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Dec 11

Categorical semiotics: Foundations for Knowledge Integration

The integration of knowledge extracted from diverse models, whether described by domain experts or generated by machine learning algorithms, has historically been challenged by the absence of a suitable framework for specifying and integrating structures, learning processes, data transformations, and data models or rules. In this work, we extend algebraic specification methods to address these challenges within such a framework. In our work, we tackle the challenging task of developing a comprehensive framework for defining and analyzing deep learning architectures. We believe that previous efforts have fallen short by failing to establish a clear connection between the constraints a model must adhere to and its actual implementation. Our methodology employs graphical structures that resemble Ehresmann's sketches, interpreted within a universe of fuzzy sets. This approach offers a unified theory that elegantly encompasses both deterministic and non-deterministic neural network designs. Furthermore, we highlight how this theory naturally incorporates fundamental concepts from computer science and automata theory. Our extended algebraic specification framework, grounded in graphical structures akin to Ehresmann's sketches, offers a promising solution for integrating knowledge across disparate models and domains. By bridging the gap between domain-specific expertise and machine-generated insights, we pave the way for more comprehensive, collaborative, and effective approaches to knowledge integration and modeling.

  • 1 authors
·
Apr 1, 2024

Cephalo: Multi-Modal Vision-Language Models for Bio-Inspired Materials Analysis and Design

We present Cephalo, a series of multimodal vision large language models (V-LLMs) designed for materials science applications, integrating visual and linguistic data for enhanced understanding and interaction within human-AI and multi-agent AI frameworks. A key innovation of Cephalo is its advanced dataset generation method, which employs a sophisticated algorithm to accurately detect and separate images and their corresponding textual descriptions from PDF documents, such as scientific papers. The method includes a careful refinement of image-text pairs through integrated vision and language processing, ensuring high-quality, contextually relevant, and well reasoned training data. Cephalo is trained on integrated image and text data extracted from thousands of scientific papers and science-focused Wikipedia pages demonstrates can interpret complex visual scenes, generate precise language descriptions, and answer queries about images effectively. The combination of a vision encoder with an autoregressive transformer supports complex natural language understanding in an integrated model, which can be coupled with other generative methods to create an image-to-text-to-image or image-to-text-to-3D pipeline. To explore the development of larger models from smaller ones, we merge sets of layers that originate from different pre-trained source models. This hybrid approach allows us to leverage the domain-specific expertise and general conversational capabilities to harness the strengths of multiple models. We examine the models in diverse use cases that incorporate biological materials, fracture and engineering analysis, protein biophysics, and bio-inspired design based on insect behavior. Generative applications include bio-inspired designs, including pollen-inspired architected materials, as well as the synthesis of bio-inspired material microstructures from a photograph of a solar eclipse.

  • 1 authors
·
May 29, 2024

InfiMed-Foundation: Pioneering Advanced Multimodal Medical Models with Compute-Efficient Pre-Training and Multi-Stage Fine-Tuning

Multimodal large language models (MLLMs) have shown remarkable potential in various domains, yet their application in the medical field is hindered by several challenges. General-purpose MLLMs often lack the specialized knowledge required for medical tasks, leading to uncertain or hallucinatory responses. Knowledge distillation from advanced models struggles to capture domain-specific expertise in radiology and pharmacology. Additionally, the computational cost of continual pretraining with large-scale medical data poses significant efficiency challenges. To address these issues, we propose InfiMed-Foundation-1.7B and InfiMed-Foundation-4B, two medical-specific MLLMs designed to deliver state-of-the-art performance in medical applications. We combined high-quality general-purpose and medical multimodal data and proposed a novel five-dimensional quality assessment framework to curate high-quality multimodal medical datasets. We employ low-to-high image resolution and multimodal sequence packing to enhance training efficiency, enabling the integration of extensive medical data. Furthermore, a three-stage supervised fine-tuning process ensures effective knowledge extraction for complex medical tasks. Evaluated on the MedEvalKit framework, InfiMed-Foundation-1.7B outperforms Qwen2.5VL-3B, while InfiMed-Foundation-4B surpasses HuatuoGPT-V-7B and MedGemma-27B-IT, demonstrating superior performance in medical visual question answering and diagnostic tasks. By addressing key challenges in data quality, training efficiency, and domain-specific knowledge extraction, our work paves the way for more reliable and effective AI-driven solutions in healthcare. InfiMed-Foundation-4B model is available at https://huggingface.co/InfiX-ai/InfiMed-Foundation-4B{InfiMed-Foundation-4B}.

  • 6 authors
·
Sep 26

RedStone: Curating General, Code, Math, and QA Data for Large Language Models

Pre-training Large Language Models (LLMs) on high-quality, meticulously curated datasets is widely recognized as critical for enhancing their performance and generalization capabilities. This study explores the untapped potential of Common Crawl as a comprehensive and flexible resource for pre-training LLMs, addressing both general-purpose language understanding and specialized domain knowledge. We introduce RedStone, an innovative and scalable pipeline engineered to extract and process data from Common Crawl, facilitating the creation of extensive and varied pre-training datasets. Unlike traditional datasets, which often require expensive curation and domain-specific expertise, RedStone leverages the breadth of Common Crawl to deliver datasets tailored to a wide array of domains. In this work, we exemplify its capability by constructing pre-training datasets across multiple fields, including general language understanding, code, mathematics, and question-answering tasks. The flexibility of RedStone allows for easy adaptation to other specialized domains, significantly lowering the barrier to creating valuable domain-specific datasets. Our findings demonstrate that Common Crawl, when harnessed through effective pipelines like RedStone, can serve as a rich, renewable source of pre-training data, unlocking new avenues for domain adaptation and knowledge discovery in LLMs. This work also underscores the importance of innovative data acquisition strategies and highlights the role of web-scale data as a powerful resource in the continued evolution of LLMs. RedStone code and data samples will be publicly available at https://aka.ms/redstone.

  • 16 authors
·
Dec 4, 2024

On Path to Multimodal Historical Reasoning: HistBench and HistAgent

Recent advances in large language models (LLMs) have led to remarkable progress across domains, yet their capabilities in the humanities, particularly history, remain underexplored. Historical reasoning poses unique challenges for AI, involving multimodal source interpretation, temporal inference, and cross-linguistic analysis. While general-purpose agents perform well on many existing benchmarks, they lack the domain-specific expertise required to engage with historical materials and questions. To address this gap, we introduce HistBench, a new benchmark of 414 high-quality questions designed to evaluate AI's capacity for historical reasoning and authored by more than 40 expert contributors. The tasks span a wide range of historical problems-from factual retrieval based on primary sources to interpretive analysis of manuscripts and images, to interdisciplinary challenges involving archaeology, linguistics, or cultural history. Furthermore, the benchmark dataset spans 29 ancient and modern languages and covers a wide range of historical periods and world regions. Finding the poor performance of LLMs and other agents on HistBench, we further present HistAgent, a history-specific agent equipped with carefully designed tools for OCR, translation, archival search, and image understanding in History. On HistBench, HistAgent based on GPT-4o achieves an accuracy of 27.54% pass@1 and 36.47% pass@2, significantly outperforming LLMs with online search and generalist agents, including GPT-4o (18.60%), DeepSeek-R1(14.49%) and Open Deep Research-smolagents(20.29% pass@1 and 25.12% pass@2). These results highlight the limitations of existing LLMs and generalist agents and demonstrate the advantages of HistAgent for historical reasoning.

  • 98 authors
·
May 26

$VILA^2$: VILA Augmented VILA

Visual language models (VLMs) have rapidly progressed, driven by the success of large language models (LLMs). While model architectures and training infrastructures advance rapidly, data curation remains under-explored. When data quantity and quality become a bottleneck, existing work either directly crawls more raw data from the Internet that does not have a guarantee of data quality or distills from black-box commercial models (e.g., GPT-4V / Gemini) causing the performance upper bounded by that model. In this work, we introduce a novel approach that includes a self-augment step and a specialist-augment step to iteratively improve data quality and model performance. In the self-augment step, a VLM recaptions its own pretraining data to enhance data quality, and then retrains from scratch using this refined dataset to improve model performance. This process can iterate for several rounds. Once self-augmentation saturates, we employ several specialist VLMs finetuned from the self-augmented VLM with domain-specific expertise, to further infuse specialist knowledge into the generalist VLM through task-oriented recaptioning and retraining. With the combined self-augmented and specialist-augmented training, we introduce VILA^2 (VILA-augmented-VILA), a VLM family that consistently improves the accuracy on a wide range of tasks over prior art, and achieves new state-of-the-art results on MMMU leaderboard among open-sourced models.

