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Dec 11

Clinical Camel: An Open-Source Expert-Level Medical Language Model with Dialogue-Based Knowledge Encoding

Large Language Models (LLMs) present immense potential in the medical field, yet concerns over data privacy, regulatory compliance, and model stability restrict their widespread adoption. Although the distillation of high-performing closed-source LLMs has proven effective for general tasks, their application in healthcare is limited due to reduced domain knowledge and remnants of alignment behavior hindering clinical tasks. To address these challenges, we propose Dialogue-Based Knowledge Encoding (DBKE). DBKE enhances models' implicit knowledge base and primes them for conversational recall, augmenting their conversational capabilities and enabling a soft alignment for subsequent use cases. By transforming dense academic source text into synthetic dialogue, DBKE broadens the model's knowledge base and enables a soft alignment that guides downstream behaviours. We present Clinical Camel, an open-source, healthcare-focused conversational model, to showcase the effectiveness of DBKE. Clinical Camel outperforms GPT-3.5 on the United States Medical Licensing Examination (USMLE) Step 1 and Step 3 with scores of 53.2 % and 58.2 %, respectively, compared to GPT-3.5's scores of 36.1 % and 55.7 %. Clinical Camel adeptly handles multi-stage clinical case problems, provides adaptive counseling, and generates clinical notes. However, it is prone to hallucinations, which pose a significant obstacle in safety-critical settings. The performance of Clinical Camel underscores the importance of continued research and development of open-source models for the safe and effective integration of LLMs in healthcare settings.

  • 6 authors
·
May 19, 2023 1

Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning

Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrary complex nested knowledge schemas. Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against GPT-3+ to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. We present examples of use of SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease causation graphs. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction (RE) methods, but has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. SPIRES is available as part of the open source OntoGPT package: https://github.com/ monarch-initiative/ontogpt.

  • 12 authors
·
Apr 5, 2023

What Does My QA Model Know? Devising Controlled Probes using Expert Knowledge

Open-domain question answering (QA) is known to involve several underlying knowledge and reasoning challenges, but are models actually learning such knowledge when trained on benchmark tasks? To investigate this, we introduce several new challenge tasks that probe whether state-of-the-art QA models have general knowledge about word definitions and general taxonomic reasoning, both of which are fundamental to more complex forms of reasoning and are widespread in benchmark datasets. As an alternative to expensive crowd-sourcing, we introduce a methodology for automatically building datasets from various types of expert knowledge (e.g., knowledge graphs and lexical taxonomies), allowing for systematic control over the resulting probes and for a more comprehensive evaluation. We find automatically constructing probes to be vulnerable to annotation artifacts, which we carefully control for. Our evaluation confirms that transformer-based QA models are already predisposed to recognize certain types of structural lexical knowledge. However, it also reveals a more nuanced picture: their performance degrades substantially with even a slight increase in the number of hops in the underlying taxonomic hierarchy, or as more challenging distractor candidate answers are introduced. Further, even when these models succeed at the standard instance-level evaluation, they leave much room for improvement when assessed at the level of clusters of semantically connected probes (e.g., all Isa questions about a concept).

  • 2 authors
·
Dec 31, 2019

CKBP v2: Better Annotation and Reasoning for Commonsense Knowledge Base Population

Commonsense Knowledge Bases (CSKB) Population, which aims at automatically expanding knowledge in CSKBs with external resources, is an important yet hard task in NLP. Fang et al. (2021a) proposed a CSKB Population (CKBP) framework with an evaluation set CKBP v1. However, CKBP v1 relies on crowdsourced annotations that suffer from a considerable number of mislabeled answers, and the evaluationset lacks alignment with the external knowledge source due to random sampling. In this paper, we introduce CKBP v2, a new high-quality CSKB Population evaluation set that addresses the two aforementioned issues by employing domain experts as annotators and incorporating diversified adversarial samples to make the evaluation data more representative. We show that CKBP v2 serves as a challenging and representative evaluation dataset for the CSKB Population task, while its development set aids in selecting a population model that leads to improved knowledge acquisition for downstream commonsense reasoning. A better population model can also help acquire more informative commonsense knowledge as additional supervision signals for both generative commonsense inference and zero-shot commonsense question answering. Specifically, the question-answering model based on DeBERTa-v3-large (He et al., 2023b) even outperforms powerful large language models in a zero-shot setting, including ChatGPT and GPT-3.5.

  • 7 authors
·
Apr 20, 2023

BiomedSQL: Text-to-SQL for Scientific Reasoning on Biomedical Knowledge Bases

Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

  • 11 authors
·
May 23 2

EXplainable Neural-Symbolic Learning (X-NeSyL) methodology to fuse deep learning representations with expert knowledge graphs: the MonuMAI cultural heritage use case

The latest Deep Learning (DL) models for detection and classification have achieved an unprecedented performance over classical machine learning algorithms. However, DL models are black-box methods hard to debug, interpret, and certify. DL alone cannot provide explanations that can be validated by a non technical audience. In contrast, symbolic AI systems that convert concepts into rules or symbols -- such as knowledge graphs -- are easier to explain. However, they present lower generalisation and scaling capabilities. A very important challenge is to fuse DL representations with expert knowledge. One way to address this challenge, as well as the performance-explainability trade-off is by leveraging the best of both streams without obviating domain expert knowledge. We tackle such problem by considering the symbolic knowledge is expressed in form of a domain expert knowledge graph. We present the eXplainable Neural-symbolic learning (X-NeSyL) methodology, designed to learn both symbolic and deep representations, together with an explainability metric to assess the level of alignment of machine and human expert explanations. The ultimate objective is to fuse DL representations with expert domain knowledge during the learning process to serve as a sound basis for explainability. X-NeSyL methodology involves the concrete use of two notions of explanation at inference and training time respectively: 1) EXPLANet: Expert-aligned eXplainable Part-based cLAssifier NETwork Architecture, a compositional CNN that makes use of symbolic representations, and 2) SHAP-Backprop, an explainable AI-informed training procedure that guides the DL process to align with such symbolic representations in form of knowledge graphs. We showcase X-NeSyL methodology using MonuMAI dataset for monument facade image classification, and demonstrate that our approach improves explainability and performance.

  • 10 authors
·
Apr 24, 2021

Deep Learning based Visually Rich Document Content Understanding: A Survey

Visually Rich Documents (VRDs) are essential in academia, finance, medical fields, and marketing due to their multimodal information content. Traditional methods for extracting information from VRDs depend on expert knowledge and manual labor, making them costly and inefficient. The advent of deep learning has revolutionized this process, introducing models that leverage multimodal information vision, text, and layout along with pretraining tasks to develop comprehensive document representations. These models have achieved state-of-the-art performance across various downstream tasks, significantly enhancing the efficiency and accuracy of information extraction from VRDs. In response to the growing demands and rapid developments in Visually Rich Document Understanding (VRDU), this paper provides a comprehensive review of deep learning-based VRDU frameworks. We systematically survey and analyze existing methods and benchmark datasets, categorizing them based on adopted strategies and downstream tasks. Furthermore, we compare different techniques used in VRDU models, focusing on feature representation and fusion, model architecture, and pretraining methods, while highlighting their strengths, limitations, and appropriate scenarios. Finally, we identify emerging trends and challenges in VRDU, offering insights into future research directions and practical applications. This survey aims to provide a thorough understanding of VRDU advancements, benefiting both academic and industrial sectors.

