new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Aug 14

CoCo: Code as CoT for Text-to-Image Preview and Rare Concept Generation

Recent advancements in Unified Multimodal Models (UMMs) have significantly advanced text-to-image (T2I) generation, particularly through the integration of Chain-of-Thought (CoT) reasoning. However, existing CoT-based T2I methods largely rely on abstract natural-language planning, which lacks the precision required for complex spatial layouts, structured visual elements, and dense textual content. In this work, we propose CoCo (Code-as-CoT), a code-driven reasoning framework that represents the reasoning process as executable code, enabling explicit and verifiable intermediate planning for image generation. Given a text prompt, CoCo first generates executable code that specifies the structural layout of the scene, which is then executed in a sandboxed environment to render a deterministic draft image. The model subsequently refines this draft through fine-grained image editing to produce the final high-fidelity result. To support this training paradigm, we construct CoCo-10K, a curated dataset containing structured draft-final image pairs designed to teach both structured draft construction and corrective visual refinement. Empirical evaluations on StructT2IBench, OneIG-Bench, and LongText-Bench show that CoCo achieves improvements of +68.83%, +54.8%, and +41.23% over direct generation, while also outperforming other generation methods empowered by CoT. These results demonstrate that executable code is an effective and reliable reasoning paradigm for precise, controllable, and structured text-to-image generation. The code is available at: https://github.com/micky-li-hd/CoCo

  • 13 authors
·
Mar 9 2

DraCo: Draft as CoT for Text-to-Image Preview and Rare Concept Generation

Recent unified multimodal large language models (MLLMs) have shown impressive capabilities, incorporating chain-of-thought (CoT) reasoning for enhanced text-to-image generation. However, existing approaches remain limited, either treating the model merely as a standalone generator or relying on abstract textual planning. To this end, we propose Draft-as-CoT (DraCo), a novel interleaved reasoning paradigm that fully leverages both textual and visual contents in CoT for better planning and verification. Our method first generates a low-resolution draft image as preview, providing more concrete and structural visual planning and guidance. Then, we employ the model's inherent understanding capability to verify potential semantic misalignments between the draft and input prompt, and performs refinement through selective corrections with super-resolution. In this way, our approach addresses two fundamental challenges: the coarse-grained nature of textual planning and the difficulty in generating rare attribute combinations. To support training, we curate DraCo-240K, aiming to enhance three atomic capabilities spanning general correction, instance manipulation, and layout reorganization. Supported by DraCo-CFG, a specialized classifier-free guidance (CFG) strategy for interleaved reasoning, DraCo achieves a tremendous increase on GenEval (+8%), Imagine-Bench (+0.91), and GenEval++ (+3%), significantly outperforming direct generation and other generation methods empowered by CoT.

  • 12 authors
·
Dec 4, 2025 2

Semantic Anchoring for Robust Personalization in Text-to-Image Diffusion Models

Text-to-image diffusion models have achieved remarkable progress in generating diverse and realistic images from textual descriptions. However, they still struggle with personalization, which requires adapting a pretrained model to depict user-specific subjects from only a few reference images. The key challenge lies in learning a new visual concept from a limited number of reference images while preserving the pretrained semantic prior that maintains text-image alignment. When the model focuses on subject fidelity, it tends to overfit the limited reference images and fails to leverage the pretrained distribution. Conversely, emphasizing prior preservation maintains semantic consistency but prevents the model from learning new personalized attributes. Building on these observations, we propose the personalization process through a semantic anchoring that guides adaptation by grounding new concepts in their corresponding distributions. We therefore reformulate personalization as the process of learning a rare concept guided by its frequent counterpart through semantic anchoring. This anchoring encourages the model to adapt new concepts in a stable and controlled manner, expanding the pretrained distribution toward personalized regions while preserving its semantic structure. As a result, the proposed method achieves stable adaptation and consistent improvements in both subject fidelity and text-image alignment compared to baseline methods. Extensive experiments and ablation studies further demonstrate the robustness and effectiveness of the proposed anchoring strategy.

  • 3 authors
·
Nov 26, 2025

MultiBanana: A Challenging Benchmark for Multi-Reference Text-to-Image Generation

Recent text-to-image generation models have acquired the ability of multi-reference generation and editing; the ability to inherit the appearance of subjects from multiple reference images and re-render them under new contexts. However, the existing benchmark datasets often focus on the generation with single or a few reference images, which prevents us from measuring the progress on how model performance advances or pointing out their weaknesses, under different multi-reference conditions. In addition, their task definitions are still vague, typically limited to axes such as "what to edit" or "how many references are given", and therefore fail to capture the intrinsic difficulty of multi-reference settings. To address this gap, we introduce MultiBanana, which is carefully designed to assesses the edge of model capabilities by widely covering multi-reference-specific problems at scale: (1) varying the number of references, (2) domain mismatch among references (e.g., photo vs. anime), (3) scale mismatch between reference and target scenes, (4) references containing rare concepts (e.g., a red banana), and (5) multilingual textual references for rendering. Our analysis among a variety of text-to-image models reveals their superior performances, typical failure modes, and areas for improvement. MultiBanana will be released as an open benchmark to push the boundaries and establish a standardized basis for fair comparison in multi-reference image generation. Our data and code are available at https://github.com/matsuolab/multibanana .

