available at https://misinfo-datasets.complexdatalab.com/.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

As a primary means of information acquisition, information retrieval (IR) systems, such as search engines, have integrated themselves into our daily lives. These systems also serve as components of dialogue, question-answering, and recommender systems. The trajectory of IR has evolved dynamically from its origins in term-based methods to its integration with advanced neural models. While the neural models excel at capturing complex contextual signals and semantic nuances, thereby reshaping the IR landscape, they still face challenges such as data scarcity, interpretability, and the generation of contextually plausible yet potentially inaccurate responses. This evolution requires a combination of both traditional methods (such as term-based sparse retrieval methods with rapid response) and modern neural architectures (such as language models with powerful language understanding capacity). Meanwhile, the emergence of large language models (LLMs), typified by ChatGPT and GPT-4, has revolutionized natural language processing due to their remarkable language understanding, generation, generalization, and reasoning abilities. Consequently, recent research has sought to leverage LLMs to improve IR systems. Given the rapid evolution of this research trajectory, it is necessary to consolidate existing methodologies and provide nuanced insights through a comprehensive overview. In this survey, we delve into the confluence of LLMs and IR systems, including crucial aspects such as query rewriters, retrievers, rerankers, and readers. Additionally, we explore promising directions within this expanding field.

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.

Pretrained transformers achieve the state of the art across tasks in natural language processing, motivating researchers to investigate their inner mechanisms. One common direction is to understand what features are important for prediction. In this paper, we apply information bottlenecks to analyze the attribution of each feature for prediction on a black-box model. We use BERT as the example and evaluate our approach both quantitatively and qualitatively. We show the effectiveness of our method in terms of attribution and the ability to provide insight into how information flows through layers. We demonstrate that our technique outperforms two competitive methods in degradation tests on four datasets. Code is available at https://github.com/bazingagin/IBA.

Generative retrieval has recently emerged as a new alternative of traditional information retrieval approaches. However, existing generative retrieval methods directly decode docid when a query is given, making it impossible to provide users with explanations as an answer for "Why this document is retrieved?". To address this limitation, we propose Hierarchical Category Path-Enhanced Generative Retrieval(HyPE), which enhances explainability by generating hierarchical category paths step-by-step before decoding docid. HyPE leverages hierarchical category paths as explanation, progressing from broad to specific semantic categories. This approach enables diverse explanations for the same document depending on the query by using shared category paths between the query and the document, and provides reasonable explanation by reflecting the document's semantic structure through a coarse-to-fine manner. HyPE constructs category paths with external high-quality semantic hierarchy, leverages LLM to select appropriate candidate paths for each document, and optimizes the generative retrieval model with path-augmented dataset. During inference, HyPE utilizes path-aware reranking strategy to aggregate diverse topic information, allowing the most relevant documents to be prioritized in the final ranked list of docids. Our extensive experiments demonstrate that HyPE not only offers a high level of explainability but also improves the retrieval performance in the document retrieval task.

Unsupervised keyphrase prediction has gained growing interest in recent years. However, existing methods typically rely on heuristically defined importance scores, which may lead to inaccurate informativeness estimation. In addition, they lack consideration for time efficiency. To solve these problems, we propose ERU-KG, an unsupervised keyphrase generation (UKG) model that consists of an informativeness and a phraseness module. The former estimates the relevance of keyphrase candidates, while the latter generate those candidates. The informativeness module innovates by learning to model informativeness through references (e.g., queries, citation contexts, and titles) and at the term-level, thereby 1) capturing how the key concepts of documents are perceived in different contexts and 2) estimating informativeness of phrases more efficiently by aggregating term informativeness, removing the need for explicit modeling of the candidates. ERU-KG demonstrates its effectiveness on keyphrase generation benchmarks by outperforming unsupervised baselines and achieving on average 89\% of the performance of a supervised model for top 10 predictions. Additionally, to highlight its practical utility, we evaluate the model on text retrieval tasks and show that keyphrases generated by ERU-KG are effective when employed as query and document expansions. Furthermore, inference speed tests reveal that ERU-KG is the fastest among baselines of similar model sizes. Finally, our proposed model can switch between keyphrase generation and extraction by adjusting hyperparameters, catering to diverse application requirements.

Large language models (LLMs), such as ChatGPT and GPT4, are making new waves in the field of natural language processing and artificial intelligence, due to their emergent ability and generalizability. However, LLMs are black-box models, which often fall short of capturing and accessing factual knowledge. In contrast, Knowledge Graphs (KGs), Wikipedia and Huapu for example, are structured knowledge models that explicitly store rich factual knowledge. KGs can enhance LLMs by providing external knowledge for inference and interpretability. Meanwhile, KGs are difficult to construct and evolving by nature, which challenges the existing methods in KGs to generate new facts and represent unseen knowledge. Therefore, it is complementary to unify LLMs and KGs together and simultaneously leverage their advantages. In this article, we present a forward-looking roadmap for the unification of LLMs and KGs. Our roadmap consists of three general frameworks, namely, 1) KG-enhanced LLMs, which incorporate KGs during the pre-training and inference phases of LLMs, or for the purpose of enhancing understanding of the knowledge learned by LLMs; 2) LLM-augmented KGs, that leverage LLMs for different KG tasks such as embedding, completion, construction, graph-to-text generation, and question answering; and 3) Synergized LLMs + KGs, in which LLMs and KGs play equal roles and work in a mutually beneficial way to enhance both LLMs and KGs for bidirectional reasoning driven by both data and knowledge. We review and summarize existing efforts within these three frameworks in our roadmap and pinpoint their future research directions.

The task of Legal Statute Identification (LSI) aims to identify the legal statutes that are relevant to a given description of Facts or evidence of a legal case. Existing methods only utilize the textual content of Facts and legal articles to guide such a task. However, the citation network among case documents and legal statutes is a rich source of additional information, which is not considered by existing models. In this work, we take the first step towards utilising both the text and the legal citation network for the LSI task. We curate a large novel dataset for this task, including Facts of cases from several major Indian Courts of Law, and statutes from the Indian Penal Code (IPC). Modeling the statutes and training documents as a heterogeneous graph, our proposed model LeSICiN can learn rich textual and graphical features, and can also tune itself to correlate these features. Thereafter, the model can be used to inductively predict links between test documents (new nodes whose graphical features are not available to the model) and statutes (existing nodes). Extensive experiments on the dataset show that our model comfortably outperforms several state-of-the-art baselines, by exploiting the graphical structure along with textual features. The dataset and our codes are available at https://github.com/Law-AI/LeSICiN.

Knowledge Graphs (KG) are of vital importance for multiple applications on the web, including information retrieval, recommender systems, and metadata annotation. Regardless of whether they are built manually by domain experts or with automatic pipelines, KGs are often incomplete. Recent work has begun to explore the use of textual descriptions available in knowledge graphs to learn vector representations of entities in order to preform link prediction. However, the extent to which these representations learned for link prediction generalize to other tasks is unclear. This is important given the cost of learning such representations. Ideally, we would prefer representations that do not need to be trained again when transferring to a different task, while retaining reasonable performance. In this work, we propose a holistic evaluation protocol for entity representations learned via a link prediction objective. We consider the inductive link prediction and entity classification tasks, which involve entities not seen during training. We also consider an information retrieval task for entity-oriented search. We evaluate an architecture based on a pretrained language model, that exhibits strong generalization to entities not observed during training, and outperforms related state-of-the-art methods (22% MRR improvement in link prediction on average). We further provide evidence that the learned representations transfer well to other tasks without fine-tuning. In the entity classification task we obtain an average improvement of 16% in accuracy compared with baselines that also employ pre-trained models. In the information retrieval task, we obtain significant improvements of up to 8.8% in NDCG@10 for natural language queries. We thus show that the learned representations are not limited KG-specific tasks, and have greater generalization properties than evaluated in previous work.

