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The integration of multi-omic data is pivotal for understanding complex diseases, but its high dimensionality and noise present significant challenges. Graph Neural Networks (GNNs) offer a robust framework for analyzing large-scale signaling pathways and protein-protein interaction networks, yet they face limitations in expressivity when capturing intricate biological relationships. To address this, we propose Graph Sequence Language Model (GraphSeqLM), a framework that enhances GNNs with biological sequence embeddings generated by Large Language Models (LLMs). These embeddings encode structural and biological properties of DNA, RNA, and proteins, augmenting GNNs with enriched features for analyzing sample-specific multi-omic data. By integrating topological, sequence-derived, and biological information, GraphSeqLM demonstrates superior predictive accuracy and outperforms existing methods, paving the way for more effective multi-omic data integration in precision medicine.

The recent surge in research interest in applying large language models (LLMs) to decision-making tasks has flourished by leveraging the extensive world knowledge embedded in LLMs. While there is a growing demand to tailor LLMs for custom decision-making tasks, finetuning them for specific tasks is resource-intensive and may diminish the model's generalization capabilities. Moreover, state-of-the-art language models like GPT-4 and Claude are primarily accessible through API calls, with their parametric weights remaining proprietary and unavailable to the public. This scenario emphasizes the growing need for new methodologies that allow learning from agent experiences without requiring parametric updates. To address these problems, we introduce the Experiential Learning (ExpeL) agent. Our agent autonomously gathers experiences and extracts knowledge using natural language from a collection of training tasks. At inference, the agent recalls its extracted insights and past experiences to make informed decisions. Our empirical results highlight the robust learning efficacy of the ExpeL agent, indicating a consistent enhancement in its performance as it accumulates experiences. We further explore the emerging capabilities and transfer learning potential of the ExpeL agent through qualitative observations and additional experiments.

Previous research has shown that constraining the gradient of loss function with respect to model-predicted probabilities can enhance the model robustness against noisy labels. These methods typically specify a fixed optimal threshold for gradient clipping through validation data to obtain the desired robustness against noise. However, this common practice overlooks the dynamic distribution of gradients from both clean and noisy-labeled samples at different stages of training, significantly limiting the model capability to adapt to the variable nature of gradients throughout the training process. To address this issue, we propose a simple yet effective approach called Optimized Gradient Clipping (OGC), which dynamically adjusts the clipping threshold based on the ratio of noise gradients to clean gradients after clipping, estimated by modeling the distributions of clean and noisy samples. This approach allows us to modify the clipping threshold at each training step, effectively controlling the influence of noise gradients. Additionally, we provide statistical analysis to certify the noise-tolerance ability of OGC. Our extensive experiments across various types of label noise, including symmetric, asymmetric, instance-dependent, and real-world noise, demonstrate the effectiveness of our approach.

Knowledge utilization is a critical aspect of LLMs, and understanding how they adapt to evolving knowledge is essential for their effective deployment. However, existing benchmarks are predominantly static, failing to capture the evolving nature of LLMs and knowledge, leading to inaccuracies and vulnerabilities such as contamination. In this paper, we introduce EvoWiki, an evolving dataset designed to reflect knowledge evolution by categorizing information into stable, evolved, and uncharted states. EvoWiki is fully auto-updatable, enabling precise evaluation of continuously changing knowledge and newly released LLMs. Through experiments with Retrieval-Augmented Generation (RAG) and Contunual Learning (CL), we evaluate how effectively LLMs adapt to evolving knowledge. Our results indicate that current models often struggle with evolved knowledge, frequently providing outdated or incorrect responses. Moreover, the dataset highlights a synergistic effect between RAG and CL, demonstrating their potential to better adapt to evolving knowledge. EvoWiki provides a robust benchmark for advancing future research on the knowledge evolution capabilities of large language models.

Insider threats (InTs) within organizations are small in number but have a disproportionate ability to damage systems, information, and infrastructure. Existing InT research studies the problem from psychological, technical, and educational perspectives. Proposed theories include research on psychological indicators, machine learning, user behavioral log analysis, and educational methods to teach employees recognition and mitigation techniques. Because InTs are a human problem, training methods that address InT detection from a behavioral perspective are critical. While numerous technological and psychological theories exist on detection, prevention, and mitigation, few training methods prioritize psychological indicators. This literature review studied peer-reviewed, InT research organized by subtopic and extracted critical theories from psychological, technical, and educational disciplines. In doing so, this is the first study to comprehensively organize research across all three approaches in a manner which properly informs the development of an InT education platform.

