arXiv subjects

Ji Wu

Publications and source records attributed to Ji Wu.

At least 73 records · Page 4Linked to original sources

arXiv2024

Reliable and diverse evaluation of LLM medical knowledge mastery

Mastering medical knowledge is crucial for medical-specific LLMs. However, despite the existence of medical benchmarks like MedQA, a unified framework that fully leverages existing knowledge bases to evaluate LLMs' mastery of medical knowledge is still lacking. In the study, we propose a novel framework PretexEval that dynamically generates reliable and diverse test samples to evaluate LLMs for any given medical knowledge base. We notice that test samples produced directly from knowledge bases by templates or LLMs may introduce factual errors and also lack diversity. To address these issues, we introduce a novel schema into our proposed evaluation framework that employs predicate equivalence transformations to produce a series of variants for any given medical knowledge point. Finally, these produced predicate variants are converted into textual language, resulting in a series of reliable and diverse test samples to evaluate whether LLMs fully master the given medical factual knowledge point. Here, we use our proposed framework to systematically investigate the mastery of medical factual knowledge of 12 well-known LLMs, based on two knowledge bases that are crucial for clinical diagnosis and treatment. The evaluation results illustrate that current LLMs still exhibit significant deficiencies in fully mastering medical knowledge, despite achieving considerable success on some famous public benchmarks. These new findings provide valuable insights for developing medical-specific LLMs, highlighting that current LLMs urgently need to strengthen their comprehensive and in-depth mastery of medical knowledge before being applied to real-world medical scenarios.

cs.CL↗

arXiv2024

From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learning

Accurate prediction of protein-ligand binding affinities is an essential challenge in structure-based drug design. Despite recent advances in data-driven methods for affinity prediction, their accuracy is still limited, partially because they only take advantage of static crystal structures while the actual binding affinities are generally determined by the thermodynamic ensembles between proteins and ligands. One effective way to approximate such a thermodynamic ensemble is to use molecular dynamics (MD) simulation. Here, an MD dataset containing 3,218 different protein-ligand complexes is curated, and Dynaformer, a graph-based deep learning model is further developed to predict the binding affinities by learning the geometric characteristics of the protein-ligand interactions from the MD trajectories. In silico experiments demonstrated that the model exhibits state-of-the-art scoring and ranking power on the CASF-2016 benchmark dataset, outperforming the methods hitherto reported. Moreover, in a virtual screening on heat shock protein 90 (HSP90) using Dynaformer, 20 candidates are identified and their binding affinities are further experimentally validated. Dynaformer displayed promising results in virtual drug screening, revealing 12 hit compounds (two are in the submicromolar range), including several novel scaffolds. Overall, these results demonstrated that the approach offer a promising avenue for accelerating the early drug discovery process.

q-bio.BM↗

arXiv2024

GKGNet: Group K-Nearest Neighbor based Graph Convolutional Network for Multi-Label Image Recognition

Multi-Label Image Recognition (MLIR) is a challenging task that aims to predict multiple object labels in a single image while modeling the complex relationships between labels and image regions. Although convolutional neural networks and vision transformers have succeeded in processing images as regular grids of pixels or patches, these representations are sub-optimal for capturing irregular and discontinuous regions of interest. In this work, we present the first fully graph convolutional model, Group K-nearest neighbor based Graph convolutional Network (GKGNet), which models the connections between semantic label embeddings and image patches in a flexible and unified graph structure. To address the scale variance of different objects and to capture information from multiple perspectives, we propose the Group KGCN module for dynamic graph construction and message passing. Our experiments demonstrate that GKGNet achieves state-of-the-art performance with significantly lower computational costs on the challenging multi-label datasets, i.e., MS-COCO and VOC2007 datasets. Codes are available at https://github.com/jin-s13/GKGNet.

cs.CV↗

arXiv2024

UniFS: Universal Few-shot Instance Perception with Point Representations

Instance perception tasks (object detection, instance segmentation, pose estimation, counting) play a key role in industrial applications of visual models. As supervised learning methods suffer from high labeling cost, few-shot learning methods which effectively learn from a limited number of labeled examples are desired. Existing few-shot learning methods primarily focus on a restricted set of tasks, presumably due to the challenges involved in designing a generic model capable of representing diverse tasks in a unified manner. In this paper, we propose UniFS, a universal few-shot instance perception model that unifies a wide range of instance perception tasks by reformulating them into a dynamic point representation learning framework. Additionally, we propose Structure-Aware Point Learning (SAPL) to exploit the higher-order structural relationship among points to further enhance representation learning. Our approach makes minimal assumptions about the tasks, yet it achieves competitive results compared to highly specialized and well optimized specialist models. Codes and data are available at https://github.com/jin-s13/UniFS.