Diffusion models have garnered considerable interest in the field of text generation. Several studies have explored text diffusion models with different structures and applied them to various tasks, including named entity recognition and summarization. However, there exists a notable disparity between the "easy-first" text generation process of current diffusion models and the "keyword-first" natural text generation process of humans, which has received limited attention. To bridge this gap, we propose InfoDiffusion, a non-autoregressive text diffusion model. Our approach introduces a "keyinfo-first" generation strategy and incorporates a noise schedule based on the amount of text information. In addition, InfoDiffusion combines self-conditioning with a newly proposed partially noising model structure. Experimental results show that InfoDiffusion outperforms the baseline model in terms of generation quality and diversity, as well as exhibiting higher sampling efficiency.

We discovered the underlying physics in Next-token Prediction (NTP). We identified the law of information conservation within NTP and proposed the First Law of Information Capacity (IC-1), demonstrating that the essence of intelligence emergence in auto-regressive models is fundamentally a process of information transfer. We also introduced Landauer's Principle into NTP, formulating the Second Law of Information Capacity (IC-2), which establishes the relationship between auto-regressive model training and energy consumption. Additionally, we presented several corollaries, which hold practical significance for production practices. Finally, we validated the compatibility and complementarity of our findings with existing theories.

To deduce new facts on a knowledge graph (KG), a link predictor learns from the graph structure and collects local evidence to find the answer to a given query. However, existing methods suffer from a severe scalability problem due to the utilization of the whole KG for prediction, which hinders their promise on large scale KGs and cannot be directly addressed by vanilla sampling methods. In this work, we propose the one-shot-subgraph link prediction to achieve efficient and adaptive prediction. The design principle is that, instead of directly acting on the whole KG, the prediction procedure is decoupled into two steps, i.e., (i) extracting only one subgraph according to the query and (ii) predicting on this single, query dependent subgraph. We reveal that the non-parametric and computation-efficient heuristics Personalized PageRank (PPR) can effectively identify the potential answers and supporting evidence. With efficient subgraph-based prediction, we further introduce the automated searching of the optimal configurations in both data and model spaces. Empirically, we achieve promoted efficiency and leading performances on five large-scale benchmarks. The code is publicly available at: https://github.com/tmlr-group/one-shot-subgraph.

Large language models' significant advances in capabilities are accompanied by significant increases in inference costs. Model routing is a simple technique for reducing inference cost, wherein one maintains a pool of candidate LLMs, and learns to route each prompt to the smallest feasible LLM. Existing works focus on learning a router for a fixed pool of LLMs. In this paper, we consider the problem of dynamic routing, where new, previously unobserved LLMs are available at test time. We propose a new approach to this problem that relies on representing each LLM as a feature vector, derived based on predictions on a set of representative prompts. Based on this, we detail two effective strategies, relying on cluster-based routing and a learned cluster map respectively. We prove that these strategies are estimates of a theoretically optimal routing rule, and provide an excess risk bound to quantify their errors. Experiments on a range of public benchmarks show the effectiveness of the proposed strategies in routing amongst more than 30 unseen LLMs.

The widespread adoption of large language models (LLMs) makes it important to recognize their strengths and limitations. We argue that in order to develop a holistic understanding of these systems we need to consider the problem that they were trained to solve: next-word prediction over Internet text. By recognizing the pressures that this task exerts we can make predictions about the strategies that LLMs will adopt, allowing us to reason about when they will succeed or fail. This approach - which we call the teleological approach - leads us to identify three factors that we hypothesize will influence LLM accuracy: the probability of the task to be performed, the probability of the target output, and the probability of the provided input. We predict that LLMs will achieve higher accuracy when these probabilities are high than when they are low - even in deterministic settings where probability should not matter. To test our predictions, we evaluate two LLMs (GPT-3.5 and GPT-4) on eleven tasks, and we find robust evidence that LLMs are influenced by probability in the ways that we have hypothesized. In many cases, the experiments reveal surprising failure modes. For instance, GPT-4's accuracy at decoding a simple cipher is 51% when the output is a high-probability word sequence but only 13% when it is low-probability. These results show that AI practitioners should be careful about using LLMs in low-probability situations. More broadly, we conclude that we should not evaluate LLMs as if they are humans but should instead treat them as a distinct type of system - one that has been shaped by its own particular set of pressures.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

Online misinformation poses an escalating threat, amplified by the Internet's open nature and increasingly capable LLMs that generate persuasive yet deceptive content. Existing misinformation detection methods typically focus on either textual content or network structure in isolation, failing to leverage the rich, dynamic interplay between website content and hyperlink relationships that characterizes real-world misinformation ecosystems. We introduce CrediBench: a large-scale data processing pipeline for constructing temporal web graphs that jointly model textual content and hyperlink structure for misinformation detection. Unlike prior work, our approach captures the dynamic evolution of general misinformation domains, including changes in both content and inter-site references over time. Our processed one-month snapshot extracted from the Common Crawl archive in December 2024 contains 45 million nodes and 1 billion edges, representing the largest web graph dataset made publicly available for misinformation research to date. From our experiments on this graph snapshot, we demonstrate the strength of both structural and webpage content signals for learning credibility scores, which measure source reliability. The pipeline and experimentation code are all available here, and the dataset is in this folder.

Large language models (LLMs) have demonstrated remarkable capabilities in numerous real-world applications. While the vast majority of research conducted from an experimental perspective is progressing rapidly, it demands substantial computational power, data, and other resources. Therefore, how to open the black-box of LLMs from a theoretical standpoint has become a critical challenge. This paper takes the theory of rate-distortion function, directed information, and Granger causality as its starting point to investigate the information-theoretic principles behind LLMs, leading to the development of semantic information theory for LLMs, where the fundamental unit is token, rather than bits that lacks any semantic meaning. By defining the probabilistic model of LLMs, we discuss structure-agnostic information-theoretic measures, such as the directed rate-distortion function in pre-training, the directed rate-reward function in post-training, and the semantic information flow in inference phase. This paper also delves deeply into the theory of token-level semantic embedding and the information-theoretically optimal vectorization method. Thereafter, we propose a general definition of autoregression LLM, where the Transformer architecture and its performance such as ELBO, generalization error bound, memory capacity, and semantic information measures can be derived theoretically. Other architectures, such as Mamba/Mamba2 and LLaDA, are also discussed in our framework. Consequently, this paper provides a theoretical framework for understanding LLMs from the perspective of semantic information theory, which also offers the necessary theoretical tools for further in-depth research.

This paper proposes a novel framework to predict traffic flows' bandwidth ahead of time. Modern network management systems share a common issue: the network situation evolves between the moment the decision is made and the moment when actions (countermeasures) are applied. This framework converts packets from real-life traffic into flows containing relevant features. Machine learning models, including Decision Tree, Random Forest, XGBoost, and Deep Neural Network, are trained on these data to predict the bandwidth at the next time instance for every flow. Predictions can be fed to the management system instead of current flows bandwidth in order to take decisions on a more accurate network state. Experiments were performed on 981,774 flows and 15 different time windows (from 0.03s to 4s). They show that the Random Forest is the best performing and most reliable model, with a predictive performance consistently better than relying on the current bandwidth (+19.73% in mean absolute error and +18.00% in root mean square error). Experimental results indicate that this framework can help network management systems to take more informed decisions using a predicted network state.

Vision Transformer models exhibit immense power yet remain opaque to human understanding, posing challenges and risks for practical applications. While prior research has attempted to demystify these models through input attribution and neuron role analysis, there's been a notable gap in considering layer-level information and the holistic path of information flow across layers. In this paper, we investigate the significance of influential neuron paths within vision Transformers, which is a path of neurons from the model input to output that impacts the model inference most significantly. We first propose a joint influence measure to assess the contribution of a set of neurons to the model outcome. And we further provide a layer-progressive neuron locating approach that efficiently selects the most influential neuron at each layer trying to discover the crucial neuron path from input to output within the target model. Our experiments demonstrate the superiority of our method finding the most influential neuron path along which the information flows, over the existing baseline solutions. Additionally, the neuron paths have illustrated that vision Transformers exhibit some specific inner working mechanism for processing the visual information within the same image category. We further analyze the key effects of these neurons on the image classification task, showcasing that the found neuron paths have already preserved the model capability on downstream tasks, which may also shed some lights on real-world applications like model pruning. The project website including implementation code is available at https://foundation-model-research.github.io/NeuronPath/.