  • 9 authors
·
Jul 24, 2024 7

CellForge: Agentic Design of Virtual Cell Models

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

The Impact of Large Language Models on Scientific Discovery: a Preliminary Study using GPT-4

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

  • 2 authors
·
Nov 13, 2023

A Survey of Graph Retrieval-Augmented Generation for Customized Large Language Models

Large language models (LLMs) have demonstrated remarkable capabilities in a wide range of tasks, yet their application to specialized domains remains challenging due to the need for deep expertise. Retrieval-augmented generation (RAG) has emerged as a promising solution to customize LLMs for professional fields by seamlessly integrating external knowledge bases, enabling real-time access to domain-specific expertise during inference. Despite its potential, traditional RAG systems, based on flat text retrieval, face three critical challenges: (i) complex query understanding in professional contexts, (ii) difficulties in knowledge integration across distributed sources, and (iii) system efficiency bottlenecks at scale. This survey presents a systematic analysis of Graph-based Retrieval-Augmented Generation (GraphRAG), a new paradigm that revolutionizes domain-specific LLM applications. GraphRAG addresses traditional RAG limitations through three key innovations: (i) graph-structured knowledge representation that explicitly captures entity relationships and domain hierarchies, (ii) efficient graph-based retrieval techniques that enable context-preserving knowledge retrieval with multihop reasoning ability, and (iii) structure-aware knowledge integration algorithms that leverage retrieved knowledge for accurate and logical coherent generation of LLMs. In this survey, we systematically analyze the technical foundations of GraphRAG and examine current implementations across various professional domains, identifying key technical challenges and promising research directions. All the related resources of GraphRAG, including research papers, open-source data, and projects, are collected for the community in blue{https://github.com/DEEP-PolyU/Awesome-GraphRAG}.

  • 10 authors
·
Jan 21

EngiBench: A Framework for Data-Driven Engineering Design Research

Engineering design optimization seeks to automatically determine the shapes, topologies, or parameters of components that maximize performance under given conditions. This process often depends on physics-based simulations, which are difficult to install, computationally expensive, and require domain-specific expertise. To mitigate these challenges, we introduce EngiBench, the first open-source library and datasets spanning diverse domains for data-driven engineering design. EngiBench provides a unified API and a curated set of benchmarks -- covering aeronautics, heat conduction, photonics, and more -- that enable fair, reproducible comparisons of optimization and machine learning algorithms, such as generative or surrogate models. We also release EngiOpt, a companion library offering a collection of such algorithms compatible with the EngiBench interface. Both libraries are modular, letting users plug in novel algorithms or problems, automate end-to-end experiment workflows, and leverage built-in utilities for visualization, dataset generation, feasibility checks, and performance analysis. We demonstrate their versatility through experiments comparing state-of-the-art techniques across multiple engineering design problems, an undertaking that was previously prohibitively time-consuming to perform. Finally, we show that these problems pose significant challenges for standard machine learning methods due to highly sensitive and constrained design manifolds.

Injecting Domain-Specific Knowledge into Large Language Models: A Comprehensive Survey

Large Language Models (LLMs) have demonstrated remarkable success in various tasks such as natural language understanding, text summarization, and machine translation. However, their general-purpose nature often limits their effectiveness in domain-specific applications that require specialized knowledge, such as healthcare, chemistry, or legal analysis. To address this, researchers have explored diverse methods to enhance LLMs by integrating domain-specific knowledge. In this survey, we provide a comprehensive overview of these methods, which we categorize into four key approaches: dynamic knowledge injection, static knowledge embedding, modular adapters, and prompt optimization. Each approach offers unique mechanisms to equip LLMs with domain expertise, balancing trade-offs between flexibility, scalability, and efficiency. We discuss how these methods enable LLMs to tackle specialized tasks, compare their advantages and disadvantages, evaluate domain-specific LLMs against general LLMs, and highlight the challenges and opportunities in this emerging field. For those interested in delving deeper into this area, we also summarize the commonly used datasets and benchmarks. To keep researchers updated on the latest studies, we maintain an open-source at: https://github.com/abilliyb/Knowledge_Injection_Survey_Papers, dedicated to documenting research in the field of specialized LLM.

  • 7 authors
·
Feb 15 2

Domain-specific optimization and diverse evaluation of self-supervised models for histopathology

Task-specific deep learning models in histopathology offer promising opportunities for improving diagnosis, clinical research, and precision medicine. However, development of such models is often limited by availability of high-quality data. Foundation models in histopathology that learn general representations across a wide range of tissue types, diagnoses, and magnifications offer the potential to reduce the data, compute, and technical expertise necessary to develop task-specific deep learning models with the required level of model performance. In this work, we describe the development and evaluation of foundation models for histopathology via self-supervised learning (SSL). We first establish a diverse set of benchmark tasks involving 17 unique tissue types and 12 unique cancer types and spanning different optimal magnifications and task types. Next, we use this benchmark to explore and evaluate histopathology-specific SSL methods followed by further evaluation on held out patch-level and weakly supervised tasks. We found that standard SSL methods thoughtfully applied to histopathology images are performant across our benchmark tasks and that domain-specific methodological improvements can further increase performance. Our findings reinforce the value of using domain-specific SSL methods in pathology, and establish a set of high quality foundation models to enable further research across diverse applications.

  • 16 authors
·
Oct 19, 2023

Bottom-up Domain-specific Superintelligence: A Reliable Knowledge Graph is What We Need

Language models traditionally used for cross-domain generalization have recently demonstrated task-specific reasoning. However, their top-down training approach on general corpora is insufficient for acquiring abstractions needed for deep domain expertise. This may require a bottom-up approach that acquires expertise by learning to compose simple domain concepts into more complex ones. A knowledge graph (KG) provides this compositional structure, where domain primitives are represented as head-relation-tail edges and their paths encode higher-level concepts. We present a task generation pipeline that synthesizes tasks directly from KG primitives, enabling models to acquire and compose them for reasoning. We fine-tune language models on the resultant KG-grounded curriculum to demonstrate domain-specific superintelligence. While broadly applicable, we validate our approach in medicine, where reliable KGs exist. Using a medical KG, we curate 24,000 reasoning tasks paired with thinking traces derived from diverse medical primitives. We fine-tune the QwQ-32B model on this curriculum to obtain QwQ-Med-3 that takes a step towards medical superintelligence. We also introduce ICD-Bench, an evaluation suite to quantify reasoning abilities across 15 medical domains. Our experiments demonstrate that QwQ-Med-3 significantly outperforms state-of-the-art reasoning models on ICD-Bench categories. Further analysis reveals that QwQ-Med-3 utilizes acquired primitives to widen the performance gap on the hardest tasks of ICD-Bench. Finally, evaluation on medical question-answer benchmarks shows that QwQ-Med-3 transfers acquired expertise to enhance the base model's performance. While the industry's approach to artificial general intelligence (AGI) emphasizes broad expertise, we envision a future in which AGI emerges from the composable interaction of efficient domain-specific superintelligent agents.

  • 3 authors
·
Jul 18

SecureBERT: A Domain-Specific Language Model for Cybersecurity

Natural Language Processing (NLP) has recently gained wide attention in cybersecurity, particularly in Cyber Threat Intelligence (CTI) and cyber automation. Increased connection and automation have revolutionized the world's economic and cultural infrastructures, while they have introduced risks in terms of cyber attacks. CTI is information that helps cybersecurity analysts make intelligent security decisions, that is often delivered in the form of natural language text, which must be transformed to machine readable format through an automated procedure before it can be used for automated security measures. This paper proposes SecureBERT, a cybersecurity language model capable of capturing text connotations in cybersecurity text (e.g., CTI) and therefore successful in automation for many critical cybersecurity tasks that would otherwise rely on human expertise and time-consuming manual efforts. SecureBERT has been trained using a large corpus of cybersecurity text.To make SecureBERT effective not just in retaining general English understanding, but also when applied to text with cybersecurity implications, we developed a customized tokenizer as well as a method to alter pre-trained weights. The SecureBERT is evaluated using the standard Masked Language Model (MLM) test as well as two additional standard NLP tasks. Our evaluation studies show that SecureBERT\url{https://github.com/ehsanaghaei/SecureBERT} outperforms existing similar models, confirming its capability for solving crucial NLP tasks in cybersecurity.