  • 3 authors
·
Aug 2, 2024

Meta Knowledge for Retrieval Augmented Large Language Models

Retrieval Augmented Generation (RAG) is a technique used to augment Large Language Models (LLMs) with contextually relevant, time-critical, or domain-specific information without altering the underlying model parameters. However, constructing RAG systems that can effectively synthesize information from large and diverse set of documents remains a significant challenge. We introduce a novel data-centric RAG workflow for LLMs, transforming the traditional retrieve-then-read system into a more advanced prepare-then-rewrite-then-retrieve-then-read framework, to achieve higher domain expert-level understanding of the knowledge base. Our methodology relies on generating metadata and synthetic Questions and Answers (QA) for each document, as well as introducing the new concept of Meta Knowledge Summary (MK Summary) for metadata-based clusters of documents. The proposed innovations enable personalized user-query augmentation and in-depth information retrieval across the knowledge base. Our research makes two significant contributions: using LLMs as evaluators and employing new comparative performance metrics, we demonstrate that (1) using augmented queries with synthetic question matching significantly outperforms traditional RAG pipelines that rely on document chunking (p < 0.01), and (2) meta knowledge-augmented queries additionally significantly improve retrieval precision and recall, as well as the final answers breadth, depth, relevancy, and specificity. Our methodology is cost-effective, costing less than $20 per 2000 research papers using Claude 3 Haiku, and can be adapted with any fine-tuning of either the language or embedding models to further enhance the performance of end-to-end RAG pipelines.

  • 6 authors
·
Aug 16, 2024

Trans-EnV: A Framework for Evaluating the Linguistic Robustness of LLMs Against English Varieties

Large Language Models (LLMs) are predominantly evaluated on Standard American English (SAE), often overlooking the diversity of global English varieties. This narrow focus may raise fairness concerns as degraded performance on non-standard varieties can lead to unequal benefits for users worldwide. Therefore, it is critical to extensively evaluate the linguistic robustness of LLMs on multiple non-standard English varieties. We introduce Trans-EnV, a framework that automatically transforms SAE datasets into multiple English varieties to evaluate the linguistic robustness. Our framework combines (1) linguistics expert knowledge to curate variety-specific features and transformation guidelines from linguistic literature and corpora, and (2) LLM-based transformations to ensure both linguistic validity and scalability. Using Trans-EnV, we transform six benchmark datasets into 38 English varieties and evaluate seven state-of-the-art LLMs. Our results reveal significant performance disparities, with accuracy decreasing by up to 46.3% on non-standard varieties. These findings highlight the importance of comprehensive linguistic robustness evaluation across diverse English varieties. Each construction of Trans-EnV was validated through rigorous statistical testing and consultation with a researcher in the field of second language acquisition, ensuring its linguistic validity. Our code and datasets are publicly available at https://github.com/jiyounglee-0523/TransEnV and https://huggingface.co/collections/jiyounglee0523/transenv-681eadb3c0c8cf363b363fb1.

  • 7 authors
·
May 27

Small but Mighty: Enhancing Time Series Forecasting with Lightweight LLMs

While LLMs have demonstrated remarkable potential in time series forecasting, their practical deployment remains constrained by excessive computational demands and memory footprints. Existing LLM-based approaches typically suffer from three critical limitations: Inefficient parameter utilization in handling numerical time series patterns; Modality misalignment between continuous temporal signals and discrete text embeddings; and Inflexibility for real-time expert knowledge integration. We present SMETimes, the first systematic investigation of sub-3B parameter SLMs for efficient and accurate time series forecasting. Our approach centers on three key innovations: A statistically-enhanced prompting mechanism that bridges numerical time series with textual semantics through descriptive statistical features; A adaptive fusion embedding architecture that aligns temporal patterns with language model token spaces through learnable parameters; And a dynamic mixture-of-experts framework enabled by SLMs' computational efficiency, adaptively combining base predictions with domain-specific models. Extensive evaluations across seven benchmark datasets demonstrate that our 3B-parameter SLM achieves state-of-the-art performance on five primary datasets while maintaining 3.8x faster training and 5.2x lower memory consumption compared to 7B-parameter LLM baselines. Notably, the proposed model exhibits better learning capabilities, achieving 12.3% lower MSE than conventional LLM. Ablation studies validate that our statistical prompting and cross-modal fusion modules respectively contribute 15.7% and 18.2% error reduction in long-horizon forecasting tasks. By redefining the efficiency-accuracy trade-off landscape, this work establishes SLMs as viable alternatives to resource-intensive LLMs for practical time series forecasting. Code and models are available at https://github.com/xiyan1234567/SMETimes.

  • 4 authors
·
Mar 5

CodexGraph: Bridging Large Language Models and Code Repositories via Code Graph Databases

Large Language Models (LLMs) excel in stand-alone code tasks like HumanEval and MBPP, but struggle with handling entire code repositories. This challenge has prompted research on enhancing LLM-codebase interaction at a repository scale. Current solutions rely on similarity-based retrieval or manual tools and APIs, each with notable drawbacks. Similarity-based retrieval often has low recall in complex tasks, while manual tools and APIs are typically task-specific and require expert knowledge, reducing their generalizability across diverse code tasks and real-world applications. To mitigate these limitations, we introduce \framework, a system that integrates LLM agents with graph database interfaces extracted from code repositories. By leveraging the structural properties of graph databases and the flexibility of the graph query language, \framework enables the LLM agent to construct and execute queries, allowing for precise, code structure-aware context retrieval and code navigation. We assess \framework using three benchmarks: CrossCodeEval, SWE-bench, and EvoCodeBench. Additionally, we develop five real-world coding applications. With a unified graph database schema, \framework demonstrates competitive performance and potential in both academic and real-world environments, showcasing its versatility and efficacy in software engineering. Our application demo: https://github.com/modelscope/modelscope-agent/tree/master/apps/codexgraph_agent.

  • 8 authors
·
Aug 7, 2024 2

The MAMe Dataset: On the relevance of High Resolution and Variable Shape image properties

In the image classification task, the most common approach is to resize all images in a dataset to a unique shape, while reducing their precision to a size which facilitates experimentation at scale. This practice has benefits from a computational perspective, but it entails negative side-effects on performance due to loss of information and image deformation. In this work we introduce the MAMe dataset, an image classification dataset with remarkable high resolution and variable shape properties. The goal of MAMe is to provide a tool for studying the impact of such properties in image classification, while motivating research in the field. The MAMe dataset contains thousands of artworks from three different museums, and proposes a classification task consisting on differentiating between 29 mediums (i.e. materials and techniques) supervised by art experts. After reviewing the singularity of MAMe in the context of current image classification tasks, a thorough description of the task is provided, together with dataset statistics. Experiments are conducted to evaluate the impact of using high resolution images, variable shape inputs and both properties at the same time. Results illustrate the positive impact in performance when using high resolution images, while highlighting the lack of solutions to exploit variable shapes. An additional experiment exposes the distinctiveness between the MAMe dataset and the prototypical ImageNet dataset. Finally, the baselines are inspected using explainability methods and expert knowledge, to gain insights on the challenges that remain ahead.

  • 7 authors
·
Jul 27, 2020

FailureSensorIQ: A Multi-Choice QA Dataset for Understanding Sensor Relationships and Failure Modes

We introduce FailureSensorIQ, a novel Multi-Choice Question-Answering (MCQA) benchmarking system designed to assess the ability of Large Language Models (LLMs) to reason and understand complex, domain-specific scenarios in Industry 4.0. Unlike traditional QA benchmarks, our system focuses on multiple aspects of reasoning through failure modes, sensor data, and the relationships between them across various industrial assets. Through this work, we envision a paradigm shift where modeling decisions are not only data-driven using statistical tools like correlation analysis and significance tests, but also domain-driven by specialized LLMs which can reason about the key contributors and useful patterns that can be captured with feature engineering. We evaluate the Industrial knowledge of over a dozen LLMs-including GPT-4, Llama, and Mistral-on FailureSensorIQ from different lens using Perturbation-Uncertainty-Complexity analysis, Expert Evaluation study, Asset-Specific Knowledge Gap analysis, ReAct agent using external knowledge-bases. Even though closed-source models with strong reasoning capabilities approach expert-level performance, the comprehensive benchmark reveals a significant drop in performance that is fragile to perturbations, distractions, and inherent knowledge gaps in the models. We also provide a real-world case study of how LLMs can drive the modeling decisions on 3 different failure prediction datasets related to various assets. We release: (a) expert-curated MCQA for various industrial assets, (b) FailureSensorIQ benchmark and Hugging Face leaderboard based on MCQA built from non-textual data found in ISO documents, and (c) LLMFeatureSelector, an LLM-based feature selection scikit-learn pipeline. The software is available at https://github.com/IBM/FailureSensorIQ.