cs.CV↗

arXiv2024

Spontaneous Speech-Based Suicide Risk Detection Using Whisper and Large Language Models

The early detection of suicide risk is important since it enables the intervention to prevent potential suicide attempts. This paper studies the automatic detection of suicide risk based on spontaneous speech from adolescents, and collects a Mandarin dataset with 15 hours of suicide speech from more than a thousand adolescents aged from ten to eighteen for our experiments. To leverage the diverse acoustic and linguistic features embedded in spontaneous speech, both the Whisper speech model and textual large language models (LLMs) are used for suicide risk detection. Both all-parameter finetuning and parameter-efficient finetuning approaches are used to adapt the pre-trained models for suicide risk detection, and multiple audio-text fusion approaches are evaluated to combine the representations of Whisper and the LLM. The proposed system achieves a detection accuracy of 0.807 and an F1-score of 0.846 on the test set with 119 subjects, indicating promising potential for real suicide risk detection applications.

cs.CL↗

arXiv2024

Bayesian Example Selection Improves In-Context Learning for Speech, Text, and Visual Modalities

Large language models (LLMs) can adapt to new tasks through in-context learning (ICL) based on a few examples presented in dialogue history without any model parameter update. Despite such convenience, the performance of ICL heavily depends on the quality of the in-context examples presented, which makes the in-context example selection approach a critical choice. This paper proposes a novel Bayesian in-Context example Selection method (ByCS) for ICL. Extending the inference probability conditioned on in-context examples based on Bayes' theorem, ByCS focuses on the inverse inference conditioned on test input. Following the assumption that accurate inverse inference probability (likelihood) will result in accurate inference probability (posterior), in-context examples are selected based on their inverse inference results. Diverse and extensive cross-tasking and cross-modality experiments are performed with speech, text, and image examples. Experimental results show the efficacy and robustness of our ByCS method on various models, tasks and modalities.

cs.CL↗

arXiv2024

Simple Data Augmentation Techniques for Chinese Disease Normalization

Disease name normalization is an important task in the medical domain. It classifies disease names written in various formats into standardized names, serving as a fundamental component in smart healthcare systems for various disease-related functions. Nevertheless, the most significant obstacle to existing disease name normalization systems is the severe shortage of training data. Consequently, we present a novel data augmentation approach that includes a series of data augmentation techniques and some supporting modules to help mitigate the problem. Our proposed methods rely on the Structural Invariance property of disease names and the Hierarchy property of the disease classification system. The goal is to equip the models with extensive understanding of the disease names and the hierarchical structure of the disease name classification system. Through extensive experimentation, we illustrate that our proposed approach exhibits significant performance improvements across various baseline models and training objectives, particularly in scenarios with limited training data.

cs.CL↗

arXiv2024

MultifacetEval: Multifaceted Evaluation to Probe LLMs in Mastering Medical Knowledge

Large language models (LLMs) have excelled across domains, also delivering notable performance on the medical evaluation benchmarks, such as MedQA. However, there still exists a significant gap between the reported performance and the practical effectiveness in real-world medical scenarios. In this paper, we aim to explore the causes of this gap by employing a multifaceted examination schema to systematically probe the actual mastery of medical knowledge by current LLMs. Specifically, we develop a novel evaluation framework MultifacetEval to examine the degree and coverage of LLMs in encoding and mastering medical knowledge at multiple facets (comparison, rectification, discrimination, and verification) concurrently. Based on the MultifacetEval framework, we construct two multifaceted evaluation datasets: MultiDiseK (by producing questions from a clinical disease knowledge base) and MultiMedQA (by rephrasing each question from a medical benchmark MedQA into multifaceted questions). The experimental results on these multifaceted datasets demonstrate that the extent of current LLMs in mastering medical knowledge is far below their performance on existing medical benchmarks, suggesting that they lack depth, precision, and comprehensiveness in mastering medical knowledge. Consequently, current LLMs are not yet ready for application in real-world medical tasks. The codes and datasets are available at https://github.com/THUMLP/MultifacetEval.

cs.CL↗

arXiv2024

M$^3$AV: A Multimodal, Multigenre, and Multipurpose Audio-Visual Academic Lecture Dataset