  • 4 authors
·
Apr 6, 2022

Agentar-Fin-R1: Enhancing Financial Intelligence through Domain Expertise, Training Efficiency, and Advanced Reasoning

Large Language Models (LLMs) exhibit considerable promise in financial applications; however, prevailing models frequently demonstrate limitations when confronted with scenarios that necessitate sophisticated reasoning capabilities, stringent trustworthiness criteria, and efficient adaptation to domain-specific requirements. We introduce the Agentar-Fin-R1 series of financial large language models (8B and 32B parameters), specifically engineered based on the Qwen3 foundation model to enhance reasoning capabilities, reliability, and domain specialization for financial applications. Our optimization approach integrates a high-quality, systematic financial task label system with a comprehensive multi-layered trustworthiness assurance framework. This framework encompasses high-quality trustworthy knowledge engineering, multi-agent trustworthy data synthesis, and rigorous data validation governance. Through label-guided automated difficulty-aware optimization, tow-stage training pipeline, and dynamic attribution systems, we achieve substantial improvements in training efficiency. Our models undergo comprehensive evaluation on mainstream financial benchmarks including Fineva, FinEval, and FinanceIQ, as well as general reasoning datasets such as MATH-500 and GPQA-diamond. To thoroughly assess real-world deployment capabilities, we innovatively propose the Finova evaluation benchmark, which focuses on agent-level financial reasoning and compliance verification. Experimental results demonstrate that Agentar-Fin-R1 not only achieves state-of-the-art performance on financial tasks but also exhibits exceptional general reasoning capabilities, validating its effectiveness as a trustworthy solution for high-stakes financial applications. The Finova bench is available at https://github.com/antgroup/Finova.

PRISMA-DFLLM: An Extension of PRISMA for Systematic Literature Reviews using Domain-specific Finetuned Large Language Models

With the proliferation of open-sourced Large Language Models (LLMs) and efficient finetuning techniques, we are on the cusp of the emergence of numerous domain-specific LLMs that have been finetuned for expertise across specialized fields and applications for which the current general-purpose LLMs are unsuitable. In academia, this technology has the potential to revolutionize the way we conduct systematic literature reviews (SLRs), access knowledge and generate new insights. This paper proposes an AI-enabled methodological framework that combines the power of LLMs with the rigorous reporting guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). By finetuning LLMs on domain-specific academic papers that have been selected as a result of a rigorous SLR process, the proposed PRISMA-DFLLM (for Domain-specific Finetuned LLMs) reporting guidelines offer the potential to achieve greater efficiency, reusability and scalability, while also opening the potential for conducting incremental living systematic reviews with the aid of LLMs. Additionally, the proposed approach for leveraging LLMs for SLRs enables the dissemination of finetuned models, empowering researchers to accelerate advancements and democratize cutting-edge research. This paper presents the case for the feasibility of finetuned LLMs to support rigorous SLRs and the technical requirements for realizing this. This work then proposes the extended PRISMA-DFLLM checklist of reporting guidelines as well as the advantages, challenges, and potential implications of implementing PRISMA-DFLLM. Finally, a future research roadmap to develop this line of AI-enabled SLRs is presented, paving the way for a new era of evidence synthesis and knowledge discovery.

  • 1 authors
·
Jun 14, 2023

Self-Specialization: Uncovering Latent Expertise within Large Language Models

Recent works have demonstrated the effectiveness of self-alignment in which a large language model is, by itself, aligned to follow general instructions through the automatic generation of instructional data using a handful of human-written seeds. Instead of general alignment, in this work, we focus on self-alignment for expert domain specialization (e.g., biomedicine), discovering it to be very effective for improving zero-shot and few-shot performance in target domains of interest. As a preliminary, we first present the benchmark results of existing aligned models within a specialized domain, which reveals the marginal effect that "generic" instruction-following training has on downstream expert domains' performance. To remedy this, we explore self-specialization that leverages domain-specific unlabelled data and a few labeled seeds for the self-alignment process. When augmented with retrieval to reduce hallucination and enhance concurrency of the alignment, self-specialization offers an effective (and efficient) way of "carving out" an expert model out of a "generalist", pre-trained LLM where different domains of expertise are originally combined in a form of "superposition". Our experimental results on a biomedical domain show that our self-specialized model (30B) outperforms its base model, MPT-30B by a large margin and even surpasses larger popular models based on LLaMA-65B, highlighting its potential and practicality for specialization, especially considering its efficiency in terms of data and parameters.

  • 8 authors
·
Sep 29, 2023

Leveraging Open Knowledge for Advancing Task Expertise in Large Language Models

The cultivation of expertise for large language models (LLMs) to solve tasks of specific areas often requires special-purpose tuning with calibrated behaviors on the expected stable outputs. To avoid huge cost brought by manual preparation of instruction datasets and training resources up to hundreds of hours, the exploitation of open knowledge including a wealth of low rank adaptation (LoRA) models and instruction datasets serves as a good starting point. However, existing methods on model and data selection focus on the performance of general-purpose capabilities while neglecting the knowledge gap exposed in domain-specific deployment. In the present study, we propose to bridge such gap by introducing few human-annotated samples (i.e., K-shot) for advancing task expertise of LLMs with open knowledge. Specifically, we develop an efficient and scalable pipeline to cost-efficiently produce task experts where K-shot data intervene in selecting the most promising expert candidates and the task-relevant instructions. A mixture-of-expert (MoE) system is built to make the best use of individual-yet-complementary knowledge between multiple experts. We unveil the two keys to the success of a MoE system, 1) the abidance by K-shot, and 2) the insistence on diversity. For the former, we ensure that models that truly possess problem-solving abilities on K-shot are selected rather than those blind guessers. Besides, during data selection, instructions that share task-relevant contexts with K-shot are prioritized. For the latter, we highlight the diversity of constituting experts and that of the fine-tuning instructions throughout the model and data selection process. Extensive experimental results confirm the superiority of our approach over existing methods on utilization of open knowledge across various tasks. Codes and models will be released later.

  • 12 authors
·
Aug 28, 2024 4

Educating LLMs like Human Students: Structure-aware Injection of Domain Knowledge

This paper presents a pioneering methodology, termed StructTuning, to efficiently transform foundation Large Language Models (LLMs) into domain specialists. It significantly minimizes the training corpus requirement to a mere 0.3% while achieving an impressive 50% of traditional knowledge injection performance. Our method is inspired by the educational processes for human students, particularly how structured domain knowledge from textbooks is absorbed and then applied to tackle real-world challenges through specific exercises. Based on this, we propose a novel two-stage knowledge injection strategy: Structure-aware Continual Pre-Training (SCPT) and Structure-aware Supervised Fine-Tuning (SSFT). In the SCPT phase, we organize the training data into an auto-generated taxonomy of domain knowledge, enabling LLMs to effectively memorize textual segments linked to specific expertise within the taxonomy's architecture. Subsequently, in the SSFT phase, we explicitly prompt models to reveal the underlying knowledge structure in their outputs, leveraging this structured domain insight to address practical problems adeptly. Our ultimate method has undergone extensive evaluations across model architectures and scales, using closed-book question-answering tasks on LongBench and MMedBench datasets. Remarkably, our method matches 50% of the improvement displayed by the state-of-the-art MMedLM2 on MMedBench, but with only 0.3% quantity of the training corpus. This breakthrough showcases the potential to scale up our StructTuning for stronger domain-specific LLMs. Code will be made public soon.