  • 7 authors
·
Nov 28, 2025 2

The Neglected Tails of Vision-Language Models

Vision-language models (VLMs) excel in zero-shot recognition but their performance varies greatly across different visual concepts. For example, although CLIP achieves impressive accuracy on ImageNet (60-80%), its performance drops below 10% for more than ten concepts like night snake, presumably due to their limited presence in the pretraining data. However, measuring the frequency of concepts in VLMs' large-scale datasets is challenging. We address this by using large language models (LLMs) to count the number of pretraining texts that contain synonyms of these concepts. Our analysis confirms that popular datasets, such as LAION, exhibit a long-tailed concept distribution, yielding biased performance in VLMs. We also find that downstream applications of VLMs, including visual chatbots (e.g., GPT-4V) and text-to-image models (e.g., Stable Diffusion), often fail to recognize or generate images of rare concepts identified by our method. To mitigate the imbalanced performance of zero-shot VLMs, we propose REtrieval-Augmented Learning (REAL). First, instead of prompting VLMs using the original class names, REAL uses their most frequent synonyms found in pretraining texts. This simple change already outperforms costly human-engineered and LLM-enriched prompts over nine benchmark datasets. Second, REAL trains a linear classifier on a small yet balanced set of pretraining data retrieved using concept synonyms. REAL surpasses the previous zero-shot SOTA, using 400x less storage and 10,000x less training time!

  • 8 authors
·
Jan 22, 2024

OmniVTG: A Large-Scale Dataset and Training Paradigm for Open-World Video Temporal Grounding

Video Temporal Grounding (VTG), the task of localizing video segments from text queries, struggles in open-world settings due to limited dataset scale and semantic diversity, causing performance gaps between common and rare concepts. To overcome these limitations, we introduce OmniVTG, a new large-scale dataset for open-world VTG, coupled with a Self-Correction Chain-of-Thought (CoT) training paradigm designed to enhance the grounding capabilities of Multimodal Large Language Models (MLLMs). Our OmniVTG is constructed via a novel Semantic Coverage Iterative Expansion pipeline, which first identifies gaps in the vocabulary of existing datasets and collects videos that are highly likely to contain these target concepts. For high-quality annotation, we leverage the insight that modern MLLMs excel at dense captioning more than direct grounding and design a caption-centric data engine to prompt MLLMs to generate dense, timestamped descriptions. Beyond the dataset, we observe that simple supervised finetuning (SFT) is insufficient, as a performance gap between rare and common concepts still persists. We find that MLLMs' video understanding ability significantly surpasses their direct grounding ability. Based on this, we propose a Self-Correction Chain-of-Thought (CoT) training paradigm. We train the MLLM to first predict, then use its understanding capabilities to reflect on and refine its own predictions. This capability is instilled via a three-stage pipeline of SFT, CoT finetuning, and reinforcement learning. Extensive experiments show our approach not only excels at open-world grounding in our OmniVTG dataset but also achieves state-of-the-art zero-shot performance on four existing VTG benchmarks. Code is available at https://github.com/oceanflowlab/OmniVTG.

  • 5 authors
·
Apr 27

AnyGroundBench: A Specialized-Domain Benchmark for Video Grounding in Vision-Language Models

Vision-Language Models (VLMs) have demonstrated immense promise in Spatio-Temporal Video Grounding (STVG). However, current evaluation protocols are largely confined to zero-shot assessments on general, daily-life benchmarks. This creates a critical disconnect from real-world applications in specialized fields, where models inevitably encounter rare visual concepts and complex spatio-temporal dynamics. Since exhaustive pre-training across infinite data distributions is infeasible, the ability to adapt to novel domains is essential. To bridge this gap, we introduce AnyGroundBench, a domain-adaptation benchmark designed to shift the STVG evaluation paradigm from static zero-shot testing to rigorous domain adaptation. Targeting five specialized domains (animal, industry, sports, surgery, and public security), AnyGroundBench pairs newly captured videos such as expert-annotated mouse behaviors with established datasets, unifying them through dense, high-fidelity spatio-temporal annotations. Crucially, the benchmark provides dedicated training subsets to systematically measure domain adaptability. We extensively evaluate 15 state-of-the-art VLMs, assessing their zero-shot generalization and In-Context Learning (ICL) capabilities under practical computational constraints. Ultimately, our findings reveal that current models fail in both zero-shot and ICL-based adaptation when confronted with specialized domains, exposing critical flaws in spatio-temporal reasoning that future research must address.

  • 9 authors
·
Jul 1 2

MoKus: Leveraging Cross-Modal Knowledge Transfer for Knowledge-Aware Concept Customization

Concept customization typically binds rare tokens to a target concept. Unfortunately, these approaches often suffer from unstable performance as the pretraining data seldom contains these rare tokens. Meanwhile, these rare tokens fail to convey the inherent knowledge of the target concept. Consequently, we introduce Knowledge-aware Concept Customization, a novel task aiming at binding diverse textual knowledge to target visual concepts. This task requires the model to identify the knowledge within the text prompt to perform high-fidelity customized generation. Meanwhile, the model should efficiently bind all the textual knowledge to the target concept. Therefore, we propose MoKus, a novel framework for knowledge-aware concept customization. Our framework relies on a key observation: cross-modal knowledge transfer, where modifying knowledge within the text modality naturally transfers to the visual modality during generation. Inspired by this observation, MoKus contains two stages: (1) In visual concept learning, we first learn the anchor representation to store the visual information of the target concept. (2) In textual knowledge updating, we update the answer for the knowledge queries to the anchor representation, enabling high-fidelity customized generation. To further comprehensively evaluate our proposed MoKus on the new task, we introduce the first benchmark for knowledge-aware concept customization: KnowCusBench. Extensive evaluations have demonstrated that MoKus outperforms state-of-the-art methods. Moreover, the cross-model knowledge transfer allows MoKus to be easily extended to other knowledge-aware applications like virtual concept creation and concept erasure. We also demonstrate the capability of our method to achieve improvements on world knowledge benchmarks.

