Self-supervised Hierarchical Representation for Medication Recommendation

Medication recommender is to suggest appropriate medication combinations based on a patient's health history, e.g., diagnoses and procedures. Existing works represent different diagnoses/procedures well separated by one-hot encodings. However, they ignore the latent hierarchical structures of these medical terms, undermining the generalization performance of the model. For example, "Respiratory Diseases", "Chronic Respiratory Diseases" and "Chronic Bronchiti" have a hierarchical relationship, progressing from general to specific. To address this issue, we propose a novel hierarchical encoder named HIER to hierarchically represent diagnoses and procedures, which is based on standard medical codes and compatible with any existing methods. Specifically, the proposed method learns relation embedding with a self-supervised objective for incorporating the neighbor hierarchical structure. Additionally, we develop the position encoding to explicitly introduce global hierarchical position. Extensive experiments demonstrate significant and consistent improvements in recommendation accuracy across four baselines and two real-world clinical datasets.

Generalizability of Graph Neural Network Force Fields for Predicting Solid-State Properties

Machine-learned force fields (MLFFs) promise to offer a computationally efficient alternative to ab initio simulations for complex molecular systems. However, ensuring their generalizability beyond training data is crucial for their wide application in studying solid materials. This work investigates the ability of a graph neural network (GNN)-based MLFF, trained on Lennard-Jones Argon, to describe solid-state phenomena not explicitly included during training. We assess the MLFF's performance in predicting phonon density of states (PDOS) for a perfect face-centered cubic (FCC) crystal structure at both zero and finite temperatures. Additionally, we evaluate vacancy migration rates and energy barriers in an imperfect crystal using direct molecular dynamics (MD) simulations and the string method. Notably, vacancy configurations were absent from the training data. Our results demonstrate the MLFF's capability to capture essential solid-state properties with good agreement to reference data, even for unseen configurations. We further discuss data engineering strategies to enhance the generalizability of MLFFs. The proposed set of benchmark tests and workflow for evaluating MLFF performance in describing perfect and imperfect crystals pave the way for reliable application of MLFFs in studying complex solid-state materials.

CTISum: A New Benchmark Dataset For Cyber Threat Intelligence Summarization

Cyber Threat Intelligence (CTI) summarization task requires the system to generate concise and accurate highlights from raw intelligence data, which plays an important role in providing decision-makers with crucial information to quickly detect and respond to cyber threats in the cybersecurity domain. However, efficient techniques for summarizing CTI reports, including facts, analytical insights, attack processes, etc., have largely been unexplored, primarily due to the lack of available dataset. To this end, we present CTISum, a new benchmark for CTI summarization task. Considering the importance of attack process, a novel fine-grained subtask of attack process summarization is proposed to enable defenders to assess risk, identify security gaps, vulnerabilities, and so on. Specifically, we first design a multi-stage annotation pipeline to gather and annotate the CTI data, and then benchmark the CTISum with a collection of extractive and abstractive summarization methods. Experimental results show that current state-of-the-art models exhibit limitations when applied to CTISum, underscoring the fact that automatically producing concise summaries of CTI reports remains an open research challenge.

Deep Neural Networks with Symplectic Preservation Properties

We propose a deep neural network architecture designed such that its output forms an invertible symplectomorphism of the input. This design draws an analogy to the real-valued non-volume-preserving (real NVP) method used in normalizing flow techniques. Utilizing this neural network type allows for learning tasks on unknown Hamiltonian systems without breaking the inherent symplectic structure of the phase space.

SoftTiger: A Clinical Foundation Model for Healthcare Workflows

We release and introduce SoftTiger, a clinical large language model (CLaM) designed as a foundation model for healthcare workflows. The narrative and unstructured nature of clinical notes is a major obstacle for healthcare intelligentization. We address a critical problem of structuring clinical notes into clinical data, according to international interoperability standards. We collect and annotate data for three critical subtasks, namely, international patient summary, clinical impression and medical encounter. We then supervised fine-tuned a state-of-the-art LLM using public and credentialed clinical data. The training is orchestrated in a way that the target model can first support basic clinical tasks such as abbreviation expansion and temporal information extraction, and then learn to perform more complex downstream clinical tasks such as impression and encounter summary. Moreover, we address, several modeling challenges in the healthcare context, e.g., extra long context window. Our blind pairwise evaluation shows that SoftTiger outperforms other popular open-source models and GPT-3.5, comparable to Gemini-pro, and only has a mild gap from GPT-4. We believe that LLMs may become a step-stone towards healthcare digitalization and democratization. Therefore, we publicly release SoftTiger models at scales of 13 billion and 70 billion parameters, as well as datasets and code for our innovative scalable evaluation, hopefully, making a significant contribution to the healthcare industry.