  • 8 authors
·
Jul 23, 2024

SCALE: Scaling up the Complexity for Advanced Language Model Evaluation

Recent strides in Large Language Models (LLMs) have saturated many NLP benchmarks (even professional domain-specific ones), emphasizing the need for novel, more challenging novel ones to properly assess LLM capabilities. In this paper, we introduce a novel NLP benchmark that poses challenges to current LLMs across four key dimensions: processing long documents (up to 50K tokens), utilizing domain specific knowledge (embodied in legal texts), multilingual understanding (covering five languages), and multitasking (comprising legal document to document Information Retrieval, Court View Generation, Leading Decision Summarization, Citation Extraction, and eight challenging Text Classification tasks). Our benchmark comprises diverse legal NLP datasets from the Swiss legal system, allowing for a comprehensive study of the underlying Non-English, inherently multilingual, federal legal system. Despite recent advances, efficiently processing long documents for intense review/analysis tasks remains an open challenge for language models. Also, comprehensive, domain-specific benchmarks requiring high expertise to develop are rare, as are multilingual benchmarks. This scarcity underscores our contribution's value, considering most public models are trained predominantly on English corpora, while other languages remain understudied, particularly for practical domain-specific NLP tasks. Our benchmark allows for testing and advancing the state-of-the-art LLMs. As part of our study, we evaluate several pre-trained multilingual language models on our benchmark to establish strong baselines as a point of reference. Despite the large size of our datasets (tens to hundreds of thousands of examples), existing publicly available models struggle with most tasks, even after in-domain pretraining. We publish all resources (benchmark suite, pre-trained models, code) under a fully permissive open CC BY-SA license.

  • 7 authors
·
Jun 15, 2023

Biomedical knowledge graph-optimized prompt generation for large language models

Large Language Models (LLMs) are being adopted at an unprecedented rate, yet still face challenges in knowledge-intensive domains like biomedicine. Solutions such as pre-training and domain-specific fine-tuning add substantial computational overhead, requiring further domain expertise. Here, we introduce a token-optimized and robust Knowledge Graph-based Retrieval Augmented Generation (KG-RAG) framework by leveraging a massive biomedical KG (SPOKE) with LLMs such as Llama-2-13b, GPT-3.5-Turbo and GPT-4, to generate meaningful biomedical text rooted in established knowledge. Compared to the existing RAG technique for Knowledge Graphs, the proposed method utilizes minimal graph schema for context extraction and uses embedding methods for context pruning. This optimization in context extraction results in more than 50% reduction in token consumption without compromising the accuracy, making a cost-effective and robust RAG implementation on proprietary LLMs. KG-RAG consistently enhanced the performance of LLMs across diverse biomedical prompts by generating responses rooted in established knowledge, accompanied by accurate provenance and statistical evidence (if available) to substantiate the claims. Further benchmarking on human curated datasets, such as biomedical true/false and multiple-choice questions (MCQ), showed a remarkable 71% boost in the performance of the Llama-2 model on the challenging MCQ dataset, demonstrating the framework's capacity to empower open-source models with fewer parameters for domain specific questions. Furthermore, KG-RAG enhanced the performance of proprietary GPT models, such as GPT-3.5 and GPT-4. In summary, the proposed framework combines explicit and implicit knowledge of KG and LLM in a token optimized fashion, thus enhancing the adaptability of general-purpose LLMs to tackle domain-specific questions in a cost-effective fashion.

  • 14 authors
·
Nov 28, 2023

TransformLLM: Adapting Large Language Models via LLM-Transformed Reading Comprehension Text

Large Language Models (LLMs) have shown promise in highly-specialized domains, however challenges are still present in aspects of accuracy and costs. These limitations restrict the usage of existing models in domain-specific tasks. While fine-tuning pre-trained models have shown promising results, this process can be computationally expensive and require massive datasets of the specialized application in hand. In this work, we bridge that gap. We have developed Phi-2-Legal and Mistral-Legal-7B, which are language models specifically designed for legal applications. These models are based on Phi-2 and Mistral-7B-v0.1, and have gone through continued pre-training with over 500 million tokens of legal texts. Our innovative approach significantly improves capabilities in legal tasks by using Large Language Models (LLMs) to convert raw training data into reading comprehension text. Our legal LLMs have demonstrated superior performance in legal benchmarks, even outperforming models trained on much larger datasets with more resources. This work emphasizes the effectiveness of continued pre-training on domain-specific texts, while using affordable LLMs for data conversion, which gives these models domain expertise while retaining general language understanding capabilities. While this work uses the legal domain as a test case, our method can be scaled and applied to any pre-training dataset, resulting in significant improvements across different tasks. These findings underscore the potential of domain-adaptive pre-training and reading comprehension for the development of highly effective domain-specific language models.

  • 3 authors
·
Oct 28, 2024

Benchmarking Large Language Models for Molecule Prediction Tasks

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

  • 3 authors
·
Mar 8, 2024

Clinical Document Corpora and Assorted Domain Proxies: A Survey of Diversity in Corpus Design, with Focus on German Text Data

We survey clinical document corpora, with focus on German textual data. Due to rigid data privacy legislation in Germany these resources, with only few exceptions, are stored in safe clinical data spaces and locked against clinic-external researchers. This situation stands in stark contrast with established workflows in the field of natural language processing where easy accessibility and reuse of data collections are common practice. Hence, alternative corpus designs have been examined to escape from this data poverty. Besides machine translation of English clinical datasets and the generation of synthetic corpora with fictitious clinical contents, several other types of domain proxies have come up as substitutes for authentic clinical documents. Common instances of close proxies are medical journal publications, clinical therapy guidelines, drug labels, etc., more distant proxies include online encyclopedic medical articles or medical contents from social media channels. After PRISM-conformant screening of 359 hits from four bibliographic systems, 75 relevant documents were finally selected for this review and 59 distinct corpora were determined. We identified 24 real clinical corpora (from 40 publications) out of which only 5 are publicly distributable. 2 translations of real corpora and 3 synthetic ones complement the set of clinical corpora. 14 corpora were categorized as close domain proxies, 16 as distant ones. There is a clear divide between the large number of non-accessible authentic clinical German-language corpora and their publicly accessible substitutes: translated or synthetic, close or more distant proxies. So on first sight, the data bottleneck seems broken. Intuitively yet, differences in genre-specific writing style, wording and medical domain expertise in this typological space are also obvious. This raises the question how valid alternative corpus designs really are.

  • 1 authors
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Nov 29, 2024

KramaBench: A Benchmark for AI Systems on Data-to-Insight Pipelines over Data Lakes

Constructing real-world data-to-insight pipelines often involves data extraction from data lakes, data integration across heterogeneous data sources, and diverse operations from data cleaning to analysis. The design and implementation of data science pipelines require domain knowledge, technical expertise, and even project-specific insights. AI systems have shown remarkable reasoning, coding, and understanding capabilities. However, it remains unclear to what extent these capabilities translate into successful design and execution of such complex pipelines. We introduce KRAMABENCH: a benchmark composed of 104 manually-curated real-world data science pipelines spanning 1700 data files from 24 data sources in 6 different domains. We show that these pipelines test the end-to-end capabilities of AI systems on data processing, requiring data discovery, wrangling and cleaning, efficient processing, statistical reasoning, and orchestrating data processing steps given a high-level task. Our evaluation tests 5 general models and 3 code generation models using our reference framework, DS-GURU, which instructs the AI model to decompose a question into a sequence of subtasks, reason through each step, and synthesize Python code that implements the proposed design. Our results on KRAMABENCH show that, although the models are sufficiently capable of solving well-specified data science code generation tasks, when extensive data processing and domain knowledge are required to construct real-world data science pipelines, existing out-of-box models fall short. Progress on KramaBench represents crucial steps towards developing autonomous data science agents for real-world applications. Our code, reference framework, and data are available at https://github.com/mitdbg/KramaBench.

