CoRelation: Boosting Automatic ICD Coding Through Contextualized Code Relation Learning

Automatic International Classification of Diseases (ICD) coding plays a crucial role in the extraction of relevant information from clinical notes for proper recording and billing. One of the most important directions for boosting the performance of automatic ICD coding is modeling ICD code relations. However, current methods insufficiently model the intricate relationships among ICD codes and often overlook the importance of context in clinical notes. In this paper, we propose a novel approach, a contextualized and flexible framework, to enhance the learning of ICD code representations. Our approach, unlike existing methods, employs a dependent learning paradigm that considers the context of clinical notes in modeling all possible code relations. We evaluate our approach on six public ICD coding datasets and the experimental results demonstrate the effectiveness of our approach compared to state-of-the-art baselines.

Force sensing to reconstruct potential energy landscapes for cluttered large obstacle traversal

Visual sensing of environmental geometry allows robots to use artificial potential fields to avoid sparse obstacles. Yet robots must further traverse cluttered large obstacles for applications like search and rescue through rubble and planetary exploration across Martain rocks. Recent studies discovered that to traverse cluttered large obstacles, multi-legged insects and insect-inspired robots make strenuous transitions across locomotor modes with major changes in body orientation. When viewed on a potential energy landscape resulting from locomotor-obstacle physical interaction, these are barrier-crossing transitions across landscape basins. This potential energy landscape approach may provide a modeling framework for cluttered large obstacle traversal. Here, we take the next step toward this vision by testing whether force sensing allows the reconstruction of the potential energy landscape. We developed a cockroach-inspired, minimalistic robot capable of sensing obstacle contact forces and torques around its body as it propelled forward against a pair of cluttered grass-like beam obstacles. We performed measurements over many traverses with systematically varied body orientations. Despite the forces and torques not being fully conservative, they well-matched the potential energy landscape gradients and the landscape reconstructed from them well-matched ground truth. In addition, inspired by cockroach observations, we found that robot head oscillation during traversal further improved the accuracies of force sensing and landscape reconstruction. We still need to study how to reconstruct landscape during a single traverse, as in applications, robots have little chance to use multiple traverses to sample the environment systematically and how to find landscape saddles for least-effort transitions to traverse.

Omni-SMoLA: Boosting Generalist Multimodal Models with Soft Mixture of Low-rank Experts

Large multi-modal models (LMMs) exhibit remarkable performance across numerous tasks. However, generalist LMMs often suffer from performance degradation when tuned over a large collection of tasks. Recent research suggests that Mixture of Experts (MoE) architectures are useful for instruction tuning, but for LMMs of parameter size around O(50-100B), the prohibitive cost of replicating and storing the expert models severely limits the number of experts we can use. We propose Omni-SMoLA, an architecture that uses the Soft MoE approach to (softly) mix many multimodal low rank experts, and avoids introducing a significant number of new parameters compared to conventional MoE models. The core intuition here is that the large model provides a foundational backbone, while different lightweight experts residually learn specialized knowledge, either per-modality or multimodally. Extensive experiments demonstrate that the SMoLA approach helps improve the generalist performance across a broad range of generative vision-and-language tasks, achieving new SoTA generalist performance that often matches or outperforms single specialized LMM baselines, as well as new SoTA specialist performance.

Accurate and interpretable drug-drug interaction prediction enabled by knowledge subgraph learning

Background: Discovering potential drug-drug interactions (DDIs) is a long-standing challenge in clinical treatments and drug developments. Recently, deep learning techniques have been developed for DDI prediction. However, they generally require a huge number of samples, while known DDIs are rare. Methods: In this work, we present KnowDDI, a graph neural network-based method that addresses the above challenge. KnowDDI enhances drug representations by adaptively leveraging rich neighborhood information from large biomedical knowledge graphs. Then, it learns a knowledge subgraph for each drug-pair to interpret the predicted DDI, where each of the edges is associated with a connection strength indicating the importance of a known DDI or resembling strength between a drug-pair whose connection is unknown. Thus, the lack of DDIs is implicitly compensated by the enriched drug representations and propagated drug similarities. Results: We evaluate KnowDDI on two benchmark DDI datasets. Results show that KnowDDI obtains the state-of-the-art prediction performance with better interpretability. We also find that KnowDDI suffers less than existing works given a sparser knowledge graph. This indicates that the propagated drug similarities play a more important role in compensating for the lack of DDIs when the drug representations are less enriched. Conclusions: KnowDDI nicely combines the efficiency of deep learning techniques and the rich prior knowledge in biomedical knowledge graphs. As an original open-source tool, KnowDDI can help detect possible interactions in a broad range of relevant interaction prediction tasks, such as protein-protein interactions, drug-target interactions and disease-gene interactions, eventually promoting the development of biomedicine and healthcare.

Hierarchical Pretraining on Multimodal Electronic Health Records

Pretraining has proven to be a powerful technique in natural language processing (NLP), exhibiting remarkable success in various NLP downstream tasks. However, in the medical domain, existing pretrained models on electronic health records (EHR) fail to capture the hierarchical nature of EHR data, limiting their generalization capability across diverse downstream tasks using a single pretrained model. To tackle this challenge, this paper introduces a novel, general, and unified pretraining framework called MEDHMP, specifically designed for hierarchically multimodal EHR data. The effectiveness of the proposed MEDHMP is demonstrated through experimental results on eight downstream tasks spanning three levels. Comparisons against eighteen baselines further highlight the efficacy of our approach.