Publishing open-source academic video recordings is an emergent and prevalent approach to sharing knowledge online. Such videos carry rich multimodal information including speech, the facial and body movements of the speakers, as well as the texts and pictures in the slides and possibly even the papers. Although multiple academic video datasets have been constructed and released, few of them support both multimodal content recognition and understanding tasks, which is partially due to the lack of high-quality human annotations. In this paper, we propose a novel multimodal, multigenre, and multipurpose audio-visual academic lecture dataset (M$^3$AV), which has almost 367 hours of videos from five sources covering computer science, mathematics, and medical and biology topics. With high-quality human annotations of the slide text and spoken words, in particular high-valued name entities, the dataset can be used for multiple audio-visual recognition and understanding tasks. Evaluations performed on contextual speech recognition, speech synthesis, and slide and script generation tasks demonstrate that the diversity of M$^3$AV makes it a challenging dataset.

cs.CL↗

arXiv2024

Conditional Language Learning with Context

Language models can learn sophisticated language understanding skills from fitting raw text. They also unselectively learn useless corpus statistics and biases, especially during finetuning on domain-specific corpora. In this paper, we propose a simple modification to causal language modeling called conditional finetuning, which performs language modeling conditioned on a context. We show that a context can "explain away" certain corpus statistics and make the model avoid learning them. In this fashion, conditional finetuning achieves selective learning from a corpus, learning knowledge useful for downstream tasks while avoiding learning useless corpus statistics like topic biases. This selective learning effect leads to less forgetting and better stability-plasticity tradeoff in domain finetuning, potentially benefitting lifelong learning with language models.

cs.CL↗

arXiv2024

Dynamic feature selection in medical predictive monitoring by reinforcement learning

In this paper, we investigate dynamic feature selection within multivariate time-series scenario, a common occurrence in clinical prediction monitoring where each feature corresponds to a bio-test result. Many existing feature selection methods fall short in effectively leveraging time-series information, primarily because they are designed for static data. Our approach addresses this limitation by enabling the selection of time-varying feature subsets for each patient. Specifically, we employ reinforcement learning to optimize a policy under maximum cost restrictions. The prediction model is subsequently updated using synthetic data generated by trained policy. Our method can seamlessly integrate with non-differentiable prediction models. We conducted experiments on a sizable clinical dataset encompassing regression and classification tasks. The results demonstrate that our approach outperforms strong feature selection baselines, particularly when subjected to stringent cost limitations. Code will be released once paper is accepted.

cs.LG↗

arXiv2024

TinyLLaVA Factory: A Modularized Codebase for Small-scale Large Multimodal Models

We present TinyLLaVA Factory, an open-source modular codebase for small-scale large multimodal models (LMMs) with a focus on simplicity of code implementations, extensibility of new features, and reproducibility of training results. Following the design philosophy of the factory pattern in software engineering, TinyLLaVA Factory modularizes the entire system into interchangeable components, with each component integrating a suite of cutting-edge models and methods, meanwhile leaving room for extensions to more features. In addition to allowing users to customize their own LMMs, TinyLLaVA Factory provides popular training recipes to let users pretrain and finetune their models with less coding effort. Empirical experiments validate the effectiveness of our codebase. The goal of TinyLLaVA Factory is to assist researchers and practitioners in exploring the wide landscape of designing and training small-scale LMMs with affordable computational resources.

cs.LG↗

arXiv2024

Can Whisper perform speech-based in-context learning?

This paper investigates the in-context learning abilities of the Whisper automatic speech recognition (ASR) models released by OpenAI. A novel speech-based in-context learning (SICL) approach is proposed for test-time adaptation, which can reduce the word error rates (WERs) with only a small number of labelled speech samples without gradient descent. Language-level adaptation experiments using Chinese dialects showed that when applying SICL to isolated word ASR, consistent and considerable relative WER reductions can be achieved using Whisper models of any size on two dialects, which is on average 32.3%. A k-nearest-neighbours-based in-context example selection technique can be applied to further improve the efficiency of SICL, which can increase the average relative WER reduction to 36.4%. The findings are verified using speaker adaptation or continuous speech recognition tasks, and both achieved considerable relative WER reductions. Detailed quantitative analyses are also provided to shed light on SICL's adaptability to phonological variances and dialect-specific lexical nuances.

eess.AS↗

arXiv2024

TinyLLaVA: A Framework of Small-scale Large Multimodal Models

We present the TinyLLaVA framework that provides a unified perspective in designing and analyzing the small-scale Large Multimodal Models (LMMs). We empirically study the effects of different vision encoders, connection modules, language models, training data and training recipes. Our extensive experiments showed that better quality of data combined with better training recipes, smaller LMMs can consistently achieve on-par performances compared to bigger LMMs. Under our framework, we train a family of small-scale LMMs. Our best model, TinyLLaVA-3.1B, achieves better overall performance against existing 7B models such as LLaVA-1.5 and Qwen-VL. We hope our findings can serve as baselines for future research in terms of data scaling, training setups and model selections. Our model weights and codes will be made public.