  • 19 authors
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Jun 6

Constrained composite Bayesian optimization for rational synthesis of polymeric particles

Polymeric nano- and micro-scale particles have critical roles in tackling critical healthcare and energy challenges with their miniature characteristics. However, tailoring their synthesis process to meet specific design targets has traditionally depended on domain expertise and costly trial-and-errors. Recently, modeling strategies, particularly Bayesian optimization (BO), have been proposed to aid materials discovery for maximized/minimized properties. Coming from practical demands, this study for the first time integrates constrained and composite Bayesian optimization (CCBO) to perform efficient target value optimization under black-box feasibility constraints and limited data for laboratory experimentation. Using a synthetic problem that simulates electrospraying, a model nanomanufacturing process, CCBO strategically avoided infeasible conditions and efficiently optimized particle production towards predefined size targets, surpassing standard BO pipelines and providing decisions comparable to human experts. Further laboratory experiments validated CCBO capability to guide the rational synthesis of poly(lactic-co-glycolic acid) (PLGA) particles with diameters of 300 nm and 3.0 mum via electrospraying. With minimal initial data and unknown experiment constraints, CCBO reached the design targets within 4 iterations. Overall, the CCBO approach presents a versatile and holistic optimization paradigm for next-generation target-driven particle synthesis empowered by artificial intelligence (AI).

  • 4 authors
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Nov 6, 2024

Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine

Generalist foundation models such as GPT-4 have displayed surprising capabilities in a wide variety of domains and tasks. Yet, there is a prevalent assumption that they cannot match specialist capabilities of fine-tuned models. For example, most explorations to date on medical competency benchmarks have leveraged domain-specific training, as exemplified by efforts on BioGPT and Med-PaLM. We build on a prior study of GPT-4's capabilities on medical challenge benchmarks in the absence of special training. Rather than using simple prompting to highlight the model's out-of-the-box capabilities, we perform a systematic exploration of prompt engineering. We find that prompting innovation can unlock deeper specialist capabilities and show that GPT-4 easily tops prior leading results for medical benchmarks. The prompting methods we explore are general purpose, and make no specific use of domain expertise, removing the need for expert-curated content. Our experimental design carefully controls for overfitting during the prompt engineering process. We introduce Medprompt, based on a composition of several prompting strategies. With Medprompt, GPT-4 achieves state-of-the-art results on all nine of the benchmark datasets in the MultiMedQA suite. The method outperforms leading specialist models such as Med-PaLM 2 by a significant margin with an order of magnitude fewer calls to the model. Steering GPT-4 with Medprompt achieves a 27% reduction in error rate on the MedQA dataset over the best methods to date achieved with specialist models and surpasses a score of 90% for the first time. Beyond medical problems, we show the power of Medprompt to generalize to other domains and provide evidence for the broad applicability of the approach via studies of the strategy on exams in electrical engineering, machine learning, philosophy, accounting, law, nursing, and clinical psychology.

  • 18 authors
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Nov 27, 2023

ReviewerToo: Should AI Join The Program Committee? A Look At The Future of Peer Review

Peer review is the cornerstone of scientific publishing, yet it suffers from inconsistencies, reviewer subjectivity, and scalability challenges. We introduce ReviewerToo, a modular framework for studying and deploying AI-assisted peer review to complement human judgment with systematic and consistent assessments. ReviewerToo supports systematic experiments with specialized reviewer personas and structured evaluation criteria, and can be partially or fully integrated into real conference workflows. We validate ReviewerToo on a carefully curated dataset of 1,963 paper submissions from ICLR 2025, where our experiments with the gpt-oss-120b model achieves 81.8% accuracy for the task of categorizing a paper as accept/reject compared to 83.9% for the average human reviewer. Additionally, ReviewerToo-generated reviews are rated as higher quality than the human average by an LLM judge, though still trailing the strongest expert contributions. Our analysis highlights domains where AI reviewers excel (e.g., fact-checking, literature coverage) and where they struggle (e.g., assessing methodological novelty and theoretical contributions), underscoring the continued need for human expertise. Based on these findings, we propose guidelines for integrating AI into peer-review pipelines, showing how AI can enhance consistency, coverage, and fairness while leaving complex evaluative judgments to domain experts. Our work provides a foundation for systematic, hybrid peer-review systems that scale with the growth of scientific publishing.

MARK: Memory Augmented Refinement of Knowledge

Large Language Models (LLMs) assist in specialized tasks but struggle to align with evolving domain knowledge without costly fine-tuning. Domain knowledge consists of: Knowledge: Immutable facts (e.g., 'A stone is solid') and generally accepted principles (e.g., ethical standards); Refined Memory: Evolving insights shaped by business needs and real-world changes. However, a significant gap often exists between a domain expert's deep, nuanced understanding and the system's domain knowledge, which can hinder accurate information retrieval and application. Our Memory-Augmented Refinement of Knowledge (MARK) framework enables LLMs to continuously learn without retraining by leveraging structured refined memory, inspired by the Society of Mind. MARK operates through specialized agents, each serving a distinct role: Residual Refined Memory Agent: Stores and retrieves domain-specific insights to maintain context over time; User Question Refined Memory Agent: Captures user-provided facts, abbreviations, and terminology for better comprehension; LLM Response Refined Memory Agent: Extracts key elements from responses for refinement and personalization. These agents analyse stored refined memory, detect patterns, resolve contradictions, and improve response accuracy. Temporal factors like recency and frequency prioritize relevant information while discarding outdated insights. MARK enhances LLMs in multiple ways: Ground Truth Strategy: Reduces hallucinations by establishing a structured reference; Domain-Specific Adaptation: Essential for fields like healthcare, law, and manufacturing, where proprietary insights are absent from public datasets; Personalized AI Assistants: Improves virtual assistants by remembering user preferences, ensuring coherent responses over time.

  • 3 authors
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May 8

RouterRetriever: Exploring the Benefits of Routing over Multiple Expert Embedding Models

Information retrieval methods often rely on a single embedding model trained on large, general-domain datasets like MSMARCO. While this approach can produce a retriever with reasonable overall performance, models trained on domain-specific data often yield better results within their respective domains. While prior work in information retrieval has tackled this through multi-task training, the topic of combining multiple domain-specific expert retrievers remains unexplored, despite its popularity in language model generation. In this work, we introduce RouterRetriever, a retrieval model that leverages multiple domain-specific experts along with a routing mechanism to select the most appropriate expert for each query. It is lightweight and allows easy addition or removal of experts without additional training. Evaluation on the BEIR benchmark demonstrates that RouterRetriever outperforms both MSMARCO-trained (+2.1 absolute nDCG@10) and multi-task trained (+3.2) models. This is achieved by employing our routing mechanism, which surpasses other routing techniques (+1.8 on average) commonly used in language modeling. Furthermore, the benefit generalizes well to other datasets, even in the absence of a specific expert on the dataset. To our knowledge, RouterRetriever is the first work to demonstrate the advantages of using multiple domain-specific expert embedding models with effective routing over a single, general-purpose embedding model in retrieval tasks.

  • 5 authors
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Sep 4, 2024

Contrastive Learning and Mixture of Experts Enables Precise Vector Embeddings

The advancement of transformer neural networks has significantly elevated the capabilities of sentence similarity models, particularly in creating effective vector representations of natural language inputs. However, these models face notable challenges in domain-specific contexts, especially in highly specialized scientific sub-fields. Traditional methods often struggle in this regime, either overgeneralizing similarities within a niche or being overly sensitive to minor differences, resulting in inaccurate text classification and subpar vector representation. In an era where retrieval augmentation and search are increasingly crucial, precise and concise numerical representations are essential. In this paper, we target this issue by assembling niche datasets using co-citations as a similarity metric, focusing on biomedical domains. We employ two key strategies for fine-tuning state-of-the-art models: 1. Domain-specific Fine-Tuning, which tailors pretrained models to a single domain, and 2. Universal Applicability with Mixture of Experts (MoE), adapting pretrained models with enforced routing for multiple domains simultaneously. Our training approach emphasizes the use of abstracts for faster training, incorporating Multiple Negative Rankings loss for efficient contrastive learning. Notably, our MoE variants, equipped with N experts, achieve the efficacy of N individual models, heralding a new era of versatile, One-Size-Fits-All transformer networks for various tasks. This methodology marks significant advancements in scientific text classification metrics and holds promise for enhancing vector database search and compilation.