  • 4 authors
·
Mar 13 3

Sparse Autoencoders Encode Both Concepts and Functions: The Downstream Geometry of Feature Effects

The wide-scale use of sparse autoencoders (SAEs) as interpretability tools is limited by inconsistent links between SAE features and model behavior. Features with clear activation descriptions may have weak or unexpected causal effects; steering can vary across prompts or oppose the intended direction; and activation-based feature selection can miss features that produce the desired output change. Prior work has studied feature geometry inside the model, where features are computed. We instead study the geometry of changes in model logits caused by feature interventions. We introduce Feature-Effect Geometry Analysis (FEGA), an unsupervised framework that removes the same active SAE feature across contexts and analyzes the resulting cloud of logit changes. Across SAE variants, consistent one-dimensional effects are rare: few features behave like reusable directions. To interpret this variation, we distinguish value-like features, tied to static information such as factual attributes, from pointer-like features, associated with context-dependent operations. Value-like features more often exhibit structured, low-dimensional effects, although these effects typically span several directions. Pointer-like features, by contrast, predominantly exhibit diffuse effects. Our results show that a feature can be interpretable and causally relevant without providing a stable direction for steering.

  • 5 authors
·
Jul 26

Ontology-Based Concept Distillation for Radiology Report Retrieval and Labeling

Retrieval-augmented learning based on radiology reports has emerged as a promising direction to improve performance on long-tail medical imaging tasks, such as rare disease detection in chest X-rays. Most existing methods rely on comparing high-dimensional text embeddings from models like CLIP or CXR-BERT, which are often difficult to interpret, computationally expensive, and not well-aligned with the structured nature of medical knowledge. We propose a novel, ontology-driven alternative for comparing radiology report texts based on clinically grounded concepts from the Unified Medical Language System (UMLS). Our method extracts standardised medical entities from free-text reports using an enhanced pipeline built on RadGraph-XL and SapBERT. These entities are linked to UMLS concepts (CUIs), enabling a transparent, interpretable set-based representation of each report. We then define a task-adaptive similarity measure based on a modified and weighted version of the Tversky Index that accounts for synonymy, negation, and hierarchical relationships between medical entities. This allows efficient and semantically meaningful similarity comparisons between reports. We demonstrate that our approach outperforms state-of-the-art embedding-based retrieval methods in a radiograph classification task on MIMIC-CXR, particularly in long-tail settings. Additionally, we use our pipeline to generate ontology-backed disease labels for MIMIC-CXR, offering a valuable new resource for downstream learning tasks. Our work provides more explainable, reliable, and task-specific retrieval strategies in clinical AI systems, especially when interpretability and domain knowledge integration are essential. Our code is available at https://github.com/Felix-012/ontology-concept-distillation

  • 3 authors
·
Aug 27, 2025

PET-DINO: Unifying Visual Cues into Grounding DINO with Prompt-Enriched Training

Open-Set Object Detection (OSOD) enables recognition of novel categories beyond fixed classes but faces challenges in aligning text representations with complex visual concepts and the scarcity of image-text pairs for rare categories. This results in suboptimal performance in specialized domains or with complex objects. Recent visual-prompted methods partially address these issues but often involve complex multi-modal designs and multi-stage optimizations, prolonging the development cycle. Additionally, effective training strategies for data-driven OSOD models remain largely unexplored. To address these challenges, we propose PET-DINO, a universal detector supporting both text and visual prompts. Our Alignment-Friendly Visual Prompt Generation (AFVPG) module builds upon an advanced text-prompted detector, addressing the limitations of text representation guidance and reducing the development cycle. We introduce two prompt-enriched training strategies: Intra-Batch Parallel Prompting (IBP) at the iteration level and Dynamic Memory-Driven Prompting (DMD) at the overall training level. These strategies enable simultaneous modeling of multiple prompt routes, facilitating parallel alignment with diverse real-world usage scenarios. Comprehensive experiments demonstrate that PET-DINO exhibits competitive zero-shot object detection capabilities across various prompt-based detection protocols. These strengths can be attributed to inheritance-based philosophy and prompt-enriched training strategies, which play a critical role in building an effective generic object detector. Project page: https://fuweifuvtoo.github.io/pet-dino.

  • 9 authors
·
Apr 6

TARA: Token-Aware LoRA for Composable Personalization in Diffusion Models

Personalized text-to-image generation aims to synthesize novel images of a specific subject or style using only a few reference images. Recent methods based on Low-Rank Adaptation (LoRA) enable efficient single-concept customization by injecting lightweight, concept-specific adapters into pre-trained diffusion models. However, combining multiple LoRA modules for multi-concept generation often leads to identity missing and visual feature leakage. In this work, we identify two key issues behind these failures: (1) token-wise interference among different LoRA modules, and (2) spatial misalignment between the attention map of a rare token and its corresponding concept-specific region. To address these issues, we propose Token-Aware LoRA (TARA), which introduces a token mask to explicitly constrain each module to focus on its associated rare token to avoid interference, and a training objective that encourages the spatial attention of a rare token to align with its concept region. Our method enables training-free multi-concept composition by directly injecting multiple independently trained TARA modules at inference time. Experimental results demonstrate that TARA enables efficient multi-concept inference and effectively preserving the visual identity of each concept by avoiding mutual interference between LoRA modules. The code and models are available at https://github.com/YuqiPeng77/TARA.