Adapting medical Large Language Models to local languages can reduce barriers to accessing healthcare services, but data scarcity remains a significant challenge, particularly for low-resource languages. To address this, we first construct a high-quality medical dataset and conduct analysis to ensure its quality. In order to leverage the generalization capability of multilingual LLMs to efficiently scale to more resource-constrained languages, we explore the internal information flow of LLMs from a multilingual perspective using Mixture of Experts (MoE) modularity. Technically, we propose a novel MoE routing method that employs language-specific experts and cross-lingual routing. Inspired by circuit theory, our routing analysis revealed a Spread Out in the End information flow mechanism: while earlier layers concentrate cross-lingual information flow, the later layers exhibit language-specific divergence. This insight directly led to the development of the Post-MoE architecture, which applies sparse routing only in the later layers while maintaining dense others. Experimental results demonstrate that this approach enhances the generalization of multilingual models to other languages while preserving interpretability. Finally, to efficiently scale the model to 50 languages, we introduce the concept of language family experts, drawing on linguistic priors, which enables scaling the number of languages without adding additional parameters.

Backpropagation, which uses the chain rule, is the de-facto standard algorithm for optimizing neural networks nowadays. Recently, Hinton (2022) proposed the forward-forward algorithm, a promising alternative that optimizes neural nets layer-by-layer, without propagating gradients throughout the network. Although such an approach has several advantages over back-propagation and shows promising results, the fact that each layer is being trained independently limits the optimization process. Specifically, it prevents the network's layers from collaborating to learn complex and rich features. In this work, we study layer collaboration in the forward-forward algorithm. We show that the current version of the forward-forward algorithm is suboptimal when considering information flow in the network, resulting in a lack of collaboration between layers of the network. We propose an improved version that supports layer collaboration to better utilize the network structure, while not requiring any additional assumptions or computations. We empirically demonstrate the efficacy of the proposed version when considering both information flow and objective metrics. Additionally, we provide a theoretical motivation for the proposed method, inspired by functional entropy theory.

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

In this work, we conceptualize the learning process as information compression. We seek to equip generative pre-trained models with human-like learning capabilities that enable data compression during inference. We present a novel approach that utilizes the Generative Pre-trained Transformer (GPT) to approximate Kolmogorov complexity, with the aim of estimating the optimal Information Distance for few-shot learning. We first propose using GPT as a prior for lossless text compression, achieving a noteworthy compression ratio. Experiment with LLAMA2-7B backbone achieves a compression ratio of 15.5 on enwik9. We justify the pre-training objective of GPT models by demonstrating its equivalence to the compression length, and, consequently, its ability to approximate the information distance for texts. Leveraging the approximated information distance, our method allows the direct application of GPT models in quantitative text similarity measurements. Experiment results show that our method overall achieves superior performance compared to embedding and prompt baselines on challenging NLP tasks, including semantic similarity, zero and one-shot text classification, and zero-shot text ranking.

In this paper, we present the findings of our Project ALPINE which stands for ``Autoregressive Learning for Planning In NEtworks." Project ALPINE initiates a theoretical investigation into the development of planning capabilities in Transformer-based language models through their autoregressive learning mechanisms, aiming to identify any potential limitations in their planning abilities. We abstract planning as a network path-finding task where the objective is to generate a valid path from a specified source node to a designated target node. In terms of expressiveness, we show that the Transformer is capable of executing path-finding by embedding the adjacency and reachability matrices within its weights. Our theoretical analysis of the gradient-based learning dynamic of the Transformer reveals that the Transformer is capable of learning both the adjacency matrix and a limited form of the reachability matrix. These theoretical insights are then validated through experiments, which demonstrate that the Transformer indeed learns the adjacency matrix and an incomplete reachability matrix, which aligns with the predictions made in our theoretical analysis. Additionally, when applying our methodology to a real-world planning benchmark, called Blocksworld, our observations remain consistent. Our theoretical and empirical analyses further unveil a potential limitation of Transformer in path-finding: it cannot identify reachability relationships through transitivity, and thus would fail when path concatenation is needed to generate a path. In summary, our findings shed new light on how the internal mechanisms of autoregressive learning enable planning in networks. This study may contribute to our understanding of the general planning capabilities in other related domains.

The rise of large language models (LLMs) had a transformative impact on search, ushering in a new era of search engines that are capable of generating search results in natural language text, imbued with citations for supporting sources. Building generative information-seeking models demands openly accessible datasets, which currently remain lacking. In this paper, we introduce a new dataset, HAGRID (Human-in-the-loop Attributable Generative Retrieval for Information-seeking Dataset) for building end-to-end generative information-seeking models that are capable of retrieving candidate quotes and generating attributed explanations. Unlike recent efforts that focus on human evaluation of black-box proprietary search engines, we built our dataset atop the English subset of MIRACL, a publicly available information retrieval dataset. HAGRID is constructed based on human and LLM collaboration. We first automatically collect attributed explanations that follow an in-context citation style using an LLM, i.e. GPT-3.5. Next, we ask human annotators to evaluate the LLM explanations based on two criteria: informativeness and attributability. HAGRID serves as a catalyst for the development of information-seeking models with better attribution capabilities.

Language models (LMs) can make a correct prediction based on many possible signals in a prompt, not all corresponding to recall of factual associations. However, current interpretations of LMs fail to take this into account. For example, given the query "Astrid Lindgren was born in" with the corresponding completion "Sweden", no difference is made between whether the prediction was based on knowing where the author was born or assuming that a person with a Swedish-sounding name was born in Sweden. In this paper, we present a model-specific recipe - PrISM - for constructing datasets with examples of four different prediction scenarios: generic language modeling, guesswork, heuristics recall and exact fact recall. We apply two popular interpretability methods to the scenarios: causal tracing (CT) and information flow analysis. We find that both yield distinct results for each scenario. Results for exact fact recall and generic language modeling scenarios confirm previous conclusions about the importance of mid-range MLP sublayers for fact recall, while results for guesswork and heuristics indicate a critical role of late last token position MLP sublayers. In summary, we contribute resources for a more extensive and granular study of fact completion in LMs, together with analyses that provide a more nuanced understanding of how LMs process fact-related queries.

Query rewriting aims to generate a new query that can complement the original query to improve the information retrieval system. Recent studies on query rewriting, such as query2doc (Q2D), query2expand (Q2E) and querey2cot (Q2C), rely on the internal knowledge of Large Language Models (LLMs) to generate a relevant passage to add information to the query. Nevertheless, the efficacy of these methodologies may markedly decline in instances where the requisite knowledge is not encapsulated within the model's intrinsic parameters. In this paper, we propose a novel structured query rewriting method called Crafting the Path tailored for retrieval systems. Crafting the Path involves a three-step process that crafts query-related information necessary for finding the passages to be searched in each step. Specifically, the Crafting the Path begins with Query Concept Comprehension, proceeds to Query Type Identification, and finally conducts Expected Answer Extraction. Experimental results show that our method outperforms previous rewriting methods, especially in less familiar domains for LLMs. We demonstrate that our method is less dependent on the internal parameter knowledge of the model and generates queries with fewer factual inaccuracies. Furthermore, we observe that Crafting the Path has less latency compared to the baselines.

A research division plays an important role of driving innovation in an organization. Drawing insights, following trends, keeping abreast of new research, and formulating strategies are increasingly becoming more challenging for both researchers and executives as the amount of information grows in both velocity and volume. In this paper we present a use case of how a corporate research community, IBM Research, utilizes Semantic Web technologies to induce a unified Knowledge Graph from both structured and textual data obtained by integrating various applications used by the community related to research projects, academic papers, datasets, achievements and recognition. In order to make the Knowledge Graph more accessible to application developers, we identified a set of common patterns for exploiting the induced knowledge and exposed them as APIs. Those patterns were born out of user research which identified the most valuable use cases or user pain points to be alleviated. We outline two distinct scenarios: recommendation and analytics for business use. We will discuss these scenarios in detail and provide an empirical evaluation on entity recommendation specifically. The methodology used and the lessons learned from this work can be applied to other organizations facing similar challenges.

