Continually Evolved Multimodal Foundation Models for Cancer Prognosis

Cancer prognosis is a critical task that involves predicting patient outcomes and survival rates. To enhance prediction accuracy, previous studies have integrated diverse data modalities, such as clinical notes, medical images, and genomic data, leveraging their complementary information. However, existing approaches face two major limitations. First, they struggle to incorporate newly arrived data with varying distributions into training, such as patient records from different hospitals, thus rendering sub-optimal generalizability and limited utility in real-world applications. Second, most multimodal integration methods rely on simplistic concatenation or task-specific pipelines, which fail to capture the complex interdependencies across modalities. To address these, we propose a continually evolving multi-modal foundation model. Extensive experiments on the TCGA dataset demonstrate the effectiveness of our approach, highlighting its potential to advance cancer prognosis by enabling robust and adaptive multimodal integration.

DeepSeek-V3 Technical Report

We present DeepSeek-V3, a strong Mixture-of-Experts (MoE) language model with 671B total parameters with 37B activated for each token. To achieve efficient inference and cost-effective training, DeepSeek-V3 adopts Multi-head Latent Attention (MLA) and DeepSeekMoE architectures, which were thoroughly validated in DeepSeek-V2. Furthermore, DeepSeek-V3 pioneers an auxiliary-loss-free strategy for load balancing and sets a multi-token prediction training objective for stronger performance. We pre-train DeepSeek-V3 on 14.8 trillion diverse and high-quality tokens, followed by Supervised Fine-Tuning and Reinforcement Learning stages to fully harness its capabilities. Comprehensive evaluations reveal that DeepSeek-V3 outperforms other open-source models and achieves performance comparable to leading closed-source models. Despite its excellent performance, DeepSeek-V3 requires only 2.788M H800 GPU hours for its full training. In addition, its training process is remarkably stable. Throughout the entire training process, we did not experience any irrecoverable loss spikes or perform any rollbacks. The model checkpoints are available at https://github.com/deepseek-ai/DeepSeek-V3.

RAMIE: Retrieval-Augmented Multi-task Information Extraction with Large Language Models on Dietary Supplements

\textbf{Objective:} We aimed to develop an advanced multi-task large language model (LLM) framework to extract multiple types of information about dietary supplements (DS) from clinical records. \textbf{Methods:} We used four core DS information extraction tasks - namely, named entity recognition (NER: 2,949 clinical sentences), relation extraction (RE: 4,892 sentences), triple extraction (TE: 2,949 sentences), and usage classification (UC: 2,460 sentences) as our multitasks. We introduced a novel Retrieval-Augmented Multi-task Information Extraction (RAMIE) Framework, including: 1) employed instruction fine-tuning techniques with task-specific prompts, 2) trained LLMs for multiple tasks with improved storage efficiency and lower training costs, and 3) incorporated retrieval augmentation generation (RAG) techniques by retrieving similar examples from the training set. We compared RAMIE's performance to LLMs with instruction fine-tuning alone and conducted an ablation study to assess the contributions of multi-task learning and RAG to improved multitasking performance. \textbf{Results:} With the aid of the RAMIE framework, Llama2-13B achieved an F1 score of 87.39 (3.51\% improvement) on the NER task and demonstrated outstanding performance on the RE task with an F1 score of 93.74 (1.15\% improvement). For the TE task, Llama2-7B scored 79.45 (14.26\% improvement), and MedAlpaca-7B achieved the highest F1 score of 93.45 (0.94\% improvement) on the UC task. The ablation study revealed that while MTL increased efficiency with a slight trade-off in performance, RAG significantly boosted overall accuracy. \textbf{Conclusion:} This study presents a novel RAMIE framework that demonstrates substantial improvements in multi-task information extraction for DS-related data from clinical records. Our framework can potentially be applied to other domains.

Deep Q-Exponential Processes

Motivated by deep neural networks, the deep Gaussian process (DGP) generalizes the standard GP by stacking multiple layers of GPs. Despite the enhanced expressiveness, GP, as an $L_2$ regularization prior, tends to be over-smooth and sub-optimal for inhomogeneous subjects, such as images with edges. Recently, Q-exponential process (Q-EP) has been proposed as an $L_q$ relaxation to GP and demonstrated with more desirable regularization properties through a parameter $q>0$ with $q=2$ corresponding to GP. Sharing the similar tractability of posterior and predictive distributions with GP, Q-EP can also be stacked to improve its modeling flexibility. In this paper, we generalize Q-EP to deep Q-EP to enjoy both proper regularization and improved expressiveness. The generalization is realized by introducing shallow Q-EP as a latent variable model and then building a hierarchy of the shallow Q-EP layers. Sparse approximation by inducing points and scalable variational strategy are applied to facilitate the inference. We demonstrate the numerical advantages of the proposed deep Q-EP model by comparing with multiple state-of-the-art deep probabilistic models.