  • 7 authors
·
Aug 12, 2025

IDEAgent: Agentic Quality-Diversity Search for Research Idea Generation

Large Language Models (LLMs) have significantly automated the process of scientific discovery over the past few years. However, existing systems share one core limitation: they generate and optimize ideas independently for either Quality or Diversity. This often leads to the generation of ideas in close proximity to one another or to a large set of trivial, unsound, or unclear concepts. In this work, we instead argue that research ideation should be treated as a conjunction of both objectives and framed as a Quality-Diversity (QD) search. In line with this perspective, we introduce IDEAgent, a multi-agent framework that manages the evolution of ideas through lineages. We jointly drive Quality using multi-objective feedback for dedicated repair and refinement, while Diversity is achieved through lightweight sequential memory and explicit comparison against completed ideas, their historical ancestors, and rejected proposals. To systematically evaluate this QD conjunction, we develop Yield, a joint metric that computes the largest set of mutually diverse ideas that satisfy a predetermined quality threshold. Finally, through evaluations across 32 topics spanning 8 domains of Computer Science, we show that IDEAgent outperforms the best baseline by 3.89x on Yield, while achieving non-zero Yield on 8x more topics. We further corroborate these findings through an analysis of quality improvements, showing that repair and refinement are crucial for building logical rigor and clarity while preserving non-obviousness. To encourage future research on QD-search-based ideation, we open-source IDEAgent at https://github.com/declare-lab/IDEAgent.

RareBench: Can LLMs Serve as Rare Diseases Specialists?

Generalist Large Language Models (LLMs), such as GPT-4, have shown considerable promise in various domains, including medical diagnosis. Rare diseases, affecting approximately 300 million people worldwide, often have unsatisfactory clinical diagnosis rates primarily due to a lack of experienced physicians and the complexity of differentiating among many rare diseases. In this context, recent news such as "ChatGPT correctly diagnosed a 4-year-old's rare disease after 17 doctors failed" underscore LLMs' potential, yet underexplored, role in clinically diagnosing rare diseases. To bridge this research gap, we introduce RareBench, a pioneering benchmark designed to systematically evaluate the capabilities of LLMs on 4 critical dimensions within the realm of rare diseases. Meanwhile, we have compiled the largest open-source dataset on rare disease patients, establishing a benchmark for future studies in this domain. To facilitate differential diagnosis of rare diseases, we develop a dynamic few-shot prompt methodology, leveraging a comprehensive rare disease knowledge graph synthesized from multiple knowledge bases, significantly enhancing LLMs' diagnostic performance. Moreover, we present an exhaustive comparative study of GPT-4's diagnostic capabilities against those of specialist physicians. Our experimental findings underscore the promising potential of integrating LLMs into the clinical diagnostic process for rare diseases. This paves the way for exciting possibilities in future advancements in this field.

  • 6 authors
·
Feb 9, 2024

Rare Disease Differential Diagnosis with Large Language Models at Scale: From Abdominal Actinomycosis to Wilson's Disease

Large language models (LLMs) have demonstrated impressive capabilities in disease diagnosis. However, their effectiveness in identifying rarer diseases, which are inherently more challenging to diagnose, remains an open question. Rare disease performance is critical with the increasing use of LLMs in healthcare settings. This is especially true if a primary care physician needs to make a rarer prognosis from only a patient conversation so that they can take the appropriate next step. To that end, several clinical decision support systems are designed to support providers in rare disease identification. Yet their utility is limited due to their lack of knowledge of common disorders and difficulty of use. In this paper, we propose RareScale to combine the knowledge LLMs with expert systems. We use jointly use an expert system and LLM to simulate rare disease chats. This data is used to train a rare disease candidate predictor model. Candidates from this smaller model are then used as additional inputs to black-box LLM to make the final differential diagnosis. Thus, RareScale allows for a balance between rare and common diagnoses. We present results on over 575 rare diseases, beginning with Abdominal Actinomycosis and ending with Wilson's Disease. Our approach significantly improves the baseline performance of black-box LLMs by over 17% in Top-5 accuracy. We also find that our candidate generation performance is high (e.g. 88.8% on gpt-4o generated chats).

  • 3 authors
·
Feb 20, 2025 2

RareLens: Towards End-to-End Rare Disease Care via Aligning Divergent Large Language Model Reasoning

Rare diseases collectively affect an estimated 3.5% to 5.9% of the population, yet more than 70% of patients are misdiagnosed and many endure years of evaluation before a diagnosis is reached, because early presentations are nonspecific and relevant expertise is scarce and unevenly distributed. Artificial intelligence could provide support, but existing systems address isolated stages of care, overwhelmingly diagnosis. They typically depend on the results of downstream investigations, and they treat the variability between models as noise to be eliminated. Here we present RareLens, a system that supports clinical decision-making across the entire rare disease trajectory by exploiting this variability. When heterogeneous large language models evaluate the same case, they generate divergent but complementary reasoning, which RareLens aligns and calibrates into a single convergent, actionable decision at each stage. Four coordinated modules perform primary-visit risk screening, diagnosis, treatment planning and prognosis. Developed and evaluated on RareBench, a real-world dataset of 157,525 cases spanning all 33 Orphanet categories and more than 7,000 conditions, RareLens outperformed every frontier model tested, including GPT-5, DeepSeek-R1, Claude-3.7-Sonnet and Gemini-2.5-Pro, at each stage. It achieved an area under the curve of 0.917 for screening and top-1 accuracies of 65.5% and 89.8% for diagnosis and treatment. In an external study spanning 1,287 cases and 23 physicians, autonomous RareLens and physicians assisted by RareLens both substantially outperformed unaided physicians. These findings indicate that aligning divergent model reasoning, rather than scaling a single model, offers a generalizable strategy for high-uncertainty clinical decision-making.