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/.

Information extraction (IE) aims to extract structural knowledge (such as entities, relations, and events) from plain natural language texts. Recently, generative Large Language Models (LLMs) have demonstrated remarkable capabilities in text understanding and generation, allowing for generalization across various domains and tasks. As a result, numerous works have been proposed to harness abilities of LLMs and offer viable solutions for IE tasks based on a generative paradigm. To conduct a comprehensive systematic review and exploration of LLM efforts for IE tasks, in this study, we survey the most recent advancements in this field. We first present an extensive overview by categorizing these works in terms of various IE subtasks and learning paradigms, then we empirically analyze the most advanced methods and discover the emerging trend of IE tasks with LLMs. Based on thorough review conducted, we identify several insights in technique and promising research directions that deserve further exploration in future studies. We maintain a public repository and consistently update related resources at: https://github.com/quqxui/Awesome-LLM4IE-Papers.

In this paper, we champion the use of structured and semantic content representation of discourse-based scholarly communication, inspired by tools like Wikipedia infoboxes or structured Amazon product descriptions. These representations provide users with a concise overview, aiding scientists in navigating the dense academic landscape. Our novel automated approach leverages the robust text generation capabilities of LLMs to produce structured scholarly contribution summaries, offering both a practical solution and insights into LLMs' emergent abilities. For LLMs, the prime focus is on improving their general intelligence as conversational agents. We argue that these models can also be applied effectively in information extraction (IE), specifically in complex IE tasks within terse domains like Science. This paradigm shift replaces the traditional modular, pipelined machine learning approach with a simpler objective expressed through instructions. Our results show that finetuned FLAN-T5 with 1000x fewer parameters than the state-of-the-art GPT-davinci is competitive for the task.

Multimodal large language models (MLLMs) have shown promising capabilities but struggle under distribution shifts, where evaluation data differ from instruction tuning distributions. Although previous works have provided empirical evaluations, we argue that establishing a formal framework that can characterize and quantify the risk of MLLMs is necessary to ensure the safe and reliable application of MLLMs in the real world. By taking an information-theoretic perspective, we propose the first theoretical framework that enables the quantification of the maximum risk of MLLMs under distribution shifts. Central to our framework is the introduction of Effective Mutual Information (EMI), a principled metric that quantifies the relevance between input queries and model responses. We derive an upper bound for the EMI difference between in-distribution (ID) and out-of-distribution (OOD) data, connecting it to visual and textual distributional discrepancies. Extensive experiments on real benchmark datasets, spanning 61 shift scenarios empirically validate our theoretical insights.

Large Language Models (LLMs) are accelerating scientific idea generation, but rigorously evaluating these numerous, often superficial, AI-generated propositions for novelty and factual accuracy is a critical bottleneck; manual verification is too slow. Existing validation methods are inadequate: LLMs as standalone verifiers may hallucinate and lack domain knowledge (our findings show 60% unawareness of relevant papers in specific domains), while traditional citation networks lack explicit causality and narrative surveys are unstructured. This underscores a core challenge: the absence of structured, verifiable, and causally-linked historical data of scientific evolution.To address this,we introduce THE-Tree (Technology History Evolution Tree), a computational framework that constructs such domain-specific evolution trees from scientific literature. THE-Tree employs a search algorithm to explore evolutionary paths. During its node expansion, it utilizes a novel "Think-Verbalize-Cite-Verify" process: an LLM proposes potential advancements and cites supporting literature. Critically, each proposed evolutionary link is then validated for logical coherence and evidential support by a recovered natural language inference mechanism that interrogates the cited literature, ensuring that each step is grounded. We construct and validate 88 THE-Trees across diverse domains and release a benchmark dataset including up to 71k fact verifications covering 27k papers to foster further research. Experiments demonstrate that i) in graph completion, our THE-Tree improves hit@1 by 8% to 14% across multiple models compared to traditional citation networks; ii) for predicting future scientific developments, it improves hit@1 metric by nearly 10%; and iii) when combined with other methods, it boosts the performance of evaluating important scientific papers by almost 100%.

Accurate remaining useful life (RUL) prediction hinges on the quality of health indicators (HIs), yet existing methods often fail to disentangle complex degradation mechanisms in multi-sensor systems or quantify uncertainty in HI reliability. This paper introduces a novel framework for HI construction, advancing three key contributions. First, we adapt Reconstruction along Projected Pathways (RaPP) as a health indicator (HI) for RUL prediction for the first time, showing that it outperforms traditional reconstruction error metrics. Second, we show that augmenting RaPP-derived HIs with aleatoric and epistemic uncertainty quantification (UQ) via Monte Carlo dropout and probabilistic latent spaces- significantly improves RUL-prediction robustness. Third, and most critically, we propose indicator groups, a paradigm that isolates sensor subsets to model system-specific degradations, giving rise to our novel method, I-GLIDE which enables interpretable, mechanism-specific diagnostics. Evaluated on data sourced from aerospace and manufacturing systems, our approach achieves marked improvements in accuracy and generalizability compared to state-of-the-art HI methods while providing actionable insights into system failure pathways. This work bridges the gap between anomaly detection and prognostics, offering a principled framework for uncertainty-aware degradation modeling in complex systems.

Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data are associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data are paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graph scenarios (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-rich graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we mention the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

Information extraction (IE) is an important task in Natural Language Processing (NLP), involving the extraction of named entities and their relationships from unstructured text. In this paper, we propose a novel approach to this task by formulating it as graph structure learning (GSL). By formulating IE as GSL, we enhance the model's ability to dynamically refine and optimize the graph structure during the extraction process. This formulation allows for better interaction and structure-informed decisions for entity and relation prediction, in contrast to previous models that have separate or untied predictions for these tasks. When compared against state-of-the-art baselines on joint entity and relation extraction benchmarks, our model, GraphER, achieves competitive results.

Social and collaborative platforms emit multivariate time-series traces in which early interactions-such as views, likes, or downloads-are followed, sometimes months or years later, by higher impact like citations, sales, or reviews. We formalize this setting as Lead-Lag Forecasting (LLF): given an early usage channel (the lead), predict a correlated but temporally shifted outcome channel (the lag). Despite the ubiquity of such patterns, LLF has not been treated as a unified forecasting problem within the time-series community, largely due to the absence of standardized datasets. To anchor research in LLF, here we present two high-volume benchmark datasets-arXiv (accesses -> citations of 2.3M papers) and GitHub (pushes/stars -> forks of 3M repositories)-and outline additional domains with analogous lead-lag dynamics, including Wikipedia (page views -> edits), Spotify (streams -> concert attendance), e-commerce (click-throughs -> purchases), and LinkedIn profile (views -> messages). Our datasets provide ideal testbeds for lead-lag forecasting, by capturing long-horizon dynamics across years, spanning the full spectrum of outcomes, and avoiding survivorship bias in sampling. We documented all technical details of data curation and cleaning, verified the presence of lead-lag dynamics through statistical and classification tests, and benchmarked parametric and non-parametric baselines for regression. Our study establishes LLF as a novel forecasting paradigm and lays an empirical foundation for its systematic exploration in social and usage data. Our data portal with downloads and documentation is available at https://lead-lag-forecasting.github.io/.

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.

Information seeking is a fundamental requirement for humans. However, existing LLM agents rely heavily on open-web search, which exposes two fundamental weaknesses: online content is noisy and unreliable, and many real-world tasks require precise, domain-specific knowledge unavailable from the web. The emergence of the Model Context Protocol (MCP) now allows agents to interface with thousands of specialized tools, seemingly resolving this limitation. Yet it remains unclear whether agents can effectively leverage such tools -- and more importantly, whether they can integrate them with general-purpose search to solve complex tasks. Therefore, we introduce InfoMosaic-Bench, the first benchmark dedicated to multi-source information seeking in tool-augmented agents. Covering six representative domains (medicine, finance, maps, video, web, and multi-domain integration), InfoMosaic-Bench requires agents to combine general-purpose search with domain-specific tools. Tasks are synthesized with InfoMosaic-Flow, a scalable pipeline that grounds task conditions in verified tool outputs, enforces cross-source dependencies, and filters out shortcut cases solvable by trivial lookup. This design guarantees both reliability and non-triviality. Experiments with 14 state-of-the-art LLM agents reveal three findings: (i) web information alone is insufficient, with GPT-5 achieving only 38.2% accuracy and 67.5% pass rate; (ii) domain tools provide selective but inconsistent benefits, improving some domains while degrading others; and (iii) 22.4% of failures arise from incorrect tool usage or selection, highlighting that current LLMs still struggle with even basic tool handling.

