Traumatic Brain Injury (TBI) presents a broad spectrum of clinical presentations and outcomes due to its inherent heterogeneity, leading to diverse recovery trajectories and varied therapeutic responses. While many studies have delved into TBI phenotyping for distinct patient populations, identifying TBI phenotypes that consistently generalize across various settings and populations remains a critical research gap. Our research addresses this by employing multivariate time-series clustering to unveil TBI's dynamic intricates. Utilizing a self-supervised learning-based approach to clustering multivariate time-Series data with missing values (SLAC-Time), we analyzed both the research-centric TRACK-TBI and the real-world MIMIC-IV datasets. Remarkably, the optimal hyperparameters of SLAC-Time and the ideal number of clusters remained consistent across these datasets, underscoring SLAC-Time's stability across heterogeneous datasets. Our analysis revealed three generalizable TBI phenotypes ({\alpha}, \b{eta}, and {\gamma}), each exhibiting distinct non-temporal features during emergency department visits, and temporal feature profiles throughout ICU stays. Specifically, phenotype {\alpha} represents mild TBI with a remarkably consistent clinical presentation. In contrast, phenotype \b{eta} signifies severe TBI with diverse clinical manifestations, and phenotype {\gamma} represents a moderate TBI profile in terms of severity and clinical diversity. Age is a significant determinant of TBI outcomes, with older cohorts recording higher mortality rates. Importantly, while certain features varied by age, the core characteristics of TBI manifestations tied to each phenotype remain consistent across diverse populations.
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Recent advances in generative models for medical imaging have shown promise in representing multiple modalities. However, the variability in modality availability across datasets limits the general applicability of the synthetic data they produce. To address this, we present a novel physics-informed generative model capable of synthesizing a variable number of brain MRI modalities, including those not present in the original dataset. Our approach utilizes latent diffusion models and a two-step generative process: first, unobserved physical tissue property maps are synthesized using a latent diffusion model, and then these maps are combined with a physical signal model to generate the final MRI scan. Our experiments demonstrate the efficacy of this approach in generating unseen MR contrasts and preserving physical plausibility. Furthermore, we validate the distributions of generated tissue properties by comparing them to those measured in real brain tissue.
Natural Language Processing (NLP) techniques have been increasingly integrated into clinical projects to advance clinical decision-making and improve patient outcomes. Such projects benefit from interdisciplinary team collaborations. This paper explores challenges and opportunities using two clinical NLP projects as case studies, where speech-language pathologists (SLPs) and NLP researchers jointly developed technology-based systems to improve clinical workflow. Through semi-structured interviews with five SLPs and four NLP researchers, we collected collaboration practices and challenges. Using Activity Theory as an analytical framework, we examined collaborative activities, challenges, and strategies to bridge interdisciplinary gaps. Our findings revealed significant knowledge boundaries and terminological barriers between SLPs and NLP researchers when both groups relied on clinical data as boundary objects to facilitate collaboration, although this approach has limitations. We highlight the potential opportunities of AI technologies as knowledge brokers to overcome interdisciplinary collaboration challenges.
Message-passing Graph Neural Networks (GNNs), which collect information from adjacent nodes achieve dismal performance on heterophilic graphs. Various schemes have been proposed to solve this problem, and propagating signed information on heterophilic edges has gained great attention. Recently, some works provided theoretical analysis that signed propagation always leads to performance improvement under a binary class scenario. However, we notice that prior analyses do not align well with multi-class benchmark datasets. This paper provides a new understanding of signed propagation for multi-class scenarios and points out two drawbacks in terms of message-passing and parameter update: (1) Message-passing: if two nodes belong to different classes but have a high similarity, signed propagation can decrease the separability. (2) Parameter update: the prediction uncertainty (e.g., conflict evidence) of signed neighbors increases during training, which can impede the stability of the algorithm. Based on the observation, we introduce two novel strategies for improving signed propagation under multi-class graphs. The proposed scheme combines calibration to secure robustness while reducing uncertainty. We show the efficacy of our theorem through extensive experiments on six benchmark graph datasets.
Estimating heterogeneous treatment effect (HTE) for survival outcomes has gained increasing attention, as it captures the variation in treatment efficacy across patients or subgroups in delaying disease progression. However, most existing methods focus on post-hoc subgroup identification rather than simultaneously estimating HTE and selecting relevant subgroups. In this paper, we propose an interpretable HTE estimation framework that integrates three meta-learners that simultaneously estimate CATE for survival outcomes and identify predictive subgroups. We evaluated the performance of our method through comprehensive simulation studies across various randomized clinical trial (RCT) settings. Additionally, we demonstrated its application in a large RCT for age-related macular degeneration (AMD), a polygenic progressive eye disease, to estimate the HTE of an antioxidant and mineral supplement on time-to-AMD progression and to identify genetics-based subgroups with enhanced treatment effects. Our method offers a direct interpretation of the estimated HTE and provides evidence to support precision healthcare.