Non-Intrusive Adaptation: Input-Centric Parameter-efficient Fine-Tuning for Versatile Multimodal Modeling

Large language models (LLMs) and vision language models (VLMs) demonstrate excellent performance on a wide range of tasks by scaling up parameter counts from O(10^9) to O(10^{12}) levels and further beyond. These large scales make it impossible to adapt and deploy fully specialized models given a task of interest. Parameter-efficient fine-tuning (PEFT) emerges as a promising direction to tackle the adaptation and serving challenges for such large models. We categorize PEFT techniques into two types: intrusive and non-intrusive. Intrusive PEFT techniques directly change a model's internal architecture. Though more flexible, they introduce significant complexities for training and serving. Non-intrusive PEFT techniques leave the internal architecture unchanged and only adapt model-external parameters, such as embeddings for input. In this work, we describe AdaLink as a non-intrusive PEFT technique that achieves competitive performance compared to SoTA intrusive PEFT (LoRA) and full model fine-tuning (FT) on various tasks. We evaluate using both text-only and multimodal tasks, with experiments that account for both parameter-count scaling and training regime (with and without instruction tuning).

Automated Evaluation of Personalized Text Generation using Large Language Models

Personalized text generation presents a specialized mechanism for delivering content that is specific to a user's personal context. While the research progress in this area has been rapid, evaluation still presents a challenge. Traditional automated metrics such as BLEU and ROUGE primarily measure lexical similarity to human-written references, and are not able to distinguish personalization from other subtle semantic aspects, thus falling short of capturing the nuances of personalized generated content quality. On the other hand, human judgments are costly to obtain, especially in the realm of personalized evaluation. Inspired by these challenges, we explore the use of large language models (LLMs) for evaluating personalized text generation, and examine their ability to understand nuanced user context. We present AuPEL, a novel evaluation method that distills three major semantic aspects of the generated text: personalization, quality and relevance, and automatically measures these aspects. To validate the effectiveness of AuPEL, we design carefully controlled experiments and compare the accuracy of the evaluation judgments made by LLMs versus that of judgements made by human annotators, and conduct rigorous analyses of the consistency and sensitivity of the proposed metric. We find that, compared to existing evaluation metrics, AuPEL not only distinguishes and ranks models based on their personalization abilities more accurately, but also presents commendable consistency and efficiency for this task. Our work suggests that using LLMs as the evaluators of personalized text generation is superior to traditional text similarity metrics, even though interesting new challenges still remain.

Outlier Weighed Layerwise Sparsity (OWL): A Missing Secret Sauce for Pruning LLMs to High Sparsity

Large Language Models (LLMs), renowned for their remarkable performance, present a challenge due to their colossal model size when it comes to practical deployment. In response to this challenge, efforts have been directed toward the application of traditional network pruning techniques to LLMs, uncovering a massive number of parameters can be pruned in one-shot without hurting performance. Building upon insights gained from pre-LLM models, prevailing LLM pruning strategies have consistently adhered to the practice of uniformly pruning all layers at equivalent sparsity. However, this observation stands in contrast to the prevailing trends observed in the field of vision models, where non-uniform layerwise sparsity typically yields substantially improved results. To elucidate the underlying reasons for this disparity, we conduct a comprehensive analysis of the distribution of token features within LLMs. In doing so, we discover a strong correlation with the emergence of outliers, defined as features exhibiting significantly greater magnitudes compared to their counterparts in feature dimensions. Inspired by this finding, we introduce a novel LLM pruning methodology that incorporates a tailored set of non-uniform layerwise sparsity ratios specifically designed for LLM pruning, termed as Outlier Weighed Layerwise sparsity (OWL). The sparsity ratio of OWL is directly proportional to the outlier ratio observed within each layer, facilitating a more effective alignment between layerwise weight sparsity and outlier ratios. Our empirical evaluation, conducted across the LLaMA-V1 family and OPT, spanning various benchmarks, demonstrates the distinct advantages offered by OWL over previous methods. For instance, our approach exhibits a remarkable performance gain, surpassing the state-of-the-art Wanda and SparseGPT by 61.22 and 6.80 perplexity at a high sparsity level of 70%, respectively.

MedDiffusion: Boosting Health Risk Prediction via Diffusion-based Data Augmentation

Health risk prediction is one of the fundamental tasks under predictive modeling in the medical domain, which aims to forecast the potential health risks that patients may face in the future using their historical Electronic Health Records (EHR). Researchers have developed several risk prediction models to handle the unique challenges of EHR data, such as its sequential nature, high dimensionality, and inherent noise. These models have yielded impressive results. Nonetheless, a key issue undermining their effectiveness is data insufficiency. A variety of data generation and augmentation methods have been introduced to mitigate this issue by expanding the size of the training data set through the learning of underlying data distributions. However, the performance of these methods is often limited due to their task-unrelated design. To address these shortcomings, this paper introduces a novel, end-to-end diffusion-based risk prediction model, named MedDiffusion. It enhances risk prediction performance by creating synthetic patient data during training to enlarge sample space. Furthermore, MedDiffusion discerns hidden relationships between patient visits using a step-wise attention mechanism, enabling the model to automatically retain the most vital information for generating high-quality data. Experimental evaluation on four real-world medical datasets demonstrates that MedDiffusion outperforms 14 cutting-edge baselines in terms of PR-AUC, F1, and Cohen's Kappa. We also conduct ablation studies and benchmark our model against GAN-based alternatives to further validate the rationality and adaptability of our model design. Additionally, we analyze generated data to offer fresh insights into the model's interpretability.