Scientific talks are a growing medium for disseminating research, and automatically identifying relevant literature that grounds or enriches a talk would be highly valuable for researchers and students alike. We introduce Reference Prediction from Talks (RPT), a new task that maps long, and unstructured scientific presentations to relevant papers. To support research on RPT, we present Talk2Ref, the first large-scale dataset of its kind, containing 6,279 talks and 43,429 cited papers (26 per talk on average), where relevance is approximated by the papers cited in the talk's corresponding source publication. We establish strong baselines by evaluating state-of-the-art text embedding models in zero-shot retrieval scenarios, and propose a dual-encoder architecture trained on Talk2Ref. We further explore strategies for handling long transcripts, as well as training for domain adaptation. Our results show that fine-tuning on Talk2Ref significantly improves citation prediction performance, demonstrating both the challenges of the task and the effectiveness of our dataset for learning semantic representations from spoken scientific content. The dataset and trained models are released under an open license to foster future research on integrating spoken scientific communication into citation recommendation systems.

Recent advances in multimodal pre-trained models have significantly improved information extraction from visually-rich documents (VrDs), in which named entity recognition (NER) is treated as a sequence-labeling task of predicting the BIO entity tags for tokens, following the typical setting of NLP. However, BIO-tagging scheme relies on the correct order of model inputs, which is not guaranteed in real-world NER on scanned VrDs where text are recognized and arranged by OCR systems. Such reading order issue hinders the accurate marking of entities by BIO-tagging scheme, making it impossible for sequence-labeling methods to predict correct named entities. To address the reading order issue, we introduce Token Path Prediction (TPP), a simple prediction head to predict entity mentions as token sequences within documents. Alternative to token classification, TPP models the document layout as a complete directed graph of tokens, and predicts token paths within the graph as entities. For better evaluation of VrD-NER systems, we also propose two revised benchmark datasets of NER on scanned documents which can reflect real-world scenarios. Experiment results demonstrate the effectiveness of our method, and suggest its potential to be a universal solution to various information extraction tasks on documents.

Accurate career path prediction can support many stakeholders, like job seekers, recruiters, HR, and project managers. However, publicly available data and tools for career path prediction are scarce. In this work, we introduce KARRIEREWEGE, a comprehensive, publicly available dataset containing over 500k career paths, significantly surpassing the size of previously available datasets. We link the dataset to the ESCO taxonomy to offer a valuable resource for predicting career trajectories. To tackle the problem of free-text inputs typically found in resumes, we enhance it by synthesizing job titles and descriptions resulting in KARRIEREWEGE+. This allows for accurate predictions from unstructured data, closely aligning with real-world application challenges. We benchmark existing state-of-the-art (SOTA) models on our dataset and a prior benchmark and observe improved performance and robustness, particularly for free-text use cases, due to the synthesized data.

We explore local vs. global evolution of knowledge systems through the framework of socio-epistemic networks (SEN), applying two complementary methods to a corpus of scientific texts. The framework comprises three interconnected layers-social, semiotic (material), and semantic-proposing a multilayered approach to understanding structural developments of knowledge. To analyse diachronic changes on the semantic layer, we first use information-theoretic measures based on relative entropy to detect semantic shifts, assess their significance, and identify key driving features. Second, variations in document embedding densities reveal changes in semantic neighbourhoods, tracking how concentration of similar documents increase, remain stable, or disperse. This enables us to trace document trajectories based on content (topics) or metadata (authorship, institution). Case studies of Joseph Silk and Hans-J\"urgen Treder illustrate how individual scholar's work aligns with broader disciplinary shifts in general relativity and gravitation research, demonstrating the applications, limitations, and further potential of this approach.

LLMs and AI chatbots have improved people's efficiency in various fields. However, the necessary knowledge for answering the question may be beyond the models' knowledge boundaries. To mitigate this issue, many researchers try to introduce external knowledge, such as knowledge graphs and Internet contents, into LLMs for up-to-date information. However, the external information from the Internet may include counterfactual information that will confuse the model and lead to an incorrect response. Thus there is a pressing need for LLMs to possess the ability to distinguish reliable information from external knowledge. Therefore, to evaluate the ability of LLMs to discern the reliability of external knowledge, we create a benchmark from existing knowledge bases. Our benchmark consists of two tasks, Question Answering and Text Generation, and for each task, we provide models with a context containing counterfactual information. Evaluation results show that existing LLMs are susceptible to interference from unreliable external knowledge with counterfactual information, and simple intervention methods make limited contributions to the alleviation of this issue.

The rapidly growing number and variety of Large Language Models (LLMs) present significant challenges in efficiently selecting the appropriate LLM for a given query, especially considering the trade-offs between performance and computational cost. Current LLM selection methods often struggle to generalize across new LLMs and different tasks because of their limited ability to leverage contextual interactions among tasks, queries, and LLMs, as well as their dependence on a transductive learning framework. To address these shortcomings, we introduce a novel inductive graph framework, named as GraphRouter, which fully utilizes the contextual information among tasks, queries, and LLMs to enhance the LLM selection process. GraphRouter constructs a heterogeneous graph comprising task, query, and LLM nodes, with interactions represented as edges, which efficiently captures the contextual information between the query's requirements and the LLM's capabilities. Through an innovative edge prediction mechanism, GraphRouter is able to predict attributes (the effect and cost of LLM response) of potential edges, allowing for optimized recommendations that adapt to both existing and newly introduced LLMs without requiring retraining. Comprehensive experiments across three distinct effect-cost weight scenarios have shown that GraphRouter substantially surpasses existing routers, delivering a minimum performance improvement of 12.3%. In addition, it achieves enhanced generalization across new LLMs settings and supports diverse tasks with at least a 9.5% boost in effect and a significant reduction in computational demands. This work endeavors to apply a graph-based approach for the contextual and adaptive selection of LLMs, offering insights for real-world applications. Our codes for GraphRouter is released at https://github.com/ulab-uiuc/GraphRouter.

The next Point of Interest (POI) recommendation task is to predict users' immediate next POI visit given their historical data. Location-Based Social Network (LBSN) data, which is often used for the next POI recommendation task, comes with challenges. One frequently disregarded challenge is how to effectively use the abundant contextual information present in LBSN data. Previous methods are limited by their numerical nature and fail to address this challenge. In this paper, we propose a framework that uses pretrained Large Language Models (LLMs) to tackle this challenge. Our framework allows us to preserve heterogeneous LBSN data in its original format, hence avoiding the loss of contextual information. Furthermore, our framework is capable of comprehending the inherent meaning of contextual information due to the inclusion of commonsense knowledge. In experiments, we test our framework on three real-world LBSN datasets. Our results show that the proposed framework outperforms the state-of-the-art models in all three datasets. Our analysis demonstrates the effectiveness of the proposed framework in using contextual information as well as alleviating the commonly encountered cold-start and short trajectory problems.

As the disruptive changes in the media economy and the proliferation of alternative news media outlets, news intent has progressively deviated from ethical standards that serve the public interest. News intent refers to the purpose or intention behind the creation of a news article. While the significance of research on news intent has been widely acknowledged, the absence of a systematic news intent understanding framework hinders further exploration of news intent and its downstream applications. To bridge this gap, we propose News INTent (NINT) frame, the first component-aware formalism for understanding the news creation intent based on research in philosophy, psychology, and cognitive science. Within this frame, we define the news intent identification task and provide a benchmark dataset with fine-grained labels along with an efficient benchmark method. Experiments demonstrate that NINT is beneficial in both the intent identification task and downstream tasks that demand a profound understanding of news. This work marks a foundational step towards a more systematic exploration of news creation intents.