  • 4 authors
·
Jan 28, 2024

Domain-Specific Pruning of Large Mixture-of-Experts Models with Few-shot Demonstrations

Mixture-of-Experts (MoE) models achieve a favorable trade-off between performance and inference efficiency by activating only a subset of experts. However, the memory overhead of storing all experts remains a major limitation, especially in large-scale MoE models such as DeepSeek-R1(671B). In this study, we investigate domain specialization and expert redundancy in large-scale MoE models and uncover a consistent behavior we term few-shot expert localization, with only a few in-domain demonstrations, the model consistently activates a sparse and stable subset of experts on tasks within the same domain. Building on this observation, we propose a simple yet effective pruning framework, EASY-EP, that leverages a few domain-specific demonstrations to identify and retain only the most relevant experts. EASY-EP comprises two key components: output-aware expert importance assessment and expert-level token contribution estimation. The former evaluates the importance of each expert for the current token by considering the gating scores and L2 norm of the outputs of activated experts, while the latter assesses the contribution of tokens based on representation similarities before and after routed experts. Experiments on DeepSeek-R1 and DeepSeek-V3-0324 show that our method can achieve comparable performances and 2.99times throughput under the same memory budget with full model with only half the experts.

  • 7 authors
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Apr 9

ModuleFormer: Learning Modular Large Language Models From Uncurated Data

Large Language Models (LLMs) have achieved remarkable results. But existing models are expensive to train and deploy, and it is also difficult to expand their knowledge beyond pre-training data without forgetting previous knowledge. This paper proposes a new neural network architecture, ModuleFormer, that leverages modularity to improve the efficiency and flexibility of large language models. ModuleFormer is based on the Sparse Mixture of Experts (SMoE). Unlike the previous SMoE-based modular language model [Gururangan et al., 2021], which requires domain-labeled data to learn domain-specific experts, ModuleFormer can induce modularity from uncurated data with its new load balancing and load concentration losses. ModuleFormer is a modular architecture that includes two different types of modules, new stick-breaking attention heads, and feedforward experts. Different modules are sparsely activated conditions on the input token during training and inference. In our experiment, we found that the modular architecture enables three important abilities for large pre-trained language models: 1) Efficiency, since ModuleFormer only activates a subset of its modules for each input token, thus it could achieve the same performance as dense LLMs with more than two times throughput; 2) Extendability, ModuleFormer is more immune to catastrophic forgetting than dense LLMs and can be easily extended with new modules to learn new knowledge that is not included in the training data; 3) Specialisation, finetuning ModuleFormer could specialize a subset of modules to the finetuning task, and the task-unrelated modules could be easily pruned for a lightweight deployment.

  • 6 authors
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Jun 7, 2023

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

VILA-M3: Enhancing Vision-Language Models with Medical Expert Knowledge

Generalist vision language models (VLMs) have made significant strides in computer vision, but they fall short in specialized fields like healthcare, where expert knowledge is essential. In traditional computer vision tasks, creative or approximate answers may be acceptable, but in healthcare, precision is paramount.Current large multimodal models like Gemini and GPT-4o are insufficient for medical tasks due to their reliance on memorized internet knowledge rather than the nuanced expertise required in healthcare. VLMs are usually trained in three stages: vision pre-training, vision-language pre-training, and instruction fine-tuning (IFT). IFT has been typically applied using a mixture of generic and healthcare data. In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models. Domain expert models developed for medical use are crucial because they are specifically trained for certain clinical tasks, e.g. to detect tumors and classify abnormalities through segmentation and classification, which learn fine-grained features of medical data-features that are often too intricate for a VLM to capture effectively especially in radiology. This paper introduces a new framework, VILA-M3, for medical VLMs that utilizes domain knowledge via expert models. Through our experiments, we show an improved state-of-the-art (SOTA) performance with an average improvement of ~9% over the prior SOTA model Med-Gemini and ~6% over models trained on the specific tasks. Our approach emphasizes the importance of domain expertise in creating precise, reliable VLMs for medical applications.

  • 22 authors
·
Nov 19, 2024

Pruning as a Domain-specific LLM Extractor

Large Language Models (LLMs) have exhibited remarkable proficiency across a wide array of NLP tasks. However, the escalation in model size also engenders substantial deployment costs. While few efforts have explored model pruning techniques to reduce the size of LLMs, they mainly center on general or task-specific weights. This leads to suboptimal performance due to lacking specificity on the target domain or generality on different tasks when applied to domain-specific challenges. This work introduces an innovative unstructured dual-pruning methodology, D-Pruner, for domain-specific compression on LLM. It extracts a compressed, domain-specific, and task-agnostic LLM by identifying LLM weights that are pivotal for general capabilities, like linguistic capability and multi-task solving, and domain-specific knowledge. More specifically, we first assess general weight importance by quantifying the error incurred upon their removal with the help of an open-domain calibration dataset. Then, we utilize this general weight importance to refine the training loss, so that it preserves generality when fitting into a specific domain. Moreover, by efficiently approximating weight importance with the refined training loss on a domain-specific calibration dataset, we obtain a pruned model emphasizing generality and specificity. Our comprehensive experiments across various tasks in healthcare and legal domains show the effectiveness of D-Pruner in domain-specific compression. Our code is available at https://github.com/psunlpgroup/D-Pruner.

  • 8 authors
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May 10, 2024

Towards Human-Guided, Data-Centric LLM Co-Pilots

Machine learning (ML) has the potential to revolutionize various domains, but its adoption is often hindered by the disconnect between the needs of domain experts and translating these needs into robust and valid ML tools. Despite recent advances in LLM-based co-pilots to democratize ML for non-technical domain experts, these systems remain predominantly focused on model-centric aspects while overlooking critical data-centric challenges. This limitation is problematic in complex real-world settings where raw data often contains complex issues, such as missing values, label noise, and domain-specific nuances requiring tailored handling. To address this we introduce CliMB-DC, a human-guided, data-centric framework for LLM co-pilots that combines advanced data-centric tools with LLM-driven reasoning to enable robust, context-aware data processing. At its core, CliMB-DC introduces a novel, multi-agent reasoning system that combines a strategic coordinator for dynamic planning and adaptation with a specialized worker agent for precise execution. Domain expertise is then systematically incorporated to guide the reasoning process using a human-in-the-loop approach. To guide development, we formalize a taxonomy of key data-centric challenges that co-pilots must address. Thereafter, to address the dimensions of the taxonomy, we integrate state-of-the-art data-centric tools into an extensible, open-source architecture, facilitating the addition of new tools from the research community. Empirically, using real-world healthcare datasets we demonstrate CliMB-DC's ability to transform uncurated datasets into ML-ready formats, significantly outperforming existing co-pilot baselines for handling data-centric challenges. CliMB-DC promises to empower domain experts from diverse domains -- healthcare, finance, social sciences and more -- to actively participate in driving real-world impact using ML.

  • 5 authors
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Jan 17

Knowledge Solver: Teaching LLMs to Search for Domain Knowledge from Knowledge Graphs

Large language models (LLMs), such as ChatGPT and GPT-4, are versatile and can solve different tasks due to their emergent ability and generalizability. However, LLMs sometimes lack domain-specific knowledge to perform tasks, which would also cause hallucination during inference. In some previous works, additional modules like graph neural networks (GNNs) are trained on retrieved knowledge from external knowledge bases, aiming to mitigate the problem of lacking domain-specific knowledge. However, incorporating additional modules: 1) would need retraining additional modules when encountering novel domains; 2) would become a bottleneck since LLMs' strong abilities are not fully utilized for retrieval. In this paper, we propose a paradigm, termed Knowledge Solver (KSL), to teach LLMs to search for essential knowledge from external knowledge bases by harnessing their own strong generalizability. Specifically, we design a simple yet effective prompt to transform retrieval into a multi-hop decision sequence, which empowers LLMs with searching knowledge ability in zero-shot manner. Additionally, KSL is able to provide complete retrieval paths and therefore increase explainability of LLMs' reasoning processes. We conduct experiments on three datasets: CommonsenseQA, OpenbookQA, and MedQA-USMLE, and found that our approach improves LLM baseline performance by a relatively large margin.