  • 27 authors
·
Jul 24

Heuresis: Search Strategies for Autonomous AI Research Agents Across Quality, Diversity and Novelty

Autonomous AI Research promises to accelerate the scientific progress of machine learning. To realise this goal, current Large Language Model (LLM)-based agents need to go beyond just writing code, to mastering the exploration of simultaneously performant, diverse and novel ideas. To this end, we introduce Heuresis, a framework that abstracts the research pipeline into a set of general and composable primitives, enabling open-ended scientific exploration in machine learning research. We implement six search strategies: a greedy baseline, two archive-based (MAP-Elites, Go-Explore), one evolutionary (Islands), and two divergent (Curiosity, Omni), and evaluate them across three axes (Quality, Diversity, and Novelty) on three domains (LLM Pretraining, On-Policy RL, and Model Unlearning), totalling 3,222 scored runs. We find that completely novel ideas are rare. No idea across our scored runs is rated as "Original", and only a few achieve only "Minor Similarity" to prior work. Moreover, novel ideas never approach the highest-performing known-recipe scores. Across all six strategies and three domains, only one such idea lands in the top-10 by quality. We also observed agents resorting to a variety of reward-hacking techniques during execution (40 confirmed fabrications across 1,628 scored runs), and detecting them was necessary to keep the search faithful to the task. Our results show that while current search and Quality-Diversity strategies enable us to steer where the generated ideas land on the quality, diversity, and novelty axes, they do not expand the quality-novelty frontier. Bridging this gap is the open challenge towards the ultimate goal of perpetual, autonomous scientific progress. Code is available at github.com/a-antoniades/Heuresis.

  • 9 authors
·
Jun 30

RARE: Retrieval-Aware Robustness Evaluation for Retrieval-Augmented Generation Systems

Retrieval-Augmented Generation (RAG) enhances recency and factuality in answers. However, existing evaluations rarely test how well these systems cope with real-world noise, conflicting between internal and external retrieved contexts, or fast-changing facts. We introduce Retrieval-Aware Robustness Evaluation (RARE), a unified framework and large-scale benchmark that jointly stress-tests query and document perturbations over dynamic, time-sensitive corpora. One of the central features of RARE is a knowledge-graph-driven synthesis pipeline (RARE-Get) that automatically extracts single and multi-hop relations from the customized corpus and generates multi-level question sets without manual intervention. Leveraging this pipeline, we construct a dataset (RARE-Set) spanning 400 expert-level time-sensitive finance, economics, and policy documents and 48,322 questions whose distribution evolves as the underlying sources change. To quantify resilience, we formalize retrieval-conditioned robustness metrics (RARE-Met) that capture a model's ability to remain correct or recover when queries, documents, or real-world retrieval results are systematically altered. Our results show that RAG systems exhibit surprising vulnerability to perturbations, with document robustness consistently being the weakest point regardless of generator size or architecture. RAG systems consistently show lower robustness on multi-hop queries than single-hop queries across all domains.

  • 8 authors
·
May 31, 2025 2

An Agentic System for Rare Disease Diagnosis with Traceable Reasoning

Rare diseases collectively affect over 300 million individuals worldwide, yet timely and accurate diagnosis remains a pervasive challenge. This is largely due to their clinical heterogeneity, low individual prevalence, and the limited familiarity most clinicians have with rare conditions. Here, we introduce DeepRare, the first rare disease diagnosis agentic system powered by a large language model (LLM), capable of processing heterogeneous clinical inputs. The system generates ranked diagnostic hypotheses for rare diseases, each accompanied by a transparent chain of reasoning that links intermediate analytic steps to verifiable medical evidence. DeepRare comprises three key components: a central host with a long-term memory module; specialized agent servers responsible for domain-specific analytical tasks integrating over 40 specialized tools and web-scale, up-to-date medical knowledge sources, ensuring access to the most current clinical information. This modular and scalable design enables complex diagnostic reasoning while maintaining traceability and adaptability. We evaluate DeepRare on eight datasets. The system demonstrates exceptional diagnostic performance among 2,919 diseases, achieving 100% accuracy for 1013 diseases. In HPO-based evaluations, DeepRare significantly outperforms other 15 methods, like traditional bioinformatics diagnostic tools, LLMs, and other agentic systems, achieving an average Recall@1 score of 57.18% and surpassing the second-best method (Reasoning LLM) by a substantial margin of 23.79 percentage points. For multi-modal input scenarios, DeepRare achieves 70.60% at Recall@1 compared to Exomiser's 53.20% in 109 cases. Manual verification of reasoning chains by clinical experts achieves 95.40% agreements. Furthermore, the DeepRare system has been implemented as a user-friendly web application http://raredx.cn/doctor.