Interpretability methods are developed to understand the working mechanisms of black-box models, which is crucial to their responsible deployment. Fulfilling this goal requires both that the explanations generated by these methods are correct and that people can easily and reliably understand them. While the former has been addressed in prior work, the latter is often overlooked, resulting in informal model understanding derived from a handful of local explanations. In this paper, we introduce explanation summary (ExSum), a mathematical framework for quantifying model understanding, and propose metrics for its quality assessment. On two domains, ExSum highlights various limitations in the current practice, helps develop accurate model understanding, and reveals easily overlooked properties of the model. We also connect understandability to other properties of explanations such as human alignment, robustness, and counterfactual minimality and plausibility.

Learning disentanglement aims at finding a low dimensional representation which consists of multiple explanatory and generative factors of the observational data. The framework of variational autoencoder (VAE) is commonly used to disentangle independent factors from observations. However, in real scenarios, factors with semantics are not necessarily independent. Instead, there might be an underlying causal structure which renders these factors dependent. We thus propose a new VAE based framework named CausalVAE, which includes a Causal Layer to transform independent exogenous factors into causal endogenous ones that correspond to causally related concepts in data. We further analyze the model identifiabitily, showing that the proposed model learned from observations recovers the true one up to a certain degree. Experiments are conducted on various datasets, including synthetic and real word benchmark CelebA. Results show that the causal representations learned by CausalVAE are semantically interpretable, and their causal relationship as a Directed Acyclic Graph (DAG) is identified with good accuracy. Furthermore, we demonstrate that the proposed CausalVAE model is able to generate counterfactual data through "do-operation" to the causal factors.

We present CoDEx, a set of knowledge graph completion datasets extracted from Wikidata and Wikipedia that improve upon existing knowledge graph completion benchmarks in scope and level of difficulty. In terms of scope, CoDEx comprises three knowledge graphs varying in size and structure, multilingual descriptions of entities and relations, and tens of thousands of hard negative triples that are plausible but verified to be false. To characterize CoDEx, we contribute thorough empirical analyses and benchmarking experiments. First, we analyze each CoDEx dataset in terms of logical relation patterns. Next, we report baseline link prediction and triple classification results on CoDEx for five extensively tuned embedding models. Finally, we differentiate CoDEx from the popular FB15K-237 knowledge graph completion dataset by showing that CoDEx covers more diverse and interpretable content, and is a more difficult link prediction benchmark. Data, code, and pretrained models are available at //bit.ly/2EPbrJs.

The design of deep graph models still remains to be investigated and the crucial part is how to explore and exploit the knowledge from different hops of neighbors in an efficient way. In this paper, we propose a novel RNN-like deep graph neural network architecture by incorporating AdaBoost into the computation of network; and the proposed graph convolutional network called AdaGCN~(AdaBoosting Graph Convolutional Network) has the ability to efficiently extract knowledge from high-order neighbors and integrate knowledge from different hops of neighbors into the network in an AdaBoost way. We also present the architectural difference between AdaGCN and existing graph convolutional methods to show the benefits of our proposal. Finally, extensive experiments demonstrate the state-of-the-art prediction performance and the computational advantage of our approach AdaGCN.

Generative Adversarial Networks (GANs) can produce images of surprising complexity and realism, but are generally modeled to sample from a single latent source ignoring the explicit spatial interaction between multiple entities that could be present in a scene. Capturing such complex interactions between different objects in the world, including their relative scaling, spatial layout, occlusion, or viewpoint transformation is a challenging problem. In this work, we propose to model object composition in a GAN framework as a self-consistent composition-decomposition network. Our model is conditioned on the object images from their marginal distributions to generate a realistic image from their joint distribution by explicitly learning the possible interactions. We evaluate our model through qualitative experiments and user evaluations in both the scenarios when either paired or unpaired examples for the individual object images and the joint scenes are given during training. Our results reveal that the learned model captures potential interactions between the two object domains given as input to output new instances of composed scene at test time in a reasonable fashion.