Empowering Multimodal LLMs with External Tools: A Comprehensive Survey

By integrating the perception capabilities of multimodal encoders with the generative power of Large Language Models (LLMs), Multimodal Large Language Models (MLLMs), exemplified by GPT-4V, have achieved great success in various multimodal tasks, pointing toward a promising pathway to artificial general intelligence. Despite this progress, the limited quality of multimodal data, poor performance on many complex downstream tasks, and inadequate evaluation protocols continue to hinder the reliability and broader applicability of MLLMs across diverse domains. Inspired by the human ability to leverage external tools for enhanced reasoning and problem-solving, augmenting MLLMs with external tools (e.g., APIs, expert models, and knowledge bases) offers a promising strategy to overcome these challenges. In this paper, we present a comprehensive survey on leveraging external tools to enhance MLLM performance. Our discussion is structured along four key dimensions about external tools: (1) how they can facilitate the acquisition and annotation of high-quality multimodal data; (2) how they can assist in improving MLLM performance on challenging downstream tasks; (3) how they enable comprehensive and accurate evaluation of MLLMs; (4) the current limitations and future directions of tool-augmented MLLMs. Through this survey, we aim to underscore the transformative potential of external tools in advancing MLLM capabilities, offering a forward-looking perspective on their development and applications. The project page of this paper is publicly available athttps://github.com/Lackel/Awesome-Tools-for-MLLMs.

  • 6 authors
·
Aug 14

WixQA: A Multi-Dataset Benchmark for Enterprise Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) is a cornerstone of modern question answering (QA) systems, enabling grounded answers based on external knowledge. Although recent progress has been driven by open-domain datasets, enterprise QA systems need datasets that mirror the concrete, domain-specific issues users raise in day-to-day support scenarios. Critically, evaluating end-to-end RAG systems requires benchmarks comprising not only question--answer pairs but also the specific knowledge base (KB) snapshot from which answers were derived. To address this need, we introduce WixQA, a benchmark suite featuring QA datasets precisely grounded in the released KB corpus, enabling holistic evaluation of retrieval and generation components. WixQA includes three distinct QA datasets derived from Wix.com customer support interactions and grounded in a snapshot of the public Wix Help Center KB: (i) WixQA-ExpertWritten, 200 real user queries with expert-authored, multi-step answers; (ii) WixQA-Simulated, 200 expert-validated QA pairs distilled from user dialogues; and (iii) WixQA-Synthetic, 6,222 LLM-generated QA pairs, with one pair systematically derived from each article in the knowledge base. We release the KB snapshot alongside the datasets under MIT license and provide comprehensive baseline results, forming a unique benchmark for evaluating enterprise RAG systems in realistic enterprise environments.

  • 7 authors
·
May 13

CulturalTeaming: AI-Assisted Interactive Red-Teaming for Challenging LLMs' (Lack of) Multicultural Knowledge

Frontier large language models (LLMs) are developed by researchers and practitioners with skewed cultural backgrounds and on datasets with skewed sources. However, LLMs' (lack of) multicultural knowledge cannot be effectively assessed with current methods for developing benchmarks. Existing multicultural evaluations primarily rely on expensive and restricted human annotations or potentially outdated internet resources. Thus, they struggle to capture the intricacy, dynamics, and diversity of cultural norms. LLM-generated benchmarks are promising, yet risk propagating the same biases they are meant to measure. To synergize the creativity and expert cultural knowledge of human annotators and the scalability and standardizability of LLM-based automation, we introduce CulturalTeaming, an interactive red-teaming system that leverages human-AI collaboration to build truly challenging evaluation dataset for assessing the multicultural knowledge of LLMs, while improving annotators' capabilities and experiences. Our study reveals that CulturalTeaming's various modes of AI assistance support annotators in creating cultural questions, that modern LLMs fail at, in a gamified manner. Importantly, the increased level of AI assistance (e.g., LLM-generated revision hints) empowers users to create more difficult questions with enhanced perceived creativity of themselves, shedding light on the promises of involving heavier AI assistance in modern evaluation dataset creation procedures. Through a series of 1-hour workshop sessions, we gather CULTURALBENCH-V0.1, a compact yet high-quality evaluation dataset with users' red-teaming attempts, that different families of modern LLMs perform with accuracy ranging from 37.7% to 72.2%, revealing a notable gap in LLMs' multicultural proficiency.

  • 10 authors
·
Apr 9, 2024

From Beginner to Expert: Modeling Medical Knowledge into General LLMs

Recently, large language model (LLM) based artificial intelligence (AI) systems have demonstrated remarkable capabilities in natural language understanding and generation. However, these models face a significant challenge when it comes to sensitive applications, such as reasoning over medical knowledge and answering medical questions in a physician-like manner. Prior studies attempted to overcome this challenge by increasing the model size (>100B) to learn more general medical knowledge, while there is still room for improvement in LLMs with smaller-scale model sizes (<100B). In this work, we start from a pre-trained general LLM model (AntGLM-10B) and fine-tune it from a medical beginner towards a medical expert (called AntGLM-Med-10B), which leverages a 3-stage optimization procedure, i.e., general medical knowledge injection, medical domain instruction tuning, and specific medical task adaptation. Our contributions are threefold: (1) We specifically investigate how to adapt a pre-trained general LLM in medical domain, especially for a specific medical task. (2) We collect and construct large-scale medical datasets for each stage of the optimization process. These datasets encompass various data types and tasks, such as question-answering, medical reasoning, multi-choice questions, and medical conversations. (3) Specifically for multi-choice questions in the medical domain, we propose a novel Verification-of-Choice approach for prompting engineering, which significantly enhances the reasoning ability of LLMs. Remarkably, by combining the above approaches, our AntGLM-Med-10B model can outperform the most of LLMs on PubMedQA, including both general and medical LLMs, even when these LLMs have larger model size.

  • 17 authors
·
Dec 2, 2023

MedReseacher-R1: Expert-Level Medical Deep Researcher via A Knowledge-Informed Trajectory Synthesis Framework

Recent developments in Large Language Model (LLM)-based agents have shown impressive capabilities spanning multiple domains, exemplified by deep research systems that demonstrate superior performance on complex information-seeking and synthesis tasks. While general-purpose deep research agents have shown impressive capabilities, they struggle significantly with medical domain challenges, as evidenced by leading proprietary systems achieving limited accuracy on complex medical benchmarks. The key limitations are: (1) the model lacks sufficient dense medical knowledge for clinical reasoning, and (2) the framework is constrained by the absence of specialized retrieval tools tailored for medical contexts.We present a medical deep research agent that addresses these challenges through two core innovations. First, we develop a novel data synthesis framework using medical knowledge graphs, extracting the longest chains from subgraphs around rare medical entities to generate complex multi-hop question-answer pairs. Second, we integrate a custom-built private medical retrieval engine alongside general-purpose tools, enabling accurate medical information synthesis. Our approach generates 2100+ diverse trajectories across 12 medical specialties, each averaging 4.2 tool interactions.Through a two-stage training paradigm combining supervised fine-tuning and online reinforcement learning with composite rewards, our MedResearcher-R1-32B model demonstrates exceptional performance, establishing new state-of-the-art results on medical benchmarks while maintaining competitive performance on general deep research tasks. Our work demonstrates that strategic domain-specific innovations in architecture, tool design, and training data construction can enable smaller open-source models to outperform much larger proprietary systems in specialized domains.