Accelerated Sampling of Rare Events using a Neural Network Bias Potential

In the field of computational physics and material science, the efficient sampling of rare events occurring at atomic scale is crucial. It aids in understanding mechanisms behind a wide range of important phenomena, including protein folding, conformal changes, chemical reactions and materials diffusion and deformation. Traditional simulation methods, such as Molecular Dynamics and Monte Carlo, often prove inefficient in capturing the timescale of these rare events by brute force. In this paper, we introduce a practical approach by combining the idea of importance sampling with deep neural networks (DNNs) that enhance the sampling of these rare events. In particular, we approximate the variance-free bias potential function with DNNs which is trained to maximize the probability of rare event transition under the importance potential function. This method is easily scalable to high-dimensional problems and provides robust statistical guarantees on the accuracy of the estimated probability of rare event transition. Furthermore, our algorithm can actively generate and learn from any successful samples, which is a novel improvement over existing methods. Using a 2D system as a test bed, we provide comparisons between results obtained from different training strategies, traditional Monte Carlo sampling and numerically solved optimal bias potential function under different temperatures. Our numerical results demonstrate the efficacy of the DNN-based importance sampling of rare events.

TigerBot: An Open Multilingual Multitask LLM

We release and introduce the TigerBot family of large language models (LLMs), consisting of base and chat models, sized from 7, 13, 70 and 180 billion parameters. We develop our models embarking from Llama-2 and BLOOM, and push the boundary further in data, training algorithm, infrastructure, and application tools. Our models yield meaningful performance gain over SOTA open-source models, e.g., Llama-2, specifically 6% gain in English and 20% gain in Chinese. TigerBot model family also achieves leading performance in major academic and industrial benchmarks and leaderboards. We believe that TigerBot represents just a snapshot of lightning-fast progression in LLM open-source community. Therefore, we are thrilled to give back by publicly releasing our models and reporting our approach behind, with additional emphases on building SOTA LLMs in a democratized way and making LLMs of use in real-world applications.

Prediction of Effective Elastic Moduli of Rocks using Graph Neural Networks

This study presents a Graph Neural Networks (GNNs)-based approach for predicting the effective elastic moduli of rocks from their digital CT-scan images. We use the Mapper algorithm to transform 3D digital rock images into graph datasets, encapsulating essential geometrical information. These graphs, after training, prove effective in predicting elastic moduli. Our GNN model shows robust predictive capabilities across various graph sizes derived from various subcube dimensions. Not only does it perform well on the test dataset, but it also maintains high prediction accuracy for unseen rocks and unexplored subcube sizes. Comparative analysis with Convolutional Neural Networks (CNNs) reveals the superior performance of GNNs in predicting unseen rock properties. Moreover, the graph representation of microstructures significantly reduces GPU memory requirements (compared to the grid representation for CNNs), enabling greater flexibility in the batch size selection. This work demonstrates the potential of GNN models in enhancing the prediction accuracy of rock properties and boosting the efficiency of digital rock analysis.

Homogenizing elastic properties of large digital rock images by combining CNN with hierarchical homogenization method

Determining effective elastic properties of rocks from their pore-scale digital images is a key goal of digital rock physics (DRP). Direct numerical simulation (DNS) of elastic behavior, however, incurs high computational cost; and surrogate machine learning (ML) model, particularly convolutional neural network (CNN), show promises to accelerate homogenization process. 3D CNN models, however, are unable to handle large images due to memory issues. To address this challenge, we propose a novel method that combines 3D CNN with hierarchical homogenization method (HHM). The surrogate 3D CNN model homogenizes only small subimages, and a DNS is used to homogenize the intermediate image obtained by assembling small subimages. The 3D CNN model is designed to output the homogenized elastic constants within the Hashin-Shtrikman (HS) bounds of the input images. The 3D CNN model is first trained on data comprising equal proportions of five sandstone (quartz mineralogy) images, and, subsequently, fine-tuned for specific rocks using transfer learning. The proposed method is applied to homogenize the rock images of size 300x300x300 and 600x600x600 voxels, and the predicted homogenized elastic moduli are shown to agree with that obtained from the brute-force DNS. The transferability of the trained 3D CNN model (using transfer learning) is further demonstrated by predicting the homogenized elastic moduli of a limestone rock with calcite mineralogy. The surrogate 3D CNN model in combination with the HHM is thus shown to be a promising tool for the homogenization of large 3D digital rock images and other random media

Evaluating the Transferability of Machine-Learned Force Fields for Material Property Modeling

Machine-learned force fields have generated significant interest in recent years as a tool for molecular dynamics (MD) simulations, with the aim of developing accurate and efficient models that can replace classical interatomic potentials. However, before these models can be confidently applied to materials simulations, they must be thoroughly tested and validated. The existing tests on the radial distribution function and mean-squared displacements are insufficient in assessing the transferability of these models. Here we present a more comprehensive set of benchmarking tests for evaluating the transferability of machine-learned force fields. We use a graph neural network (GNN)-based force field coupled with the OpenMM package to carry out MD simulations for Argon as a test case. Our tests include computational X-ray photon correlation spectroscopy (XPCS) signals, which capture the density fluctuation at various length scales in the liquid phase, as well as phonon density-of-state in the solid phase and the liquid-solid phase transition behavior. Our results show that the model can accurately capture the behavior of the solid phase only when the configurations from the solid phase are included in the training dataset. This underscores the importance of appropriately selecting the training data set when developing machine-learned force fields. The tests presented in this work provide a necessary foundation for the development and application of machine-learned force fields for materials simulations.