  • 3 authors
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Sep 6, 2023

Mixing It Up: The Cocktail Effect of Multi-Task Fine-Tuning on LLM Performance -- A Case Study in Finance

The application of large language models (LLMs) in domain-specific contexts, including finance, has expanded rapidly. Domain-specific LLMs are typically evaluated based on their performance in various downstream tasks relevant to the domain. In this work, we present a detailed analysis of fine-tuning LLMs for such tasks. Somewhat counterintuitively, we find that in domain-specific cases, fine-tuning exclusively on the target task is not always the most effective strategy. Instead, multi-task finetuning - where models are trained on a cocktail of related tasks - can significantly enhance performance. We demonstrate how this approach enables a small model, such as Phi-3-Mini, to achieve state-of-the-art results, even surpassing the much larger GPT-4-o model on financial benchmarks. Our study involves a large-scale experiment, conducting over 200 training experiments using several widely adopted LLMs as baselines, and empirically confirms the benefits of multi-task fine-tuning. Additionally, we explore the use of general instruction data as a form of regularization, suggesting that it helps minimize performance degradation. We also investigate the inclusion of mathematical data, finding improvements in numerical reasoning that transfer effectively to financial tasks. Finally, we note that while fine-tuning for downstream tasks leads to targeted improvements in task performance, it does not necessarily result in broader gains in domain knowledge or complex domain reasoning abilities.

  • 6 authors
·
Oct 1, 2024

BLADE: Enhancing Black-box Large Language Models with Small Domain-Specific Models

Large Language Models (LLMs) like ChatGPT and GPT-4 are versatile and capable of addressing a diverse range of tasks. However, general LLMs, which are developed on open-domain data, may lack the domain-specific knowledge essential for tasks in vertical domains, such as legal, medical, etc. To address this issue, previous approaches either conduct continuous pre-training with domain-specific data or employ retrieval augmentation to support general LLMs. Unfortunately, these strategies are either cost-intensive or unreliable in practical applications. To this end, we present a novel framework named BLADE, which enhances Black-box LArge language models with small Domain-spEcific models. BLADE consists of a black-box LLM and a small domain-specific LM. The small LM preserves domain-specific knowledge and offers specialized insights, while the general LLM contributes robust language comprehension and reasoning capabilities. Specifically, our method involves three steps: 1) pre-training the small LM with domain-specific data, 2) fine-tuning this model using knowledge instruction data, and 3) joint Bayesian optimization of the general LLM and the small LM. Extensive experiments conducted on public legal and medical benchmarks reveal that BLADE significantly outperforms existing approaches. This shows the potential of BLADE as an effective and cost-efficient solution in adapting general LLMs for vertical domains.

  • 8 authors
·
Mar 27, 2024

KGQuiz: Evaluating the Generalization of Encoded Knowledge in Large Language Models

Large language models (LLMs) demonstrate remarkable performance on knowledge-intensive tasks, suggesting that real-world knowledge is encoded in their model parameters. However, besides explorations on a few probing tasks in limited knowledge domains, it is not well understood how to evaluate LLMs' knowledge systematically and how well their knowledge abilities generalize, across a spectrum of knowledge domains and progressively complex task formats. To this end, we propose KGQuiz, a knowledge-intensive benchmark to comprehensively investigate the knowledge generalization abilities of LLMs. KGQuiz is a scalable framework constructed from triplet-based knowledge, which covers three knowledge domains and consists of five tasks with increasing complexity: true-or-false, multiple-choice QA, blank filling, factual editing, and open-ended knowledge generation. To gain a better understanding of LLMs' knowledge abilities and their generalization, we evaluate 10 open-source and black-box LLMs on the KGQuiz benchmark across the five knowledge-intensive tasks and knowledge domains. Extensive experiments demonstrate that LLMs achieve impressive performance in straightforward knowledge QA tasks, while settings and contexts requiring more complex reasoning or employing domain-specific facts still present significant challenges. We envision KGQuiz as a testbed to analyze such nuanced variations in performance across domains and task formats, and ultimately to understand, evaluate, and improve LLMs' knowledge abilities across a wide spectrum of knowledge domains and tasks.

  • 7 authors
·
Oct 15, 2023

AstroMLab 4: Benchmark-Topping Performance in Astronomy Q&A with a 70B-Parameter Domain-Specialized Reasoning Model

General-purpose large language models, despite their broad capabilities, often struggle with specialized domain knowledge, a limitation particularly pronounced in more accessible, lower-parameter versions. This gap hinders their deployment as effective agents in demanding fields such as astronomy. Building on our prior work with AstroSage-8B, this study introduces AstroSage-70B, a significantly larger and more advanced domain-specialized natural-language AI assistant. It is designed for research and education across astronomy, astrophysics, space science, astroparticle physics, cosmology, and astronomical instrumentation. Developed from the Llama-3.1-70B foundation, AstroSage-70B underwent extensive continued pre-training on a vast corpus of astronomical literature, followed by supervised fine-tuning and model merging. Beyond its 70-billion parameter scale, this model incorporates refined datasets, judiciously chosen learning hyperparameters, and improved training procedures, achieving state-of-the-art performance on complex astronomical tasks. Notably, we integrated reasoning chains into the SFT dataset, enabling AstroSage-70B to either answer the user query immediately, or first emit a human-readable thought process. Evaluated on the AstroMLab-1 benchmark -- comprising 4,425 questions from literature withheld during training -- AstroSage-70B achieves state-of-the-art performance. It surpasses all other tested open-weight and proprietary models, including leading systems like o3, Gemini-2.5-Pro, Claude-3.7-Sonnet, Deepseek-R1, and Qwen-3-235B, even those with API costs two orders of magnitude higher. This work demonstrates that domain specialization, when applied to large-scale models, can enable them to outperform generalist counterparts in specialized knowledge areas like astronomy, thereby advancing the frontier of AI capabilities in the field.

  • 10 authors
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May 23

Generalized Domain Conditioned Adaptation Network

Domain Adaptation (DA) attempts to transfer knowledge learned in the labeled source domain to the unlabeled but related target domain without requiring large amounts of target supervision. Recent advances in DA mainly proceed by aligning the source and target distributions. Despite the significant success, the adaptation performance still degrades accordingly when the source and target domains encounter a large distribution discrepancy. We consider this limitation may attribute to the insufficient exploration of domain-specialized features because most studies merely concentrate on domain-general feature learning in task-specific layers and integrate totally-shared convolutional networks (convnets) to generate common features for both domains. In this paper, we relax the completely-shared convnets assumption adopted by previous DA methods and propose Domain Conditioned Adaptation Network (DCAN), which introduces domain conditioned channel attention module with a multi-path structure to separately excite channel activation for each domain. Such a partially-shared convnets module allows domain-specialized features in low-level to be explored appropriately. Further, given the knowledge transferability varying along with convolutional layers, we develop Generalized Domain Conditioned Adaptation Network (GDCAN) to automatically determine whether domain channel activations should be separately modeled in each attention module. Afterward, the critical domain-specialized knowledge could be adaptively extracted according to the domain statistic gaps. As far as we know, this is the first work to explore the domain-wise convolutional channel activations separately for deep DA networks. Additionally, to effectively match high-level feature distributions across domains, we consider deploying feature adaptation blocks after task-specific layers, which can explicitly mitigate the domain discrepancy.

  • 6 authors
·
Mar 23, 2021

Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. In this paper, we challenge this assumption by showing that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language models. To facilitate this investigation, we compile a comprehensive biomedical NLP benchmark from publicly-available datasets. Our experiments show that domain-specific pretraining serves as a solid foundation for a wide range of biomedical NLP tasks, leading to new state-of-the-art results across the board. Further, in conducting a thorough evaluation of modeling choices, both for pretraining and task-specific fine-tuning, we discover that some common practices are unnecessary with BERT models, such as using complex tagging schemes in named entity recognition (NER). To help accelerate research in biomedical NLP, we have released our state-of-the-art pretrained and task-specific models for the community, and created a leaderboard featuring our BLURB benchmark (short for Biomedical Language Understanding & Reasoning Benchmark) at https://aka.ms/BLURB.