  • 12 authors
·
Jun 25, 2025 1

Efficient Prediction of Pass@k Scaling in Large Language Models

Assessing the capabilities and risks of frontier AI systems is a critical area of research, and recent work has shown that repeated sampling from models can dramatically increase both. For instance, repeated sampling has been shown to increase their capabilities, such as solving difficult math and coding problems, but it has also been shown to increase their potential for harm, such as being jailbroken. Such results raise a crucial question for both capability and safety forecasting: how can one accurately predict a model's behavior when scaled to a massive number of attempts, given a vastly smaller sampling budget? This question is directly relevant to model providers, who serve hundreds of millions of users daily, and to governmental regulators, who seek to prevent harms. To answer this questions, we make three contributions. First, we find that standard methods for fitting these laws suffer from statistical shortcomings that hinder predictive accuracy, especially in data-limited scenarios. Second, we remedy these shortcomings by introducing a robust estimation framework, which uses a beta-binomial distribution to generate more accurate predictions from limited data. Third, we propose a dynamic sampling strategy that allocates a greater budget to harder problems. Combined, these innovations enable more reliable prediction of rare risks and capabilities at a fraction of the computational cost.

  • 7 authors
·
Oct 5, 2025

Assessing and Enhancing Large Language Models in Rare Disease Question-answering

Despite the impressive capabilities of Large Language Models (LLMs) in general medical domains, questions remain about their performance in diagnosing rare diseases. To answer this question, we aim to assess the diagnostic performance of LLMs in rare diseases, and explore methods to enhance their effectiveness in this area. In this work, we introduce a rare disease question-answering (ReDis-QA) dataset to evaluate the performance of LLMs in diagnosing rare diseases. Specifically, we collected 1360 high-quality question-answer pairs within the ReDis-QA dataset, covering 205 rare diseases. Additionally, we annotated meta-data for each question, facilitating the extraction of subsets specific to any given disease and its property. Based on the ReDis-QA dataset, we benchmarked several open-source LLMs, revealing that diagnosing rare diseases remains a significant challenge for these models. To facilitate retrieval augmentation generation for rare disease diagnosis, we collect the first rare diseases corpus (ReCOP), sourced from the National Organization for Rare Disorders (NORD) database. Specifically, we split the report of each rare disease into multiple chunks, each representing a different property of the disease, including their overview, symptoms, causes, effects, related disorders, diagnosis, and standard therapies. This structure ensures that the information within each chunk aligns consistently with a question. Experiment results demonstrate that ReCOP can effectively improve the accuracy of LLMs on the ReDis-QA dataset by an average of 8%. Moreover, it significantly guides LLMs to generate trustworthy answers and explanations that can be traced back to existing literature.

  • 10 authors
·
Aug 15, 2024

Predicting Rare Events by Shrinking Towards Proportional Odds

Training classifiers is difficult with severe class imbalance, but many rare events are the culmination of a sequence with much more common intermediate outcomes. For example, in online marketing a user first sees an ad, then may click on it, and finally may make a purchase; estimating the probability of purchases is difficult because of their rarity. We show both theoretically and through data experiments that the more abundant data in earlier steps may be leveraged to improve estimation of probabilities of rare events. We present PRESTO, a relaxation of the proportional odds model for ordinal regression. Instead of estimating weights for one separating hyperplane that is shifted by separate intercepts for each of the estimated Bayes decision boundaries between adjacent pairs of categorical responses, we estimate separate weights for each of these transitions. We impose an L1 penalty on the differences between weights for the same feature in adjacent weight vectors in order to shrink towards the proportional odds model. We prove that PRESTO consistently estimates the decision boundary weights under a sparsity assumption. Synthetic and real data experiments show that our method can estimate rare probabilities in this setting better than both logistic regression on the rare category, which fails to borrow strength from more abundant categories, and the proportional odds model, which is too inflexible.

  • 2 authors
·
May 29, 2023

Erasing Concepts from Text-to-Image Diffusion Models with Few-shot Unlearning

Generating images from text has become easier because of the scaling of diffusion models and advancements in the field of vision and language. These models are trained using vast amounts of data from the Internet. Hence, they often contain undesirable content such as copyrighted material. As it is challenging to remove such data and retrain the models, methods for erasing specific concepts from pre-trained models have been investigated. We propose a novel concept-erasure method that updates the text encoder using few-shot unlearning in which a few real images are used. The discussion regarding the generated images after erasing a concept has been lacking. While there are methods for specifying the transition destination for concepts, the validity of the specified concepts is unclear. Our method implicitly achieves this by transitioning to the latent concepts inherent in the model or the images. Our method can erase a concept within 10 s, making concept erasure more accessible than ever before. Implicitly transitioning to related concepts leads to more natural concept erasure. We applied the proposed method to various concepts and confirmed that concept erasure can be achieved tens to hundreds of times faster than with current methods. By varying the parameters to be updated, we obtained results suggesting that, like previous research, knowledge is primarily accumulated in the feed-forward networks of the text encoder. Our code is available at https://github.com/fmp453/few-shot-erasing

  • 2 authors
·
May 12, 2024

Navigating Ideation Space: Decomposed Conceptual Representations for Positioning Scientific Ideas