Patho-R1: A Multimodal Reinforcement Learning-Based Pathology Expert Reasoner

Recent advances in vision language models (VLMs) have enabled broad progress in the general medical field. However, pathology still remains a more challenging subdomain, with current pathology specific VLMs exhibiting limitations in both diagnostic accuracy and reasoning plausibility. Such shortcomings are largely attributable to the nature of current pathology datasets, which are primarily composed of image description pairs that lack the depth and structured diagnostic paradigms employed by real world pathologists. In this study, we leverage pathology textbooks and real world pathology experts to construct high-quality, reasoning-oriented datasets. Building on this, we introduce Patho-R1, a multimodal RL-based pathology Reasoner, trained through a three-stage pipeline: (1) continued pretraining on 3.5 million image-text pairs for knowledge infusion; (2) supervised fine-tuning on 500k high-quality Chain-of-Thought samples for reasoning incentivizing; (3) reinforcement learning using Group Relative Policy Optimization and Decoupled Clip and Dynamic sAmpling Policy Optimization strategies for multimodal reasoning quality refinement. To further assess the alignment quality of our dataset, we propose PathoCLIP, trained on the same figure-caption corpus used for continued pretraining. Comprehensive experimental results demonstrate that both PathoCLIP and Patho-R1 achieve robust performance across a wide range of pathology-related tasks, including zero-shot classification, cross-modal retrieval, Visual Question Answering, and Multiple Choice Question. Our project is available at the Patho-R1 repository: https://github.com/Wenchuan-Zhang/Patho-R1.

  • 9 authors
·
May 16

LLM The Genius Paradox: A Linguistic and Math Expert's Struggle with Simple Word-based Counting Problems

Interestingly, LLMs yet struggle with some basic tasks that humans find trivial to handle, e.g., counting the number of character r's in the word "strawberry". There are several popular conjectures (e.g., tokenization, architecture and training data) regarding the reason for deficiency of LLMs in simple word-based counting problems, sharing the similar belief that such failure stems from model pretraining hence probably inevitable during deployment. In this paper, we carefully design multiple evaluation settings to investigate validity of prevalent conjectures. Meanwhile, we measure transferability of advanced mathematical and coding reasoning capabilities from specialized LLMs to simple counting tasks. Although specialized LLMs suffer from counting problems as well, we find conjectures about inherent deficiency of LLMs invalid and further seek opportunities to elicit knowledge and capabilities from LLMs that are beneficial to counting tasks. Compared with strategies such as finetuning and in-context learning that are commonly adopted to enhance performance on new or challenging tasks, we show that engaging reasoning is the most robust and efficient way to help LLMs better perceive tasks with more accurate responses. We hope our conjecture validation design could provide insights into the study of future critical failure modes of LLMs. Based on challenges in transferring advanced capabilities to much simpler tasks, we call for more attention to model capability acquisition and evaluation. We also highlight the importance of cultivating consciousness of "reasoning before responding" during model pretraining.

  • 2 authors
·
Oct 18, 2024

VITA-VLA: Efficiently Teaching Vision-Language Models to Act via Action Expert Distillation

Vision-Language Action (VLA) models significantly advance robotic manipulation by leveraging the strong perception capabilities of pretrained vision-language models (VLMs). By integrating action modules into these pretrained models, VLA methods exhibit improved generalization. However, training them from scratch is costly. In this work, we propose a simple yet effective distillation-based framework that equips VLMs with action-execution capability by transferring knowledge from pretrained small action models. Our architecture retains the original VLM structure, adding only an action token and a state encoder to incorporate physical inputs. To distill action knowledge, we adopt a two-stage training strategy. First, we perform lightweight alignment by mapping VLM hidden states into the action space of the small action model, enabling effective reuse of its pretrained action decoder and avoiding expensive pretraining. Second, we selectively fine-tune the language model, state encoder, and action modules, enabling the system to integrate multimodal inputs with precise action generation. Specifically, the action token provides the VLM with a direct handle for predicting future actions, while the state encoder allows the model to incorporate robot dynamics not captured by vision alone. This design yields substantial efficiency gains over training large VLA models from scratch. Compared with previous state-of-the-art methods, our method achieves 97.3% average success rate on LIBERO (11.8% improvement) and 93.5% on LIBERO-LONG (24.5% improvement). In real-world experiments across five manipulation tasks, our method consistently outperforms the teacher model, achieving 82.0% success rate (17% improvement), which demonstrate that action distillation effectively enables VLMs to generate precise actions while substantially reducing training costs.

  • 15 authors
·
Oct 10

Bidirectional LMs are Better Knowledge Memorizers? A Benchmark for Real-world Knowledge Injection

Despite significant advances in large language models (LLMs), their knowledge memorization capabilities remain underexplored, due to the lack of standardized and high-quality test ground. In this paper, we introduce a novel, real-world and large-scale knowledge injection benchmark that evolves continuously over time without requiring human intervention. Specifically, we propose WikiDYK, which leverages recently-added and human-written facts from Wikipedia's "Did You Know..." entries. These entries are carefully selected by expert Wikipedia editors based on criteria such as verifiability and clarity. Each entry is converted into multiple question-answer pairs spanning diverse task formats from easy cloze prompts to complex multi-hop questions. WikiDYK contains 12,290 facts and 77,180 questions, which is also seamlessly extensible with future updates from Wikipedia editors. Extensive experiments using continued pre-training reveal a surprising insight: despite their prevalence in modern LLMs, Causal Language Models (CLMs) demonstrate significantly weaker knowledge memorization capabilities compared to Bidirectional Language Models (BiLMs), exhibiting a 23% lower accuracy in terms of reliability. To compensate for the smaller scales of current BiLMs, we introduce a modular collaborative framework utilizing ensembles of BiLMs as external knowledge repositories to integrate with LLMs. Experiment shows that our framework further improves the reliability accuracy by up to 29.1%.

  • 8 authors
·
May 18 2

MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research

Scientific research demands sophisticated reasoning over multimodal data, a challenge especially prevalent in biology. Despite recent advances in multimodal large language models (MLLMs) for AI-assisted research, existing multimodal reasoning benchmarks only target up to college-level difficulty, while research-level benchmarks emphasize lower-level perception, falling short of the complex multimodal reasoning needed for scientific discovery. To bridge this gap, we introduce MicroVQA, a visual-question answering (VQA) benchmark designed to assess three reasoning capabilities vital in research workflows: expert image understanding, hypothesis generation, and experiment proposal. MicroVQA consists of 1,042 multiple-choice questions (MCQs) curated by biology experts across diverse microscopy modalities, ensuring VQA samples represent real scientific practice. In constructing the benchmark, we find that standard MCQ generation methods induce language shortcuts, motivating a new two-stage pipeline: an optimized LLM prompt structures question-answer pairs into MCQs; then, an agent-based `RefineBot' updates them to remove shortcuts. Benchmarking on state-of-the-art MLLMs reveal a peak performance of 53\%; models with smaller LLMs only slightly underperform top models, suggesting that language-based reasoning is less challenging than multimodal reasoning; and tuning with scientific articles enhances performance. Expert analysis of chain-of-thought responses shows that perception errors are the most frequent, followed by knowledge errors and then overgeneralization errors. These insights highlight the challenges in multimodal scientific reasoning, showing MicroVQA is a valuable resource advancing AI-driven biomedical research. MicroVQA is available at https://huggingface.co/datasets/jmhb/microvqa, and project page at https://jmhb0.github.io/microvqa.