Large Language Models for Disease Diagnosis: A Scoping Review

Automatic disease diagnosis has become increasingly valuable in clinical practice. The advent of large language models (LLMs) has catalyzed a paradigm shift in artificial intelligence, with growing evidence supporting the efficacy of LLMs in diagnostic tasks. Despite the growing attention in this field, many critical research questions remain under-explored. For instance, what diseases and LLM techniques have been investigated for diagnostic tasks? How can suitable LLM techniques and evaluation methods be selected for clinical decision-making? To answer these questions, we performed a comprehensive analysis of LLM-based methods for disease diagnosis. This scoping review examined the types of diseases, associated organ systems, relevant clinical data, LLM techniques, and evaluation methods reported in existing studies. Furthermore, we offered guidelines for data preprocessing and the selection of appropriate LLM techniques and evaluation strategies for diagnostic tasks. We also assessed the limitations of current research and delineated the challenges and future directions in this research field. In summary, our review outlined a blueprint for LLM-based disease diagnosis, helping to streamline and guide future research endeavors.

Interpretable Differential Diagnosis with Dual-Inference Large Language Models

Methodological advancements to automate the generation of differential diagnosis (DDx) to predict a list of potential diseases as differentials given patients' symptom descriptions are critical to clinical reasoning and applications such as decision support. However, providing reasoning or interpretation for these differential diagnoses is more meaningful. Fortunately, large language models (LLMs) possess powerful language processing abilities and have been proven effective in various related tasks. Motivated by this potential, we investigate the use of LLMs for interpretable DDx. First, we develop a new DDx dataset with expert-derived interpretation on 570 public clinical notes. Second, we propose a novel framework, named Dual-Inf, that enables LLMs to conduct bidirectional inference for interpretation. Both human and automated evaluation demonstrate the effectiveness of Dual-Inf in predicting differentials and diagnosis explanations. Specifically, the performance improvement of Dual-Inf over the baseline methods exceeds 32% w.r.t. BERTScore in DDx interpretation. Furthermore, experiments verify that Dual-Inf (1) makes fewer errors in interpretation, (2) has great generalizability, (3) is promising for rare disease diagnosis and explanation.

Graph Anomaly Detection with Noisy Labels by Reinforcement Learning

Graph anomaly detection (GAD) has been widely applied in many areas, e.g., fraud detection in finance and robot accounts in social networks. Existing methods are dedicated to identifying the outlier nodes that deviate from normal ones. While they heavily rely on high-quality annotation, which is hard to obtain in real-world scenarios, this could lead to severely degraded performance based on noisy labels. Thus, we are motivated to cut the edges of suspicious nodes to alleviate the impact of noise. However, it remains difficult to precisely identify the nodes with noisy labels. Moreover, it is hard to quantitatively evaluate the regret of cutting the edges, which may have either positive or negative influences. To this end, we propose a novel framework REGAD, i.e., REinforced Graph Anomaly Detector. Specifically, we aim to maximize the performance improvement (AUC) of a base detector by cutting noisy edges approximated through the nodes with high-confidence labels. (i) We design a tailored action and search space to train a policy network to carefully prune edges step by step, where only a few suspicious edges are prioritized in each step. (ii) We design a policy-in-the-loop mechanism to iteratively optimize the policy based on the feedback from base detector. The overall performance is evaluated by the cumulative rewards. Extensive experiments are conducted on three datasets under different anomaly ratios. The results indicate the superior performance of our proposed REGAD.

Denoising-Aware Contrastive Learning for Noisy Time Series

Time series self-supervised learning (SSL) aims to exploit unlabeled data for pre-training to mitigate the reliance on labels. Despite the great success in recent years, there is limited discussion on the potential noise in the time series, which can severely impair the performance of existing SSL methods. To mitigate the noise, the de facto strategy is to apply conventional denoising methods before model training. However, this pre-processing approach may not fully eliminate the effect of noise in SSL for two reasons: (i) the diverse types of noise in time series make it difficult to automatically determine suitable denoising methods; (ii) noise can be amplified after mapping raw data into latent space. In this paper, we propose denoising-aware contrastive learning (DECL), which uses contrastive learning objectives to mitigate the noise in the representation and automatically selects suitable denoising methods for every sample. Extensive experiments on various datasets verify the effectiveness of our method. The code is open-sourced.

Improving Generalizability of Graph Anomaly Detection Models via Data Augmentation

Graph anomaly detection (GAD) is a vital task since even a few anomalies can pose huge threats to benign users. Recent semi-supervised GAD methods, which can effectively leverage the available labels as prior knowledge, have achieved superior performances than unsupervised methods. In practice, people usually need to identify anomalies on new (sub)graphs to secure their business, but they may lack labels to train an effective detection model. One natural idea is to directly adopt a trained GAD model to the new (sub)graph for testing. However, we find that existing semi-supervised GAD methods suffer from poor generalization issue, i.e., well-trained models could not perform well on an unseen area (i.e., not accessible in training) of the same graph. It may cause great troubles. In this paper, we base on the phenomenon and propose a general and novel research problem of generalized graph anomaly detection that aims to effectively identify anomalies on both the training-domain graph and unseen testing graph to eliminate potential dangers. Nevertheless, it is a challenging task since only limited labels are available, and the normal background may differ between training and testing data. Accordingly, we propose a data augmentation method named \textit{AugAN} (\uline{Aug}mentation for \uline{A}nomaly and \uline{N}ormal distributions) to enrich training data and boost the generalizability of GAD models. Experiments verify the effectiveness of our method in improving model generalizability.