HAL (Hyper Articles en Ligne) is the French national publication repository, used by most higher education and research organizations for their open science policy. As a digital library, it is a rich repository of scholarly documents, but its potential for advanced research has been underutilized. We present HALvest, a unique dataset that bridges the gap between citation networks and the full text of papers submitted on HAL. We craft our dataset by filtering HAL for scholarly publications, resulting in approximately 700,000 documents, spanning 34 languages across 13 identified domains, suitable for language model training, and yielding approximately 16.5 billion tokens (with 8 billion in French and 7 billion in English, the most represented languages). We transform the metadata of each paper into a citation network, producing a directed heterogeneous graph. This graph includes uniquely identified authors on HAL, as well as all open submitted papers, and their citations. We provide a baseline for authorship attribution using the dataset, implement a range of state-of-the-art models in graph representation learning for link prediction, and discuss the usefulness of our generated knowledge graph structure.

In this paper we develop a dynamic form of Bayesian optimization for machine learning models with the goal of rapidly finding good hyperparameter settings. Our method uses the partial information gained during the training of a machine learning model in order to decide whether to pause training and start a new model, or resume the training of a previously-considered model. We specifically tailor our method to machine learning problems by developing a novel positive-definite covariance kernel to capture a variety of training curves. Furthermore, we develop a Gaussian process prior that scales gracefully with additional temporal observations. Finally, we provide an information-theoretic framework to automate the decision process. Experiments on several common machine learning models show that our approach is extremely effective in practice.

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their expansive application in sensitive domains requires a comprehensive understanding of their decision-making processes -- necessitating a framework for GNN explainability. An explanation function for GNNs takes a pre-trained GNN along with a graph as input, to produce a `sufficient statistic' subgraph with respect to the graph label. A main challenge in studying GNN explainability is to provide fidelity measures that evaluate the performance of these explanation functions. This paper studies this foundational challenge, spotlighting the inherent limitations of prevailing fidelity metrics, including Fid_+, Fid_-, and Fid_Delta. Specifically, a formal, information-theoretic definition of explainability is introduced and it is shown that existing metrics often fail to align with this definition across various statistical scenarios. The reason is due to potential distribution shifts when subgraphs are removed in computing these fidelity measures. Subsequently, a robust class of fidelity measures are introduced, and it is shown analytically that they are resilient to distribution shift issues and are applicable in a wide range of scenarios. Extensive empirical analysis on both synthetic and real datasets are provided to illustrate that the proposed metrics are more coherent with gold standard metrics. The source code is available at https://trustai4s-lab.github.io/fidelity.

Interpreting the inner function of neural networks is crucial for the trustworthy development and deployment of these black-box models. Prior interpretability methods focus on correlation-based measures to attribute model decisions to individual examples. However, these measures are susceptible to noise and spurious correlations encoded in the model during the training phase (e.g., biased inputs, model overfitting, or misspecification). Moreover, this process has proven to result in noisy and unstable attributions that prevent any transparent understanding of the model's behavior. In this paper, we develop a robust interventional-based method grounded by causal analysis to capture cause-effect mechanisms in pre-trained neural networks and their relation to the prediction. Our novel approach relies on path interventions to infer the causal mechanisms within hidden layers and isolate relevant and necessary information (to model prediction), avoiding noisy ones. The result is task-specific causal explanatory graphs that can audit model behavior and express the actual causes underlying its performance. We apply our method to vision models trained on classification tasks. On image classification tasks, we provide extensive quantitative experiments to show that our approach can capture more stable and faithful explanations than standard attribution-based methods. Furthermore, the underlying causal graphs reveal the neural interactions in the model, making it a valuable tool in other applications (e.g., model repair).

Within this study, we propose a new approach for natural language processing using Bayesian networks to predict and analyze the context and how this approach can be applied to the Community Question Answering domain. We discuss how Bayesian networks can detect semantic relationships and dependencies between entities, and this is connected to different score-based approaches of structure-learning. We compared the Bayesian networks with different score metrics, such as the BIC, BDeu, K2 and Chow-Liu trees. Our proposed approach out-performs the baseline model at the precision metric. We also discuss the influence of penalty terms on the structure of Bayesian networks and how they can be used to analyze the relationships between entities. In addition, we examine the visualization of directed acyclic graphs to analyze semantic relationships. The article further identifies issues with detecting certain semantic classes that are separated in the structure of directed acyclic graphs. Finally, we evaluate potential improvements for the Bayesian network approach.

In this paper, the problem of semantic information extraction for resource constrained text data transmission is studied. In the considered model, a sequence of text data need to be transmitted within a communication resource-constrained network, which only allows limited data transmission. Thus, at the transmitter, the original text data is extracted with natural language processing techniques. Then, the extracted semantic information is captured in a knowledge graph. An additional probability dimension is introduced in this graph to capture the importance of each information. This semantic information extraction problem is posed as an optimization framework whose goal is to extract most important semantic information for transmission. To find an optimal solution for this problem, a Floyd's algorithm based solution coupled with an efficient sorting mechanism is proposed. Numerical results testify the effectiveness of the proposed algorithm with regards to two novel performance metrics including semantic uncertainty and semantic similarity.

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.

Fake news detection has been a critical task for maintaining the health of the online news ecosystem. However, very few existing works consider the temporal shift issue caused by the rapidly-evolving nature of news data in practice, resulting in significant performance degradation when training on past data and testing on future data. In this paper, we observe that the appearances of news events on the same topic may display discernible patterns over time, and posit that such patterns can assist in selecting training instances that could make the model adapt better to future data. Specifically, we design an effective framework FTT (Forecasting Temporal Trends), which could forecast the temporal distribution patterns of news data and then guide the detector to fast adapt to future distribution. Experiments on the real-world temporally split dataset demonstrate the superiority of our proposed framework. The code is available at https://github.com/ICTMCG/FTT-ACL23.

Large language models (LLMs) have achieved unprecedented performance by leveraging vast pretraining corpora, yet their performance remains suboptimal in knowledge-intensive domains such as medicine and scientific research, where high factual precision is required. While synthetic data provides a promising avenue for augmenting domain knowledge, existing methods frequently generate redundant samples that do not align with the model's true knowledge gaps. To overcome this limitation, we propose a novel Structural Entropy-guided Knowledge Navigator (SENATOR) framework that addresses the intrinsic knowledge deficiencies of LLMs. Our approach employs the Structure Entropy (SE) metric to quantify uncertainty along knowledge graph paths and leverages Monte Carlo Tree Search (MCTS) to selectively explore regions where the model lacks domain-specific knowledge. Guided by these insights, the framework generates targeted synthetic data for supervised fine-tuning, enabling continuous self-improvement. Experimental results on LLaMA-3 and Qwen2 across multiple domain-specific benchmarks show that SENATOR effectively detects and repairs knowledge deficiencies, achieving notable performance improvements. The code and data for our methods and experiments are available at https://github.com/weiyifan1023/senator.

Knowledge Graphs (KGs) have been used to support a wide range of applications, from web search to personal assistant. In this paper, we describe three generations of knowledge graphs: entity-based KGs, which have been supporting general search and question answering (e.g., at Google and Bing); text-rich KGs, which have been supporting search and recommendations for products, bio-informatics, etc. (e.g., at Amazon and Alibaba); and the emerging integration of KGs and LLMs, which we call dual neural KGs. We describe the characteristics of each generation of KGs, the crazy ideas behind the scenes in constructing such KGs, and the techniques developed over time to enable industry impact. In addition, we use KGs as examples to demonstrate a recipe to evolve research ideas from innovations to production practice, and then to the next level of innovations, to advance both science and business.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

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.

Training data influence estimation methods quantify the contribution of training documents to a model's output, making them a promising source of information for example-based explanations. As humans cannot interpret thousands of documents, only a small subset of the training data can be presented as an explanation. Although the choice of which documents to include directly affects explanation quality, previous evaluations of such systems have largely ignored any selection strategies. To address this, we propose a novel selection relevance score, a retraining-free metric that quantifies how useful a set of examples is for explaining a model's output. We validate this score through fine-tuning experiments, confirming that it can predict whether a set of examples supports or undermines the model's predictions. Using this metric, we further show that common selection strategies often underperform random selection. Motivated by this finding, we propose a strategy that balances influence and representativeness, enabling better use of selection budgets than naively selecting the highest-ranking examples.