  • 23 authors
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Mar 17 2

Astrea: A MOE-based Visual Understanding Model with Progressive Alignment

Vision-Language Models (VLMs) based on Mixture-of-Experts (MoE) architectures have emerged as a pivotal paradigm in multimodal understanding, offering a powerful framework for integrating visual and linguistic information. However, the increasing complexity and diversity of tasks present significant challenges in coordinating load balancing across heterogeneous visual experts, where optimizing one specialist's performance often compromises others' capabilities. To address task heterogeneity and expert load imbalance, we propose Astrea, a novel multi-expert collaborative VLM architecture based on progressive pre-alignment. Astrea introduces three key innovations: 1) A heterogeneous expert coordination mechanism that integrates four specialized models (detection, segmentation, classification, captioning) into a comprehensive expert matrix covering essential visual comprehension elements; 2) A dynamic knowledge fusion strategy featuring progressive pre-alignment to harmonize experts within the VLM latent space through contrastive learning, complemented by probabilistically activated stochastic residual connections to preserve knowledge continuity; 3) An enhanced optimization framework utilizing momentum contrastive learning for long-range dependency modeling and adaptive weight allocators for real-time expert contribution calibration. Extensive evaluations across 12 benchmark tasks spanning VQA, image captioning, and cross-modal retrieval demonstrate Astrea's superiority over state-of-the-art models, achieving an average performance gain of +4.7\%. This study provides the first empirical demonstration that progressive pre-alignment strategies enable VLMs to overcome task heterogeneity limitations, establishing new methodological foundations for developing general-purpose multimodal agents.

  • 15 authors
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Mar 12

The Digital Cybersecurity Expert: How Far Have We Come?

The increasing deployment of large language models (LLMs) in the cybersecurity domain underscores the need for effective model selection and evaluation. However, traditional evaluation methods often overlook specific cybersecurity knowledge gaps that contribute to performance limitations. To address this, we develop CSEBenchmark, a fine-grained cybersecurity evaluation framework based on 345 knowledge points expected of cybersecurity experts. Drawing from cognitive science, these points are categorized into factual, conceptual, and procedural types, enabling the design of 11,050 tailored multiple-choice questions. We evaluate 12 popular LLMs on CSEBenchmark and find that even the best-performing model achieves only 85.42% overall accuracy, with particular knowledge gaps in the use of specialized tools and uncommon commands. Different LLMs have unique knowledge gaps. Even large models from the same family may perform poorly on knowledge points where smaller models excel. By identifying and addressing specific knowledge gaps in each LLM, we achieve up to an 84% improvement in correcting previously incorrect predictions across three existing benchmarks for two cybersecurity tasks. Furthermore, our assessment of each LLM's knowledge alignment with specific cybersecurity roles reveals that different models align better with different roles, such as GPT-4o for the Google Senior Intelligence Analyst and Deepseek-V3 for the Amazon Privacy Engineer. These findings underscore the importance of aligning LLM selection with the specific knowledge requirements of different cybersecurity roles for optimal performance.

  • 8 authors
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Apr 16

PRBench: Large-Scale Expert Rubrics for Evaluating High-Stakes Professional Reasoning

Frontier model progress is often measured by academic benchmarks, which offer a limited view of performance in real-world professional contexts. Existing evaluations often fail to assess open-ended, economically consequential tasks in high-stakes domains like Legal and Finance, where practical returns are paramount. To address this, we introduce Professional Reasoning Bench (PRBench), a realistic, open-ended, and difficult benchmark of real-world problems in Finance and Law. We open-source its 1,100 expert-authored tasks and 19,356 expert-curated criteria, making it, to our knowledge, the largest public, rubric-based benchmark for both legal and finance domains. We recruit 182 qualified professionals, holding JDs, CFAs, or 6+ years of experience, who contributed tasks inspired by their actual workflows. This process yields significant diversity, with tasks spanning 114 countries and 47 US jurisdictions. Our expert-curated rubrics are validated through a rigorous quality pipeline, including independent expert validation. Subsequent evaluation of 20 leading models reveals substantial room for improvement, with top scores of only 0.39 (Finance) and 0.37 (Legal) on our Hard subsets. We further catalog associated economic impacts of the prompts and analyze performance using human-annotated rubric categories. Our analysis shows that models with similar overall scores can diverge significantly on specific capabilities. Common failure modes include inaccurate judgments, a lack of process transparency and incomplete reasoning, highlighting critical gaps in their reliability for professional adoption.

  • 24 authors
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Nov 14

ExpertRAG: Efficient RAG with Mixture of Experts -- Optimizing Context Retrieval for Adaptive LLM Responses

ExpertRAG is a novel theoretical framework that integrates Mixture-of-Experts (MoE) architectures with Retrieval Augmented Generation (RAG) to advance the efficiency and accuracy of knowledge-intensive language modeling. We propose a dynamic retrieval gating mechanism coupled with expert routing, enabling the model to selectively consult an external knowledge store or rely on specialized internal experts based on the query's needs. The paper lays out the theoretical foundations of ExpertRAG, including a probabilistic formulation that treats retrieval and expert selection as latent decisions, and mathematical justifications for its efficiency in both computation and knowledge utilization. We derive formulae to quantify the expected computational cost savings from selective retrieval and the capacity gains from sparse expert utilization. A comparative analysis positions ExpertRAG against standard RAG (with always-on retrieval) and pure MoE models (e.g., Switch Transformer, Mixtral) to highlight its unique balance between parametric knowledge and non-parametric retrieval. We also outline an experimental validation strategy, proposing benchmarks and evaluation protocols to test ExpertRAG's performance on factual recall, generalization, and inference efficiency. The proposed framework, although presented theoretically, is supported by insights from prior work in RAG and MoE, and is poised to provide more factual, efficient, and adaptive generation by leveraging the best of both paradigms. In summary, ExpertRAG contributes a new perspective on scaling and augmenting language models, backed by a thorough analysis and a roadmap for empirical validation.

  • 1 authors
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Mar 23

Xolver: Multi-Agent Reasoning with Holistic Experience Learning Just Like an Olympiad Team

Despite impressive progress on complex reasoning, current large language models (LLMs) typically operate in isolation - treating each problem as an independent attempt, without accumulating or integrating experiential knowledge. In contrast, expert problem solvers - such as Olympiad or programming contest teams - leverage a rich tapestry of experiences: absorbing mentorship from coaches, developing intuition from past problems, leveraging knowledge of tool usage and library functionality, adapting strategies based on the expertise and experiences of peers, continuously refining their reasoning through trial and error, and learning from other related problems even during competition. We introduce Xolver, a training-free multi-agent reasoning framework that equips a black-box LLM with a persistent, evolving memory of holistic experience. Xolver integrates diverse experience modalities, including external and self-retrieval, tool use, collaborative interactions, agent-driven evaluation, and iterative refinement. By learning from relevant strategies, code fragments, and abstract reasoning patterns at inference time, Xolver avoids generating solutions from scratch - marking a transition from isolated inference toward experience-aware language agents. Built on both open-weight and proprietary models, Xolver consistently outperforms specialized reasoning agents. Even with lightweight backbones (e.g., QWQ-32B), it often surpasses advanced models including Qwen3-235B, Gemini 2.5 Pro, o3, and o4-mini-high. With o3-mini-high, it achieves new best results on GSM8K (98.1%), AIME'24 (94.4%), AIME'25 (93.7%), Math-500 (99.8%), and LiveCodeBench-V5 (91.6%) - highlighting holistic experience learning as a key step toward generalist agents capable of expert-level reasoning. Code and data are available at https://kagnlp.github.io/xolver.github.io/.

  • 4 authors
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Jun 17 2

CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.