cs.LG↗

arXiv2023

Transferring speech-generic and depression-specific knowledge for Alzheimer's disease detection

The detection of Alzheimer's disease (AD) from spontaneous speech has attracted increasing attention while the sparsity of training data remains an important issue. This paper handles the issue by knowledge transfer, specifically from both speech-generic and depression-specific knowledge. The paper first studies sequential knowledge transfer from generic foundation models pretrained on large amounts of speech and text data. A block-wise analysis is performed for AD diagnosis based on the representations extracted from different intermediate blocks of different foundation models. Apart from the knowledge from speech-generic representations, this paper also proposes to simultaneously transfer the knowledge from a speech depression detection task based on the high comorbidity rates of depression and AD. A parallel knowledge transfer framework is studied that jointly learns the information shared between these two tasks. Experimental results show that the proposed method improves AD and depression detection, and produces a state-of-the-art F1 score of 0.928 for AD diagnosis on the commonly used ADReSSo dataset.

cs.CL↗

arXiv2023

QuadricsNet: Learning Concise Representation for Geometric Primitives in Point Clouds

This paper presents a novel framework to learn a concise geometric primitive representation for 3D point clouds. Different from representing each type of primitive individually, we focus on the challenging problem of how to achieve a concise and uniform representation robustly. We employ quadrics to represent diverse primitives with only 10 parameters and propose the first end-to-end learning-based framework, namely QuadricsNet, to parse quadrics in point clouds. The relationships between quadrics mathematical formulation and geometric attributes, including the type, scale and pose, are insightfully integrated for effective supervision of QuaidricsNet. Besides, a novel pattern-comprehensive dataset with quadrics segments and objects is collected for training and evaluation. Experiments demonstrate the effectiveness of our concise representation and the robustness of QuadricsNet. Our code is available at \url{https://github.com/MichaelWu99-lab/QuadricsNet}

cs.RO↗

arXiv2023

THiFLY Research at SemEval-2023 Task 7: A Multi-granularity System for CTR-based Textual Entailment and Evidence Retrieval

The NLI4CT task aims to entail hypotheses based on Clinical Trial Reports (CTRs) and retrieve the corresponding evidence supporting the justification. This task poses a significant challenge, as verifying hypotheses in the NLI4CT task requires the integration of multiple pieces of evidence from one or two CTR(s) and the application of diverse levels of reasoning, including textual and numerical. To address these problems, we present a multi-granularity system for CTR-based textual entailment and evidence retrieval in this paper. Specifically, we construct a Multi-granularity Inference Network (MGNet) that exploits sentence-level and token-level encoding to handle both textual entailment and evidence retrieval tasks. Moreover, we enhance the numerical inference capability of the system by leveraging a T5-based model, SciFive, which is pre-trained on the medical corpus. Model ensembling and a joint inference method are further utilized in the system to increase the stability and consistency of inference. The system achieves f1-scores of 0.856 and 0.853 on textual entailment and evidence retrieval tasks, resulting in the best performance on both subtasks. The experimental results corroborate the effectiveness of our proposed method. Our code is publicly available at https://github.com/THUMLP/NLI4CT.

cs.CL↗

arXiv2023

How can Deep Learning Retrieve the Write-Missing Additional Diagnosis from Chinese Electronic Medical Record For DRG

The purpose of write-missing diagnosis detection is to find diseases that have been clearly diagnosed from medical records but are missed in the discharge diagnosis. Unlike the definition of missed diagnosis, the write-missing diagnosis is clearly manifested in the medical record without further reasoning. The write-missing diagnosis is a common problem, often caused by physician negligence. The write-missing diagnosis will result in an incomplete diagnosis of medical records. While under DRG grouping, the write-missing diagnoses will miss important additional diagnoses (CC, MCC), thus affecting the correct rate of DRG enrollment. Under the circumstance that countries generally start to adopt DRG enrollment and payment, the problem of write-missing diagnosis is a common and serious problem. The current manual-based method is expensive due to the complex content of the full medical record. We think this problem is suitable to be solved as natural language processing. But to the best of our knowledge, no researchers have conducted research on this problem based on natural language processing methods. We propose a framework for solving the problem of write-missing diagnosis, which mainly includes three modules: disease recall module, disease context logic judgment module, and disease relationship comparison module. Through this framework, we verify that the problem of write-missing diagnosis can be solved well, and the results are interpretable. At the same time, we propose advanced solutions for the disease context logic judgment module and disease relationship comparison module, which have obvious advantages compared with the mainstream methods of the same type of problems. Finally, we verified the value of our proposed framework under DRG medical insurance payment in a tertiary hospital.

cs.CL↗