Quantum Relative Entropy (QRE) programming is a recently popular and challenging class of convex optimization problems with significant applications in quantum computing and quantum information theory. We are interested in modern interior point (IP) methods based on optimal self-concordant barriers for the QRE cone. A range of theoretical and numerical challenges associated with such barrier functions and the QRE cones have hindered the scalability of IP methods. To address these challenges, we propose a series of numerical and linear algebraic techniques and heuristics aimed at enhancing the efficiency of gradient and Hessian computations for the self-concordant barrier function, solving linear systems, and performing matrix-vector products. We also introduce and deliberate about some interesting concepts related to QRE such as symmetric quantum relative entropy (SQRE). We also introduce a two-phase method for performing facial reduction that can significantly improve the performance of QRE programming. Our new techniques have been implemented in the latest version (DDS 2.2) of the software package DDS. In addition to handling QRE constraints, DDS accepts any combination of several other conic and non-conic convex constraints. Our comprehensive numerical experiments encompass several parts including 1) a comparison of DDS 2.2 with Hypatia for the nearest correlation matrix problem, 2) using DDS for combining QRE constraints with various other constraint types, and 3) calculating the key rate for quantum key distribution (QKD) channels and presenting results for several QKD protocols.
Echo State Networks (ESNs) are recurrent neural networks usually employed for modeling nonlinear dynamic systems with relatively ease of training. By incorporating physical laws into the training of ESNs, Physics-Informed ESNs (PI-ESNs) were proposed initially to model chaotic dynamic systems without external inputs. They require less data for training since Ordinary Differential Equations (ODEs) of the considered system help to regularize the ESN. In this work, the PI-ESN is extended with external inputs to model controllable nonlinear dynamic systems. Additionally, an existing self-adaptive balancing loss method is employed to balance the contributions of the residual regression term and the physics-informed loss term in the total loss function. The experiments with two nonlinear systems modeled by ODEs, the Van der Pol oscillator and the four-tank system, and with one differential-algebraic (DAE) system, an electric submersible pump, revealed that the proposed PI-ESN outperforms the conventional ESN, especially in scenarios with limited data availability, showing that PI-ESNs can regularize an ESN model with external inputs previously trained on just a few datapoints, reducing its overfitting and improving its generalization error (up to 92% relative reduction in the test error). Further experiments demonstrated that the proposed PI-ESN is robust to parametric uncertainties in the ODE equations and that model predictive control using PI-ESN outperforms the one using plain ESN, particularly when training data is scarce.
Large Language Models (LLMs) have shown excellent generalization capabilities that have led to the development of numerous models. These models propose various new architectures, tweaking existing architectures with refined training strategies, increasing context length, using high-quality training data, and increasing training time to outperform baselines. Analyzing new developments is crucial for identifying changes that enhance training stability and improve generalization in LLMs. This survey paper comprehensively analyses the LLMs architectures and their categorization, training strategies, training datasets, and performance evaluations and discusses future research directions. Moreover, the paper also discusses the basic building blocks and concepts behind LLMs, followed by a complete overview of LLMs, including their important features and functions. Finally, the paper summarizes significant findings from LLM research and consolidates essential architectural and training strategies for developing advanced LLMs. Given the continuous advancements in LLMs, we intend to regularly update this paper by incorporating new sections and featuring the latest LLM models.
We consider the problem of explaining the predictions of graph neural networks (GNNs), which otherwise are considered as black boxes. Existing methods invariably focus on explaining the importance of graph nodes or edges but ignore the substructures of graphs, which are more intuitive and human-intelligible. In this work, we propose a novel method, known as SubgraphX, to explain GNNs by identifying important subgraphs. Given a trained GNN model and an input graph, our SubgraphX explains its predictions by efficiently exploring different subgraphs with Monte Carlo tree search. To make the tree search more effective, we propose to use Shapley values as a measure of subgraph importance, which can also capture the interactions among different subgraphs. To expedite computations, we propose efficient approximation schemes to compute Shapley values for graph data. Our work represents the first attempt to explain GNNs via identifying subgraphs explicitly and directly. Experimental results show that our SubgraphX achieves significantly improved explanations, while keeping computations at a reasonable level.
Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.
Semantic Role Labeling (SRL) is believed to be a crucial step towards natural language understanding and has been widely studied. Recent years, end-to-end SRL with recurrent neural networks (RNN) has gained increasing attention. However, it remains a major challenge for RNNs to handle structural information and long range dependencies. In this paper, we present a simple and effective architecture for SRL which aims to address these problems. Our model is based on self-attention which can directly capture the relationships between two tokens regardless of their distance. Our single model achieves F$_1=83.4$ on the CoNLL-2005 shared task dataset and F$_1=82.7$ on the CoNLL-2012 shared task dataset, which outperforms the previous state-of-the-art results by $1.8$ and $1.0$ F$_1$ score respectively. Besides, our model is computationally efficient, and the parsing speed is 50K tokens per second on a single Titan X GPU.
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