  • 10 authors
·
Apr 27, 2024

Leveraging Vision-Centric Multi-Modal Expertise for 3D Object Detection

Current research is primarily dedicated to advancing the accuracy of camera-only 3D object detectors (apprentice) through the knowledge transferred from LiDAR- or multi-modal-based counterparts (expert). However, the presence of the domain gap between LiDAR and camera features, coupled with the inherent incompatibility in temporal fusion, significantly hinders the effectiveness of distillation-based enhancements for apprentices. Motivated by the success of uni-modal distillation, an apprentice-friendly expert model would predominantly rely on camera features, while still achieving comparable performance to multi-modal models. To this end, we introduce VCD, a framework to improve the camera-only apprentice model, including an apprentice-friendly multi-modal expert and temporal-fusion-friendly distillation supervision. The multi-modal expert VCD-E adopts an identical structure as that of the camera-only apprentice in order to alleviate the feature disparity, and leverages LiDAR input as a depth prior to reconstruct the 3D scene, achieving the performance on par with other heterogeneous multi-modal experts. Additionally, a fine-grained trajectory-based distillation module is introduced with the purpose of individually rectifying the motion misalignment for each object in the scene. With those improvements, our camera-only apprentice VCD-A sets new state-of-the-art on nuScenes with a score of 63.1% NDS.

  • 7 authors
·
Oct 24, 2023

Dense2MoE: Restructuring Diffusion Transformer to MoE for Efficient Text-to-Image Generation

Diffusion Transformer (DiT) has demonstrated remarkable performance in text-to-image generation; however, its large parameter size results in substantial inference overhead. Existing parameter compression methods primarily focus on pruning, but aggressive pruning often leads to severe performance degradation due to reduced model capacity. To address this limitation, we pioneer the transformation of a dense DiT into a Mixture of Experts (MoE) for structured sparsification, reducing the number of activated parameters while preserving model capacity. Specifically, we replace the Feed-Forward Networks (FFNs) in DiT Blocks with MoE layers, reducing the number of activated parameters in the FFNs by 62.5\%. Furthermore, we propose the Mixture of Blocks (MoB) to selectively activate DiT blocks, thereby further enhancing sparsity. To ensure an effective dense-to-MoE conversion, we design a multi-step distillation pipeline, incorporating Taylor metric-based expert initialization, knowledge distillation with load balancing, and group feature loss for MoB optimization. We transform large diffusion transformers (e.g., FLUX.1 [dev]) into an MoE structure, reducing activated parameters by 60\% while maintaining original performance and surpassing pruning-based approaches in extensive experiments. Overall, Dense2MoE establishes a new paradigm for efficient text-to-image generation.

  • 5 authors
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Oct 10

MoLE: Enhancing Human-centric Text-to-image Diffusion via Mixture of Low-rank Experts

Text-to-image diffusion has attracted vast attention due to its impressive image-generation capabilities. However, when it comes to human-centric text-to-image generation, particularly in the context of faces and hands, the results often fall short of naturalness due to insufficient training priors. We alleviate the issue in this work from two perspectives. 1) From the data aspect, we carefully collect a human-centric dataset comprising over one million high-quality human-in-the-scene images and two specific sets of close-up images of faces and hands. These datasets collectively provide a rich prior knowledge base to enhance the human-centric image generation capabilities of the diffusion model. 2) On the methodological front, we propose a simple yet effective method called Mixture of Low-rank Experts (MoLE) by considering low-rank modules trained on close-up hand and face images respectively as experts. This concept draws inspiration from our observation of low-rank refinement, where a low-rank module trained by a customized close-up dataset has the potential to enhance the corresponding image part when applied at an appropriate scale. To validate the superiority of MoLE in the context of human-centric image generation compared to state-of-the-art, we construct two benchmarks and perform evaluations with diverse metrics and human studies. Datasets, model, and code are released at https://sites.google.com/view/mole4diffuser/.

  • 6 authors
·
Oct 30, 2024

Histopathological Image Classification based on Self-Supervised Vision Transformer and Weak Labels

Whole Slide Image (WSI) analysis is a powerful method to facilitate the diagnosis of cancer in tissue samples. Automating this diagnosis poses various issues, most notably caused by the immense image resolution and limited annotations. WSIs commonly exhibit resolutions of 100Kx100K pixels. Annotating cancerous areas in WSIs on the pixel level is prohibitively labor-intensive and requires a high level of expert knowledge. Multiple instance learning (MIL) alleviates the need for expensive pixel-level annotations. In MIL, learning is performed on slide-level labels, in which a pathologist provides information about whether a slide includes cancerous tissue. Here, we propose Self-ViT-MIL, a novel approach for classifying and localizing cancerous areas based on slide-level annotations, eliminating the need for pixel-wise annotated training data. Self-ViT- MIL is pre-trained in a self-supervised setting to learn rich feature representation without relying on any labels. The recent Vision Transformer (ViT) architecture builds the feature extractor of Self-ViT-MIL. For localizing cancerous regions, a MIL aggregator with global attention is utilized. To the best of our knowledge, Self-ViT- MIL is the first approach to introduce self-supervised ViTs in MIL-based WSI analysis tasks. We showcase the effectiveness of our approach on the common Camelyon16 dataset. Self-ViT-MIL surpasses existing state-of-the-art MIL-based approaches in terms of accuracy and area under the curve (AUC).

  • 6 authors
·
Oct 17, 2022

LoRAMoE: Revolutionizing Mixture of Experts for Maintaining World Knowledge in Language Model Alignment

Supervised fine-tuning (SFT) is a crucial step for large language models (LLMs), enabling them to align with human instructions and enhance their capabilities in downstream tasks. When the models are required to align with a broader range of downstream tasks, or there is a desire to notably improve the performance on a specific task, a substantial increase in fine-tuning data often emerges as the solution. However, we find that large-scale increases in instruction data can disrupt the world knowledge previously stored in the LLMs, i.e., world knowledge forgetting. In this paper, we introduce LoRAMoE to address the above challenge. The LoRAMoE is a plugin version of Mixture of Experts (MoE). The plugin form ensures the integrity of world knowledge by freezing the backbone model during the training phase. We then propose the use of localized balancing constraints to coordinate parts of experts for task utilization, meanwhile enabling other experts to fully leverage the world knowledge stored in the models. Experimental results demonstrate that LoRAMoE can reasonably coordinate experts based on data type during inference, and even dramatically increasing instruction data does not result in knowledge forgetting. Moreover, LoRAMoE provides additional benefits for the performance of downstream tasks, indicating the potential of our approach for multi-task learning.

  • 16 authors
·
Dec 15, 2023

Does Localization Inform Editing? Surprising Differences in Causality-Based Localization vs. Knowledge Editing in Language Models

Language models learn a great quantity of factual information during pretraining, and recent work localizes this information to specific model weights like mid-layer MLP weights. In this paper, we find that we can change how a fact is stored in a model by editing weights that are in a different location than where existing methods suggest that the fact is stored. This is surprising because we would expect that localizing facts to specific model parameters would tell us where to manipulate knowledge in models, and this assumption has motivated past work on model editing methods. Specifically, we show that localization conclusions from representation denoising (also known as Causal Tracing) do not provide any insight into which model MLP layer would be best to edit in order to override an existing stored fact with a new one. This finding raises questions about how past work relies on Causal Tracing to select which model layers to edit. Next, we consider several variants of the editing problem, including erasing and amplifying facts. For one of our editing problems, editing performance does relate to localization results from representation denoising, but we find that which layer we edit is a far better predictor of performance. Our results suggest, counterintuitively, that better mechanistic understanding of how pretrained language models work may not always translate to insights about how to best change their behavior. Our code is available at https://github.com/google/belief-localization

  • 4 authors
·
Jan 10, 2023

MechGPT, a language-based strategy for mechanics and materials modeling that connects knowledge across scales, disciplines and modalities

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

  • 1 authors
·
Oct 16, 2023

Local or Global: Selective Knowledge Assimilation for Federated Learning with Limited Labels

Many existing FL methods assume clients with fully-labeled data, while in realistic settings, clients have limited labels due to the expensive and laborious process of labeling. Limited labeled local data of the clients often leads to their local model having poor generalization abilities to their larger unlabeled local data, such as having class-distribution mismatch with the unlabeled data. As a result, clients may instead look to benefit from the global model trained across clients to leverage their unlabeled data, but this also becomes difficult due to data heterogeneity across clients. In our work, we propose FedLabel where clients selectively choose the local or global model to pseudo-label their unlabeled data depending on which is more of an expert of the data. We further utilize both the local and global models' knowledge via global-local consistency regularization which minimizes the divergence between the two models' outputs when they have identical pseudo-labels for the unlabeled data. Unlike other semi-supervised FL baselines, our method does not require additional experts other than the local or global model, nor require additional parameters to be communicated. We also do not assume any server-labeled data or fully labeled clients. For both cross-device and cross-silo settings, we show that FedLabel outperforms other semi-supervised FL baselines by 8-24%, and even outperforms standard fully supervised FL baselines (100% labeled data) with only 5-20% of labeled data.