Scientific discovery is a cumulative process and requires new ideas to be situated within an ever-expanding landscape of existing knowledge. An emerging and critical challenge is how to identify conceptually relevant prior work from rapidly growing literature, and assess how a new idea differentiates from existing research. Current embedding approaches typically conflate distinct conceptual aspects into single representations and cannot support fine-grained literature retrieval; meanwhile, LLM-based evaluators are subject to sycophancy biases, failing to provide discriminative novelty assessment. To tackle these challenges, we introduce the Ideation Space, a structured representation that decomposes scientific knowledge into three distinct dimensions, i.e., research problem, methodology, and core findings, each learned through contrastive training. This framework enables principled measurement of conceptual distance between ideas, and modeling of ideation transitions that capture the logical connections within a proposed idea. Building upon this representation, we propose a Hierarchical Sub-Space Retrieval framework for efficient, targeted literature retrieval, and a Decomposed Novelty Assessment algorithm that identifies which aspects of an idea are novel. Extensive experiments demonstrate substantial improvements, where our approach achieves Recall@30 of 0.329 (16.7% over baselines), our ideation transition retrieval reaches Hit Rate@30 of 0.643, and novelty assessment attains 0.37 correlation with expert judgments. In summary, our work provides a promising paradigm for future research on accelerating and evaluating scientific discovery.

  • 4 authors
·
Jan 13

The Consciousness Prior

A new prior is proposed for learning representations of high-level concepts of the kind we manipulate with language. This prior can be combined with other priors in order to help disentangling abstract factors from each other. It is inspired by cognitive neuroscience theories of consciousness, seen as a bottleneck through which just a few elements, after having been selected by attention from a broader pool, are then broadcast and condition further processing, both in perception and decision-making. The set of recently selected elements one becomes aware of is seen as forming a low-dimensional conscious state. This conscious state is combining the few concepts constituting a conscious thought, i.e., what one is immediately conscious of at a particular moment. We claim that this architectural and information-processing constraint corresponds to assumptions about the joint distribution between high-level concepts. To the extent that these assumptions are generally true (and the form of natural language seems consistent with them), they can form a useful prior for representation learning. A low-dimensional thought or conscious state is analogous to a sentence: it involves only a few variables and yet can make a statement with very high probability of being true. This is consistent with a joint distribution (over high-level concepts) which has the form of a sparse factor graph, i.e., where the dependencies captured by each factor of the factor graph involve only very few variables while creating a strong dip in the overall energy function. The consciousness prior also makes it natural to map conscious states to natural language utterances or to express classical AI knowledge in a form similar to facts and rules, albeit capturing uncertainty as well as efficient search mechanisms implemented by attention mechanisms.

  • 1 authors
·
Sep 25, 2017

Can LLMs Generate Novel Research Ideas? A Large-Scale Human Study with 100+ NLP Researchers

Recent advancements in large language models (LLMs) have sparked optimism about their potential to accelerate scientific discovery, with a growing number of works proposing research agents that autonomously generate and validate new ideas. Despite this, no evaluations have shown that LLM systems can take the very first step of producing novel, expert-level ideas, let alone perform the entire research process. We address this by establishing an experimental design that evaluates research idea generation while controlling for confounders and performs the first head-to-head comparison between expert NLP researchers and an LLM ideation agent. By recruiting over 100 NLP researchers to write novel ideas and blind reviews of both LLM and human ideas, we obtain the first statistically significant conclusion on current LLM capabilities for research ideation: we find LLM-generated ideas are judged as more novel (p < 0.05) than human expert ideas while being judged slightly weaker on feasibility. Studying our agent baselines closely, we identify open problems in building and evaluating research agents, including failures of LLM self-evaluation and their lack of diversity in generation. Finally, we acknowledge that human judgements of novelty can be difficult, even by experts, and propose an end-to-end study design which recruits researchers to execute these ideas into full projects, enabling us to study whether these novelty and feasibility judgements result in meaningful differences in research outcome.

  • 3 authors
·
Sep 6, 2024 3

Treasure Hunt: Real-time Targeting of the Long Tail using Training-Time Markers

One of the most profound challenges of modern machine learning is performing well on the long-tail of rare and underrepresented features. Large general-purpose models are trained for many tasks, but work best on high-frequency use cases. After training, it is hard to adapt a model to perform well on specific use cases underrepresented in the training corpus. Relying on prompt engineering or few-shot examples to maximize the output quality on a particular test case can be frustrating, as models can be highly sensitive to small changes, react in unpredicted ways or rely on a fixed system prompt for maintaining performance. In this work, we ask: "Can we optimize our training protocols to both improve controllability and performance on underrepresented use cases at inference time?" We revisit the divide between training and inference techniques to improve long-tail performance while providing users with a set of control levers the model is trained to be responsive to. We create a detailed taxonomy of data characteristics and task provenance to explicitly control generation attributes and implicitly condition generations at inference time. We fine-tune a base model to infer these markers automatically, which makes them optional at inference time. This principled and flexible approach yields pronounced improvements in performance, especially on examples from the long tail of the training distribution. While we observe an average lift of 5.7% win rates in open-ended generation quality with our markers, we see over 9.1% gains in underrepresented domains. We also observe relative lifts of up to 14.1% on underrepresented tasks like CodeRepair and absolute improvements of 35.3% on length instruction following evaluations.