High-throughput drug screening -- using cell imaging or gene expression measurements as readouts of drug effect -- is a critical tool in biotechnology to assess and understand the relationship between the chemical structure and biological activity of a drug. Since large-scale screens have to be divided into multiple experiments, a key difficulty is dealing with batch effects, which can introduce systematic errors and non-biological associations in the data. We propose InfoCORE, an Information maximization approach for COnfounder REmoval, to effectively deal with batch effects and obtain refined molecular representations. InfoCORE establishes a variational lower bound on the conditional mutual information of the latent representations given a batch identifier. It adaptively reweighs samples to equalize their implied batch distribution. Extensive experiments on drug screening data reveal InfoCORE's superior performance in a multitude of tasks including molecular property prediction and molecule-phenotype retrieval. Additionally, we show results for how InfoCORE offers a versatile framework and resolves general distribution shifts and issues of data fairness by minimizing correlation with spurious features or removing sensitive attributes. The code is available at https://github.com/uhlerlab/InfoCORE.

Time series forecasting plays a crucial role in data mining, driving rapid advancements across numerous industries. With the emergence of large models, time series foundation models (TSFMs) have exhibited remarkable generalization capabilities, such as zero-shot learning, through large-scale pre-training. Meanwhile, Retrieval-Augmented Generation (RAG) methods have been widely employed to enhance the performance of foundation models on unseen data, allowing models to access to external knowledge. In this paper, we introduce TimeRAF, a Retrieval-Augmented Forecasting model that enhance zero-shot time series forecasting through retrieval-augmented techniques. We develop customized time series knowledge bases that are tailored to the specific forecasting tasks. TimeRAF employs an end-to-end learnable retriever to extract valuable information from the knowledge base. Additionally, we propose Channel Prompting for knowledge integration, which effectively extracts relevant information from the retrieved knowledge along the channel dimension. Extensive experiments demonstrate the effectiveness of our model, showing significant improvement across various domains and datasets.

Whole-Slide Image (WSI) is an important tool for evaluating the prognosis of cancer patients. Present WSI-based prognosis studies generally follow a conventional paradigm -- cancer-specific model development -- where one cancer disease corresponds to one model and this model cannot make use of the prognostic knowledge from others. Despite its notable success in recent years, this paradigm has inherent limitations and has always been struggling with practical requirements: (i) scaling to the rare tumor diseases with very limited samples and (ii) benefiting from the generalizable prognostic knowledge in other cancers. To this end, this paper presents the first systematic study on Prognostic Knowledge Transfer in Pathology, called Path-PKT. It comprises three main parts. (1) We curate a large dataset (UNI2-h-DSS) with 13 cancers and use it to evaluate the transferability of prognostic knowledge between different cancers computationally. (2) We design experiments to understand what factors affect knowledge transfer and what causes positive transfers. (3) Motivated by empirical findings, we propose a new baseline approach (MoE-PKT) with a routing mechanism to utilize the generalizable prognostic knowledge in other cancers. Finally, we show the transferability of source models to rare tumor diseases. This study could lay solid foundations for the study of knowledge transfer in WSI-based cancer prognosis. Source code is available at https://github.com/liupei101/Path-PKT.

With the recent addition of Retrieval-Augmented Generation (RAG), the scope and importance of Information Retrieval (IR) has expanded. As a result, the importance of a deeper understanding of IR models also increases. However, interpretability in IR remains under-explored, especially when it comes to the models' inner mechanisms. In this paper, we explore the possibility of adapting Integrated Gradient-based methods in an IR context to identify the role of individual neurons within the model. In particular, we provide new insights into the role of what we call "relevance" neurons, as well as how they deal with unseen data. Finally, we carry out an in-depth pruning study to validate our findings.

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.

In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as semantic networks) cannot. An olog is similar to a relational database schema; in fact an olog can serve as a data repository if desired. Unlike database schemas, which are generally difficult to create or modify, ologs are designed to be user-friendly enough that authoring or reconfiguring an olog is a matter of course rather than a difficult chore. It is hoped that learning to author ologs is much simpler than learning a database definition language, despite their similarity. We describe ologs carefully and illustrate with many examples. As an application we show that any primitive recursive function can be described by an olog. We also show that ologs can be aligned or connected together into a larger network using functors. The various methods of information flow and institutions can then be used to integrate local and global world-views. We finish by providing several different avenues for future research.

Entity linking is a prominent thread of research focused on structured data creation by linking spans of text to an ontology or knowledge source. We revisit the use of structured prediction for entity linking which classifies each individual input token as an entity, and aggregates the token predictions. Our system, called SpEL (Structured prediction for Entity Linking) is a state-of-the-art entity linking system that uses some new ideas to apply structured prediction to the task of entity linking including: two refined fine-tuning steps; a context sensitive prediction aggregation strategy; reduction of the size of the model's output vocabulary, and; we address a common problem in entity-linking systems where there is a training vs. inference tokenization mismatch. Our experiments show that we can outperform the state-of-the-art on the commonly used AIDA benchmark dataset for entity linking to Wikipedia. Our method is also very compute efficient in terms of number of parameters and speed of inference.

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.

The causal capabilities of large language models (LLMs) are a matter of significant debate, with critical implications for the use of LLMs in societally impactful domains such as medicine, science, law, and policy. We conduct a "behavorial" study of LLMs to benchmark their capability in generating causal arguments. Across a wide range of tasks, we find that LLMs can generate text corresponding to correct causal arguments with high probability, surpassing the best-performing existing methods. Algorithms based on GPT-3.5 and 4 outperform existing algorithms on a pairwise causal discovery task (97%, 13 points gain), counterfactual reasoning task (92%, 20 points gain) and event causality (86% accuracy in determining necessary and sufficient causes in vignettes). We perform robustness checks across tasks and show that the capabilities cannot be explained by dataset memorization alone, especially since LLMs generalize to novel datasets that were created after the training cutoff date. That said, LLMs exhibit unpredictable failure modes, and we discuss the kinds of errors that may be improved and what are the fundamental limits of LLM-based answers. Overall, by operating on the text metadata, LLMs bring capabilities so far understood to be restricted to humans, such as using collected knowledge to generate causal graphs or identifying background causal context from natural language. As a result, LLMs may be used by human domain experts to save effort in setting up a causal analysis, one of the biggest impediments to the widespread adoption of causal methods. Given that LLMs ignore the actual data, our results also point to a fruitful research direction of developing algorithms that combine LLMs with existing causal techniques. Code and datasets are available at https://github.com/py-why/pywhy-llm.

Forecasting is a critical task in decision-making across numerous domains. While historical numerical data provide a start, they fail to convey the complete context for reliable and accurate predictions. Human forecasters frequently rely on additional information, such as background knowledge and constraints, which can efficiently be communicated through natural language. However, in spite of recent progress with LLM-based forecasters, their ability to effectively integrate this textual information remains an open question. To address this, we introduce "Context is Key" (CiK), a time-series forecasting benchmark that pairs numerical data with diverse types of carefully crafted textual context, requiring models to integrate both modalities; crucially, every task in CiK requires understanding textual context to be solved successfully. We evaluate a range of approaches, including statistical models, time series foundation models, and LLM-based forecasters, and propose a simple yet effective LLM prompting method that outperforms all other tested methods on our benchmark. Our experiments highlight the importance of incorporating contextual information, demonstrate surprising performance when using LLM-based forecasting models, and also reveal some of their critical shortcomings. This benchmark aims to advance multimodal forecasting by promoting models that are both accurate and accessible to decision-makers with varied technical expertise. The benchmark can be visualized at https://servicenow.github.io/context-is-key-forecasting/v0/.