  • 3 authors
·
Jul 17, 2023

Dynamic Experts Search: Enhancing Reasoning in Mixture-of-Experts LLMs at Test Time

Test-Time Scaling (TTS) enhances the reasoning ability of large language models (LLMs) by allocating additional computation during inference. However, existing approaches primarily rely on output-level sampling while overlooking the role of model architecture. In mainstream Mixture-of-Experts (MoE) LLMs, we observe that varying the number of activated experts yields complementary solution sets with stable accuracy, revealing a new and underexplored source of diversity. Motivated by this observation, we propose Dynamic Experts Search (DES), a TTS strategy that elevates expert activation into a controllable dimension of the search space. DES integrates two key components: (1) Dynamic MoE, which enables direct control of expert counts during inference to generate diverse reasoning trajectories without additional cost; and (2) Expert Configuration Inheritance, which preserves consistent expert counts within a reasoning path while varying them across runs, thereby balancing stability and diversity throughout the search. Extensive experiments across MoE architectures, verifiers and reasoning benchmarks (i.e., math, code and knowledge) demonstrate that DES reliably outperforms TTS baselines, enhancing accuracy and stability without additional cost. These results highlight DES as a practical and scalable form of architecture-aware TTS, illustrating how structural flexibility in modern LLMs can advance reasoning.

  • 4 authors
·
Sep 26 1

Gamma: Toward Generic Image Assessment with Mixture of Assessment Experts

Image assessment aims to evaluate the quality and aesthetics of images and has been applied across various scenarios, such as natural and AIGC scenes. Existing methods mostly address these sub-tasks or scenes individually. While some works attempt to develop unified image assessment models, they have struggled to achieve satisfactory performance or cover a broad spectrum of assessment scenarios. In this paper, we present Gamma, a Generic imAge assessMent model using Mixture of Assessment Experts, which can effectively assess images from diverse scenes through mixed-dataset training. Achieving unified training in image assessment presents significant challenges due to annotation biases across different datasets. To address this issue, we first propose a Mixture of Assessment Experts (MoAE) module, which employs shared and adaptive experts to dynamically learn common and specific knowledge for different datasets, respectively. In addition, we introduce a Scene-based Differential Prompt (SDP) strategy, which uses scene-specific prompts to provide prior knowledge and guidance during the learning process, further boosting adaptation for various scenes. Our Gamma model is trained and evaluated on 12 datasets spanning 6 image assessment scenarios. Extensive experiments show that our unified Gamma outperforms other state-of-the-art mixed-training methods by significant margins while covering more scenes. Codes are available at https://github.com/zht8506/Gamma.

  • 6 authors
·
Mar 9

Zebra-Llama: A Context-Aware Large Language Model for Democratizing Rare Disease Knowledge

Rare diseases present unique challenges in healthcare, often suffering from delayed diagnosis and fragmented information landscapes. The scarcity of reliable knowledge in these conditions poses a distinct challenge for Large Language Models (LLMs) in supporting clinical management and delivering precise patient information underscoring the need for focused training on these 'zebra' cases. We present Zebra-Llama, a specialized context-aware language model with high precision Retrieval Augmented Generation (RAG) capability, focusing on Ehlers-Danlos Syndrome (EDS) as our case study. EDS, affecting 1 in 5,000 individuals, exemplifies the complexities of rare diseases with its diverse symptoms, multiple subtypes, and evolving diagnostic criteria. By implementing a novel context-aware fine-tuning methodology trained on questions derived from medical literature, patient experiences, and clinical resources, along with expertly curated responses, Zebra-Llama demonstrates unprecedented capabilities in handling EDS-related queries. On a test set of real-world questions collected from EDS patients and clinicians, medical experts evaluated the responses generated by both models, revealing Zebra-Llama's substantial improvements over base model (Llama 3.1-8B-Instruct) in thoroughness (77.5% vs. 70.1%), accuracy (83.0% vs. 78.8%), clarity (74.7% vs. 72.0%) and citation reliability (70.6% vs. 52.3%). Released as an open-source resource, Zebra-Llama not only provides more accessible and reliable EDS information but also establishes a framework for developing specialized AI solutions for other rare conditions. This work represents a crucial step towards democratizing expert-level knowledge in rare disease management, potentially transforming how healthcare providers and patients navigate the complex landscape of rare diseases.

  • 8 authors
·
Nov 4, 2024 1

Meta-DMoE: Adapting to Domain Shift by Meta-Distillation from Mixture-of-Experts

In this paper, we tackle the problem of domain shift. Most existing methods perform training on multiple source domains using a single model, and the same trained model is used on all unseen target domains. Such solutions are sub-optimal as each target domain exhibits its own specialty, which is not adapted. Furthermore, expecting single-model training to learn extensive knowledge from multiple source domains is counterintuitive. The model is more biased toward learning only domain-invariant features and may result in negative knowledge transfer. In this work, we propose a novel framework for unsupervised test-time adaptation, which is formulated as a knowledge distillation process to address domain shift. Specifically, we incorporate Mixture-of-Experts (MoE) as teachers, where each expert is separately trained on different source domains to maximize their specialty. Given a test-time target domain, a small set of unlabeled data is sampled to query the knowledge from MoE. As the source domains are correlated to the target domains, a transformer-based aggregator then combines the domain knowledge by examining the interconnection among them. The output is treated as a supervision signal to adapt a student prediction network toward the target domain. We further employ meta-learning to enforce the aggregator to distill positive knowledge and the student network to achieve fast adaptation. Extensive experiments demonstrate that the proposed method outperforms the state-of-the-art and validates the effectiveness of each proposed component. Our code is available at https://github.com/n3il666/Meta-DMoE.

  • 6 authors
·
Oct 7, 2022

The SAM2-to-SAM3 Gap in the Segment Anything Model Family: Why Prompt-Based Expertise Fails in Concept-Driven Image Segmentation

This paper investigates the fundamental discontinuity between the latest two Segment Anything Models: SAM2 and SAM3. We explain why the expertise in prompt-based segmentation of SAM2 does not transfer to the multimodal concept-driven paradigm of SAM3. SAM2 operates through spatial prompts points, boxes, and masks yielding purely geometric and temporal segmentation. In contrast, SAM3 introduces a unified vision-language architecture capable of open-vocabulary reasoning, semantic grounding, contrastive alignment, and exemplar-based concept understanding. We structure this analysis through five core components: (1) a Conceptual Break Between Prompt-Based and Concept-Based Segmentation, contrasting spatial prompt semantics of SAM2 with multimodal fusion and text-conditioned mask generation of SAM3; (2) Architectural Divergence, detailing pure vision-temporal design of SAM2 versus integration of vision-language encoders, geometry and exemplar encoders, fusion modules, DETR-style decoders, object queries, and ambiguity-handling via Mixture-of-Experts in SAM3; (3) Dataset and Annotation Differences, contrasting SA-V video masks with multimodal concept-annotated corpora of SAM3; (4) Training and Hyperparameter Distinctions, showing why SAM2 optimization knowledge does not apply to SAM3; and (5) Evaluation, Metrics, and Failure Modes, outlining the transition from geometric IoU metrics to semantic, open-vocabulary evaluation. Together, these analyses establish SAM3 as a new class of segmentation foundation model and chart future directions for the emerging concept-driven segmentation era.