  • 5 authors
·
Jun 17, 2025 4

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

Flow of Reasoning: Efficient Training of LLM Policy with Divergent Thinking

Divergent thinking, the cognitive process of generating diverse solutions, is a hallmark of human creativity and problem-solving. For machines, sampling diverse solution trajectories in complex reasoning problems is crucial for robust outcomes, data augmentation, and enhanced model generalization. Large language models (LLMs) often struggle with generating high-quality, diverse reasoning. While supervised fine-tuning helps with quality, it requires extensive supervision data to capture the full diversity of solutions. Alternatively, reinforcement learning methods like PPO aim to find limited highest-reward solutions while neglecting the solution diversity, akin to convergent thinking. To address these limitations, we propose Flow of Reasoning (FoR) -- an efficient LLM training approach enabling diverse reasoning with minimal data. FoR formulates multi-step LLM reasoning as a Markovian flow from an initial state to terminal states. The formulation allows to adapt principled GFlowNet approaches to train the LLM as a policy, which is able to sample multiple reasoning paths with probabilities proportional to the unnormalized reward. Empirical results show that, with limited training data (e.g., 15 examples), FoR can discover diverse high-quality solutions that excel greatly beyond current state-of-the-art methods across three tasks, including embodied reasoning (BlocksWorld), math puzzle solving (Game24), and logical reasoning (PrOntoQA). Code is available at https://github.com/Yu-Fangxu/FoR.

  • 5 authors
·
Jun 9, 2024

Boosting EfficientNets Ensemble Performance via Pseudo-Labels and Synthetic Images by pix2pixHD for Infection and Ischaemia Classification in Diabetic Foot Ulcers

Diabetic foot ulcers are a common manifestation of lesions on the diabetic foot, a syndrome acquired as a long-term complication of diabetes mellitus. Accompanying neuropathy and vascular damage promote acquisition of pressure injuries and tissue death due to ischaemia. Affected areas are prone to infections, hindering the healing progress. The research at hand investigates an approach on classification of infection and ischaemia, conducted as part of the Diabetic Foot Ulcer Challenge (DFUC) 2021. Different models of the EfficientNet family are utilized in ensembles. An extension strategy for the training data is applied, involving pseudo-labeling for unlabeled images, and extensive generation of synthetic images via pix2pixHD to cope with severe class imbalances. The resulting extended training dataset features 8.68 times the size of the baseline and shows a real to synthetic image ratio of 1:3. Performances of models and ensembles trained on the baseline and extended training dataset are compared. Synthetic images featured a broad qualitative variety. Results show that models trained on the extended training dataset as well as their ensemble benefit from the large extension. F1-Scores for rare classes receive outstanding boosts, while those for common classes are either not harmed or boosted moderately. A critical discussion concretizes benefits and identifies limitations, suggesting improvements. The work concludes that classification performance of individual models as well as that of ensembles can be boosted utilizing synthetic images. Especially performance for rare classes benefits notably.

  • 3 authors
·
Nov 30, 2021

Improving large language models with concept-aware fine-tuning

Large language models (LLMs) have become the cornerstone of modern AI. However, the existing paradigm of next-token prediction fundamentally limits their ability to form coherent, high-level concepts, making it a critical barrier to human-like understanding and reasoning. Take the phrase "ribonucleic acid" as an example: an LLM will first decompose it into tokens, i.e., artificial text fragments ("rib", "on", ...), then learn each token sequentially, rather than grasping the phrase as a unified, coherent semantic entity. This fragmented representation hinders deeper conceptual understanding and, ultimately, the development of truly intelligent systems. In response, we introduce Concept-Aware Fine-Tuning (CAFT), a novel multi-token training method that redefines how LLMs are fine-tuned. By enabling the learning of sequences that span multiple tokens, this method fosters stronger concept-aware learning. Our experiments demonstrate significant improvements compared to conventional next-token finetuning methods across diverse tasks, including traditional applications like text summarization and domain-specific ones like de novo protein design. Multi-token prediction was previously only possible in the prohibitively expensive pretraining phase; CAFT, to our knowledge, is the first to bring the multi-token setting to the post-training phase, thus effectively democratizing its benefits for the broader community of practitioners and researchers. Finally, the unexpected effectiveness of our proposed method suggests wider implications for the machine learning research community. All code and data are available at https://github.com/michaelchen-lab/caft-llm

  • 4 authors
·
Jun 9, 2025 2

Calibrated Surprise: An Information-Theoretic Account of Creative Quality

In the era of large language models, creative writing quality lacks a computable theoretical anchor. The dominant approaches are rubric scoring -- decomposing holistic aesthetic judgment into sub-scores -- and RLHF preference signals -- replacing quality with group votes. Both bypass the statistical structure of the text itself. This paper provides an information-theoretic foundation to fill this gap. We propose 'calibrated surprise' as the information-theoretic essence of excellent creative writing. This judgment matches reading intuition and covers its opposite. This literary judgment admits a precise mathematical formulation. Under full-dimensional constraints Y, feasible writing choices are forced into an extremely narrow space. The rare survivors are, from the unconstrained perspective, exactly the least predictable choices. Both are measured precisely by Shannon mutual information I(X;Y) = H(X) - H(X|Y) -- 'calibrated' corresponds to H(X|Y) approaching 0; 'surprising' corresponds to H(X) going high. The subtraction structure of the formula naturally separates 'well-grounded surprise' from 'pure noise'. We use token-level logprobs from Qwen1.5-7B as an operational proxy for the ideal reader's probability distribution. Across 20 pairs (12 Chinese / 8 English) of high-quality vs. systematically degraded literary passages, 20/20 pairs support the core prediction: high-quality passages have systematically higher I(X;Y) than their degraded versions.

  • 2 authors
·
Jun 3