  • 9 authors
·
Jul 30, 2020 1

Beyond Finite Data: Towards Data-free Out-of-distribution Generalization via Extrapolation

Out-of-distribution (OOD) generalization is a favorable yet challenging property for deep neural networks. The core challenges lie in the limited availability of source domains that help models learn an invariant representation from the spurious features. Various domain augmentation have been proposed but largely rely on interpolating existing domains and frequently face difficulties in creating truly "novel" domains. Humans, on the other hand, can easily extrapolate novel domains, thus, an intriguing question arises: How can neural networks extrapolate like humans and achieve OOD generalization? We introduce a novel approach to domain extrapolation that leverages reasoning ability and the extensive knowledge encapsulated within large language models (LLMs) to synthesize entirely new domains. Starting with the class of interest, we query the LLMs to extract relevant knowledge for these novel domains. We then bridge the gap between the text-centric knowledge derived from LLMs and the pixel input space of the model using text-to-image generation techniques. By augmenting the training set of domain generalization datasets with high-fidelity, photo-realistic images of these new domains, we achieve significant improvements over all existing methods, as demonstrated in both single and multi-domain generalization across various benchmarks. With the ability to extrapolate any domains for any class, our method has the potential to learn a generalized model for any task without any data. To illustrate, we put forth a much more difficult setting termed, data-free domain generalization, that aims to learn a generalized model in the absence of any collected data. Our empirical findings support the above argument and our methods exhibit commendable performance in this setting, even surpassing the supervised setting by approximately 1-2\% on datasets such as VLCS.

  • 7 authors
·
Mar 8, 2024

TaskMatrix.AI: Completing Tasks by Connecting Foundation Models with Millions of APIs

Artificial Intelligence (AI) has made incredible progress recently. On the one hand, advanced foundation models like ChatGPT can offer powerful conversation, in-context learning and code generation abilities on a broad range of open-domain tasks. They can also generate high-level solution outlines for domain-specific tasks based on the common sense knowledge they have acquired. However, they still face difficulties with some specialized tasks because they lack enough domain-specific data during pre-training or they often have errors in their neural network computations on those tasks that need accurate executions. On the other hand, there are also many existing models and systems (symbolic-based or neural-based) that can do some domain-specific tasks very well. However, due to the different implementation or working mechanisms, they are not easily accessible or compatible with foundation models. Therefore, there is a clear and pressing need for a mechanism that can leverage foundation models to propose task solution outlines and then automatically match some of the sub-tasks in the outlines to the off-the-shelf models and systems with special functionalities to complete them. Inspired by this, we introduce TaskMatrix.AI as a new AI ecosystem that connects foundation models with millions of APIs for task completion. Unlike most previous work that aimed to improve a single AI model, TaskMatrix.AI focuses more on using existing foundation models (as a brain-like central system) and APIs of other AI models and systems (as sub-task solvers) to achieve diversified tasks in both digital and physical domains. As a position paper, we will present our vision of how to build such an ecosystem, explain each key component, and use study cases to illustrate both the feasibility of this vision and the main challenges we need to address next.

  • 14 authors
·
Mar 28, 2023

Adapting While Learning: Grounding LLMs for Scientific Problems with Intelligent Tool Usage Adaptation

Large Language Models (LLMs) demonstrate promising capabilities in solving simple scientific problems but often produce hallucinations for complex ones. While integrating LLMs with tools can increase reliability, this approach typically results in over-reliance on tools, diminishing the model's ability to solve simple problems through basic reasoning. In contrast, human experts first assess problem complexity using domain knowledge before choosing an appropriate solution approach. Inspired by this human problem-solving process, we propose a novel two-component fine-tuning method. In the first component World Knowledge Distillation (WKD), LLMs learn directly from solutions generated using tool's information to internalize domain knowledge. In the second component Tool Usage Adaptation (TUA), we partition problems into easy and hard categories based on the model's direct answering accuracy. While maintaining the same alignment target for easy problems as in WKD, we train the model to intelligently switch to tool usage for more challenging problems. We validate our method on six scientific benchmark datasets, spanning mathematics, climate science and epidemiology. On average, our models demonstrate a 28.18% improvement in answer accuracy and a 13.89% increase in tool usage precision across all datasets, surpassing state-of-the-art models including GPT-4o and Claude-3.5.

  • 6 authors
·
Nov 1, 2024 3

CySecBERT: A Domain-Adapted Language Model for the Cybersecurity Domain

The field of cybersecurity is evolving fast. Experts need to be informed about past, current and - in the best case - upcoming threats, because attacks are becoming more advanced, targets bigger and systems more complex. As this cannot be addressed manually, cybersecurity experts need to rely on machine learning techniques. In the texutual domain, pre-trained language models like BERT have shown to be helpful, by providing a good baseline for further fine-tuning. However, due to the domain-knowledge and many technical terms in cybersecurity general language models might miss the gist of textual information, hence doing more harm than good. For this reason, we create a high-quality dataset and present a language model specifically tailored to the cybersecurity domain, which can serve as a basic building block for cybersecurity systems that deal with natural language. The model is compared with other models based on 15 different domain-dependent extrinsic and intrinsic tasks as well as general tasks from the SuperGLUE benchmark. On the one hand, the results of the intrinsic tasks show that our model improves the internal representation space of words compared to the other models. On the other hand, the extrinsic, domain-dependent tasks, consisting of sequence tagging and classification, show that the model is best in specific application scenarios, in contrast to the others. Furthermore, we show that our approach against catastrophic forgetting works, as the model is able to retrieve the previously trained domain-independent knowledge. The used dataset and trained model are made publicly available

  • 4 authors
·
Dec 6, 2022

PromptAgent: Strategic Planning with Language Models Enables Expert-level Prompt Optimization

Highly effective, task-specific prompts are often heavily engineered by experts to integrate detailed instructions and domain insights based on a deep understanding of both instincts of large language models (LLMs) and the intricacies of the target task. However, automating the generation of such expert-level prompts remains elusive. Existing prompt optimization methods tend to overlook the depth of domain knowledge and struggle to efficiently explore the vast space of expert-level prompts. Addressing this, we present PromptAgent, an optimization method that autonomously crafts prompts equivalent in quality to those handcrafted by experts. At its core, PromptAgent views prompt optimization as a strategic planning problem and employs a principled planning algorithm, rooted in Monte Carlo tree search, to strategically navigate the expert-level prompt space. Inspired by human-like trial-and-error exploration, PromptAgent induces precise expert-level insights and in-depth instructions by reflecting on model errors and generating constructive error feedback. Such a novel framework allows the agent to iteratively examine intermediate prompts (states), refine them based on error feedbacks (actions), simulate future rewards, and search for high-reward paths leading to expert prompts. We apply PromptAgent to 12 tasks spanning three practical domains: BIG-Bench Hard (BBH), as well as domain-specific and general NLP tasks, showing it significantly outperforms strong Chain-of-Thought and recent prompt optimization baselines. Extensive analyses emphasize its capability to craft expert-level, detailed, and domain-insightful prompts with great efficiency and generalizability.

  • 9 authors
·
Oct 25, 2023

X-Reasoner: Towards Generalizable Reasoning Across Modalities and Domains

Recent proprietary models (e.g., o3) have begun to demonstrate strong multimodal reasoning capabilities. Yet, most existing open-source research concentrates on training text-only reasoning models, with evaluations limited to mainly mathematical and general-domain tasks. Therefore, it remains unclear how to effectively extend reasoning capabilities beyond text input and general domains. This paper explores a fundamental research question: Is reasoning generalizable across modalities and domains? Our findings support an affirmative answer: General-domain text-based post-training can enable such strong generalizable reasoning. Leveraging this finding, we introduce X-Reasoner, a vision-language model post-trained solely on general-domain text for generalizable reasoning, using a two-stage approach: an initial supervised fine-tuning phase with distilled long chain-of-thoughts, followed by reinforcement learning with verifiable rewards. Experiments show that X-Reasoner successfully transfers reasoning capabilities to both multimodal and out-of-domain settings, outperforming existing state-of-the-art models trained with in-domain and multimodal data across various general and medical benchmarks (Figure 1). Additionally, we find that X-Reasoner's performance in specialized domains can be further enhanced through continued training on domain-specific text-only data. Building upon this, we introduce X-Reasoner-Med, a medical-specialized variant that achieves new state of the art on numerous text-only and multimodal medical benchmarks.