Hallucination reduction with CASAL: Contrastive Activation Steering For Amortized Learning

Large Language Models (LLMs) exhibit impressive capabilities but often hallucinate, confidently providing incorrect answers instead of admitting ignorance. Prior work has shown that models encode linear representations of their own knowledge and that activation steering can reduce hallucinations. These approaches, however, require real-time monitoring and intervention during inference. We introduce Contrastive Activation Steering for Amortized Learning (CASAL), an efficient algorithm that connects interpretability with amortized optimization. CASAL directly bakes the benefits of activation steering into model's weights. Once trained, LLMs answer questions they know while abstaining from answering those they do not. CASAL's light-weight design requires training only a submodule of a single transformer layer and yet reduces hallucination by 30%-40% across multiple short-form QA benchmarks. CASAL is 30x more compute-efficient and 20x more data-efficient than strong LoRA-based baselines such as SFT and DPO, boosting its practical applicability in data scarce domains. Importantly, CASAL also generalizes effectively to out-of-distribution (OOD) domains. We showcase CASAL's flexibility in mitigating hallucinations in both text-only and vision-language models. To our knowledge, CASAL is the first steering-based training method that has been shown to be effective for both dense and Mixture-of-Experts (MoE) models. CASAL represents a promising step forward for applying interpretability-inspired method for practical deployment in production systems.

  • 8 authors
·
Sep 25

Training A Small Emotional Vision Language Model for Visual Art Comprehension

This paper develops small vision language models to understand visual art, which, given an art work, aims to identify its emotion category and explain this prediction with natural language. While small models are computationally efficient, their capacity is much limited compared with large models. To break this trade-off, this paper builds a small emotional vision language model (SEVLM) by emotion modeling and input-output feature alignment. On the one hand, based on valence-arousal-dominance (VAD) knowledge annotated by psychology experts, we introduce and fuse emotional features derived through VAD dictionary and a VAD head to align VAD vectors of predicted emotion explanation and the ground truth. This allows the vision language model to better understand and generate emotional texts, compared with using traditional text embeddings alone. On the other hand, we design a contrastive head to pull close embeddings of the image, its emotion class, and explanation, which aligns model outputs and inputs. On two public affective explanation datasets, we show that the proposed techniques consistently improve the visual art understanding performance of baseline SEVLMs. Importantly, the proposed model can be trained and evaluated on a single RTX 2080 Ti while exhibiting very strong performance: it not only outperforms the state-of-the-art small models but is also competitive compared with LLaVA 7B after fine-tuning and GPT4(V). The code is available at https://github.com/BetterZH/SEVLM-code.

  • 4 authors
·
Mar 17, 2024

Towards Practical Plug-and-Play Diffusion Models

Diffusion-based generative models have achieved remarkable success in image generation. Their guidance formulation allows an external model to plug-and-play control the generation process for various tasks without finetuning the diffusion model. However, the direct use of publicly available off-the-shelf models for guidance fails due to their poor performance on noisy inputs. For that, the existing practice is to fine-tune the guidance models with labeled data corrupted with noises. In this paper, we argue that this practice has limitations in two aspects: (1) performing on inputs with extremely various noises is too hard for a single guidance model; (2) collecting labeled datasets hinders scaling up for various tasks. To tackle the limitations, we propose a novel strategy that leverages multiple experts where each expert is specialized in a particular noise range and guides the reverse process of the diffusion at its corresponding timesteps. However, as it is infeasible to manage multiple networks and utilize labeled data, we present a practical guidance framework termed Practical Plug-And-Play (PPAP), which leverages parameter-efficient fine-tuning and data-free knowledge transfer. We exhaustively conduct ImageNet class conditional generation experiments to show that our method can successfully guide diffusion with small trainable parameters and no labeled data. Finally, we show that image classifiers, depth estimators, and semantic segmentation models can guide publicly available GLIDE through our framework in a plug-and-play manner. Our code is available at https://github.com/riiid/PPAP.

  • 7 authors
·
Dec 12, 2022

Establishing Knowledge Preference in Language Models

Language models are known to encode a great amount of factual knowledge through pretraining. However, such knowledge might be insufficient to cater to user requests, requiring the model to integrate external knowledge sources and adhere to user-provided specifications. When answering questions about ongoing events, the model should use recent news articles to update its response; when asked to provide recommendations, the model should prioritize user specifications over retrieved product reviews; when some facts are edited in the model, the updated facts should override all prior knowledge learned by the model even if they are conflicting. In all of the cases above, the model faces a decision between its own parametric knowledge, (retrieved) contextual knowledge, and user instruction knowledge. In this paper, we (1) unify such settings into the problem of knowledge preference and define a three-level preference hierarchy over these knowledge sources; (2) compile a collection of existing datasets IfQA, MQuAKE, and MRQA covering a combination of settings (with/without user specifications, with/without context documents) to systematically evaluate how well models obey the intended knowledge preference; and (3) propose a dataset synthesis method that composes diverse question-answer pairs with user assumptions and related context to directly fine-tune LMs for instilling the hierarchy of knowledge. We demonstrate that a 7B model, fine-tuned on only a few thousand examples automatically generated by our proposed method, effectively achieves superior performance (more than 18% improvement across all evaluation benchmarks) in adhering to the desired knowledge preference hierarchy.

  • 6 authors
·
Jul 17, 2024

Using clarification questions to improve software developers' Web search

Context: Recent research indicates that Web queries written by software developers are not very successful in retrieving relevant results, performing measurably worse compared to general purpose Web queries. Most approaches up to this point have addressed this problem with software engineering-specific automated query reformulation techniques, which work without developer involvement but are limited by the content of the original query. In other words, these techniques automatically improve the existing query but can not contribute new, previously unmentioned, concepts. Objective: In this paper, we propose a technique to guide software developers in manually improving their own Web search queries. We examine a conversational approach that follows unsuccessful queries with a clarification question aimed at eliciting additional query terms, thus providing to the developer a clear dimension along which the query could be improved. Methods: We describe a set of clarification questions derived from a corpus of software developer queries and a neural approach to recommending them for a newly issued query. Results: Our evaluation indicates that the recommendation technique is accurate, predicting a valid clarification question 80% of the time and outperforms simple baselines, as well as, state-of-the-art Learning To Rank (LTR) baselines. Conclusion: As shown in the experimental results, the described approach is capable at recommending appropriate clarification questions to software developers and considered useful by a sample of developers ranging from novices to experienced professionals.

  • 2 authors
·
Jul 26, 2022

T2Ranking: A large-scale Chinese Benchmark for Passage Ranking

Passage ranking involves two stages: passage retrieval and passage re-ranking, which are important and challenging topics for both academics and industries in the area of Information Retrieval (IR). However, the commonly-used datasets for passage ranking usually focus on the English language. For non-English scenarios, such as Chinese, the existing datasets are limited in terms of data scale, fine-grained relevance annotation and false negative issues. To address this problem, we introduce T2Ranking, a large-scale Chinese benchmark for passage ranking. T2Ranking comprises more than 300K queries and over 2M unique passages from real-world search engines. Expert annotators are recruited to provide 4-level graded relevance scores (fine-grained) for query-passage pairs instead of binary relevance judgments (coarse-grained). To ease the false negative issues, more passages with higher diversities are considered when performing relevance annotations, especially in the test set, to ensure a more accurate evaluation. Apart from the textual query and passage data, other auxiliary resources are also provided, such as query types and XML files of documents which passages are generated from, to facilitate further studies. To evaluate the dataset, commonly used ranking models are implemented and tested on T2Ranking as baselines. The experimental results show that T2Ranking is challenging and there is still scope for improvement. The full data and all codes are available at https://github.com/THUIR/T2Ranking/

  • 11 authors
·
Apr 7, 2023