Neural networks -- especially those that use large, pre-trained language models -- have improved search engines in various ways. Most prominently, they can estimate the relevance of a passage or document to a user's query. In this work, we depart from this direction by exploring whether neural networks can effectively predict which of a document's passages are unlikely to be relevant to any query submitted to the search engine. We refer to this query-agnostic estimation of passage relevance as a passage's quality. We find that our novel methods for estimating passage quality allow passage corpora to be pruned considerably while maintaining statistically equivalent effectiveness; our best methods can consistently prune >25% of passages in a corpora, across various retrieval pipelines. Such substantial pruning reduces the operating costs of neural search engines in terms of computing resources, power usage, and carbon footprint -- both when processing queries (thanks to a smaller index size) and when indexing (lightweight models can prune low-quality passages prior to the costly dense or learned sparse encoding step). This work sets the stage for developing more advanced neural "learning-what-to-index" methods.

Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors.

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.

This paper introduces a pioneering approach to artificial intelligence research, embodied in our O1 Replication Journey. In response to the announcement of OpenAI's groundbreaking O1 model, we embark on a transparent, real-time exploration to replicate its capabilities while reimagining the process of conducting and communicating AI research. Our methodology addresses critical challenges in modern AI research, including the insularity of prolonged team-based projects, delayed information sharing, and the lack of recognition for diverse contributions. By providing comprehensive, real-time documentation of our replication efforts, including both successes and failures, we aim to foster open science, accelerate collective advancement, and lay the groundwork for AI-driven scientific discovery. Our research progress report diverges significantly from traditional research papers, offering continuous updates, full process transparency, and active community engagement throughout the research journey. Technologically, we proposed the journey learning paradigm, which encourages models to learn not just shortcuts, but the complete exploration process, including trial and error, reflection, and backtracking. With only 327 training samples and without any additional tricks, journey learning outperformed conventional supervised learning by over 8\% on the MATH dataset, demonstrating its extremely powerful potential. We believe this to be the most crucial component of O1 technology that we have successfully decoded. We share valuable resources including technical hypotheses and insights, cognitive exploration maps, custom-developed tools, etc at https://github.com/GAIR-NLP/O1-Journey.

Previous works on knowledge-to-text generation take as input a few RDF triples or key-value pairs conveying the knowledge of some entities to generate a natural language description. Existing datasets, such as WIKIBIO, WebNLG, and E2E, basically have a good alignment between an input triple/pair set and its output text. However, in practice, the input knowledge could be more than enough, since the output description may only cover the most significant knowledge. In this paper, we introduce a large-scale and challenging dataset to facilitate the study of such a practical scenario in KG-to-text. Our dataset involves retrieving abundant knowledge of various types of main entities from a large knowledge graph (KG), which makes the current graph-to-sequence models severely suffer from the problems of information loss and parameter explosion while generating the descriptions. We address these challenges by proposing a multi-graph structure that is able to represent the original graph information more comprehensively. Furthermore, we also incorporate aggregation methods that learn to extract the rich graph information. Extensive experiments demonstrate the effectiveness of our model architecture.

Recent studies have shown that large language models (LLMs) can assess relevance and support information retrieval (IR) tasks such as document ranking and relevance judgment generation. However, the internal mechanisms by which off-the-shelf LLMs understand and operationalize relevance remain largely unexplored. In this paper, we systematically investigate how different LLM modules contribute to relevance judgment through the lens of mechanistic interpretability. Using activation patching techniques, we analyze the roles of various model components and identify a multi-stage, progressive process in generating either pointwise or pairwise relevance judgment. Specifically, LLMs first extract query and document information in the early layers, then process relevance information according to instructions in the middle layers, and finally utilize specific attention heads in the later layers to generate relevance judgments in the required format. Our findings provide insights into the mechanisms underlying relevance assessment in LLMs, offering valuable implications for future research on leveraging LLMs for IR tasks.

We propose a novel Chain Guided Retriever-reader ({\tt CGR}) framework to model the reasoning chain for multi-hop Science Question Answering. Our framework is capable of performing explainable reasoning without the need of any corpus-specific annotations, such as the ground-truth reasoning chain, or human-annotated entity mentions. Specifically, we first generate reasoning chains from a semantic graph constructed by Abstract Meaning Representation of retrieved evidence facts. A Chain-aware loss, concerning both local and global chain information, is also designed to enable the generated chains to serve as distant supervision signals for training the retriever, where reinforcement learning is also adopted to maximize the utility of the reasoning chains. Our framework allows the retriever to capture step-by-step clues of the entire reasoning process, which is not only shown to be effective on two challenging multi-hop Science QA tasks, namely OpenBookQA and ARC-Challenge, but also favors explainability.

Knowledge Graph Embedding (KGE) models are used to learn continuous representations of entities and relations. A key task in the literature is predicting missing links between entities. However, Knowledge Graphs are not just sets of links but also have semantics underlying their structure. Semantics is crucial in several downstream tasks, such as query answering or reasoning. We introduce the subgraph inference task, where a model has to generate likely and semantically valid subgraphs. We propose IntelliGraphs, a set of five new Knowledge Graph datasets. The IntelliGraphs datasets contain subgraphs with semantics expressed in logical rules for evaluating subgraph inference. We also present the dataset generator that produced the synthetic datasets. We designed four novel baseline models, which include three models based on traditional KGEs. We evaluate their expressiveness and show that these models cannot capture the semantics. We believe this benchmark will encourage the development of machine learning models that emphasize semantic understanding.

Predictive models often need to work with incomplete information in real-world tasks. Consequently, they must provide reliable probability or confidence estimation, especially in large-scale decision-making and planning tasks. Current large language models (LLMs) are insufficient for accurate estimations, but they can generate relevant factors that may affect the probabilities, produce coarse-grained probabilities when the information is more complete, and help determine which factors are relevant to specific downstream contexts. In this paper, we make use of these capabilities of LLMs to provide a significantly more accurate probabilistic estimation. We propose BIRD, a novel probabilistic inference framework that aligns a Bayesian network with LLM abductions and then estimates more accurate probabilities in a deduction step. We show BIRD provides reliable probability estimations that are 30% better than those provided directly by LLM baselines. These estimates further contribute to better and more trustworthy decision making.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

Discovering the intended items of user queries from a massive repository of items is one of the main goals of an e-commerce search system. Relevance prediction is essential to the search system since it helps improve performance. When online serving a relevance model, the model is required to perform fast and accurate inference. Currently, the widely used models such as Bi-encoder and Cross-encoder have their limitations in accuracy or inference speed respectively. In this work, we propose a novel model called the Entity-Based Relevance Model (EBRM). We identify the entities contained in an item and decompose the QI (query-item) relevance problem into multiple QE (query-entity) relevance problems; we then aggregate their results to form the QI prediction using a soft logic formulation. The decomposition allows us to use a Cross-encoder QE relevance module for high accuracy as well as cache QE predictions for fast online inference. Utilizing soft logic makes the prediction procedure interpretable and intervenable. We also show that pretraining the QE module with auto-generated QE data from user logs can further improve the overall performance. The proposed method is evaluated on labeled data from e-commerce websites. Empirical results show that it achieves promising improvements with computation efficiency.

Large language models (LLMs) have rapidly evolved from text generators into powerful problem solvers. Yet, many open tasks demand critical thinking, multi-source, and verifiable outputs, which are beyond single-shot prompting or standard retrieval-augmented generation. Recently, numerous studies have explored Deep Research (DR), which aims to combine the reasoning capabilities of LLMs with external tools, such as search engines, thereby empowering LLMs to act as research agents capable of completing complex, open-ended tasks. This survey presents a comprehensive and systematic overview of deep research systems, including a clear roadmap, foundational components, practical implementation techniques, important challenges, and future directions. Specifically, our main contributions are as follows: (i) we formalize a three-stage roadmap and distinguish deep research from related paradigms; (ii) we introduce four key components: query planning, information acquisition, memory management, and answer generation, each paired with fine-grained sub-taxonomies; (iii) we summarize optimization techniques, including prompting, supervised fine-tuning, and agentic reinforcement learning; and (iv) we consolidate evaluation criteria and open challenges, aiming to guide and facilitate future development. As the field of deep research continues to evolve rapidly, we are committed to continuously updating this survey to reflect the latest progress in this area.

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.