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Aug 24

Surgical Refusal Ablation: Disentangling Safety from Intelligence via Concept-Guided Spectral Cleaning

Safety-aligned language models systematically refuse harmful requests. While activation steering can modulate refusal, ablating the raw "refusal vector" calculated from contrastive harmful and harmless prompts often causes collateral damage and distribution drift. We argue this degradation occurs because the raw vector is polysemantic, entangling the refusal signal with core capability circuits and linguistic style. We introduce Surgical Refusal Ablation (SRA) to distill these steering directions. SRA constructs a registry of independent Concept Atoms representing protected capabilities and stylistic confounds, then uses ridge-regularized spectral residualization to orthogonalize the refusal vector against these directions. This yields a clean refusal direction that targets refusal-relevant structure while minimizing disruption to the model's semantic geometry. Across five models (Qwen3-VL and Ministral series), SRA achieves deep refusal reduction (0-2%) with negligible perplexity impact on Wikitext-2 (mean delta PPL approx. 0.02) and minimal distribution drift. Notably, standard ablation on Qwen3-VL-4B induces severe drift (first-token KL = 2.088), whereas SRA maintains the original distribution (KL = 0.044) while achieving the same 0% refusal rate. Using teacher-forced perplexity on GSM8K and MBPP as a high-resolution capability proxy, we show SRA preserves math and code distributions. These results suggest that common "model damage" is often "Ghost Noise," defined as the spectral bleeding of the dirty refusal direction into capability subspaces.

  • 1 authors
·
Jan 12

Do Sparse Autoencoders Capture Concept Manifolds?

Sparse autoencoders (SAEs) are widely used to extract interpretable features from neural network representations, often under the implicit assumption that concepts correspond to independent linear directions. However, a growing body of evidence suggests that many concepts are instead organized along low-dimensional manifolds encoding continuous geometric relationships. This raises three basic questions: what does it mean for an SAE to capture a manifold, when do existing SAE architectures do so, and how? We develop a theoretical framework that answers these questions and show that SAEs can capture manifolds in two fundamentally different ways: globally, by allocating a compact group of atoms whose linear span contains the entire manifold, or locally, by distributing it across features that each selectively tile a restricted region of the underlying geometry. Empirically, we find that SAEs suboptimally recover continuous structures, mixing the global subspace and local tiling solutions in a fragmented regime we call dilution. This explains why manifold structure is rarely visible at the level of individual concepts and motivates post-hoc unsupervised discovery methods that search for coherent groups of atoms rather than isolated directions. More broadly, our results suggest that future representation learning methods should treat geometric objects, not just individual directions, as the basic units of interpretability.

  • 12 authors
·
Apr 29

Feature Lottery? A Bifurcation Theory of Concept Emergence

Neural networks acquire structured representations at specific moments during training, yet identifying these transitions typically relies on retrospective, label-dependent metrics. We introduce a bifurcation theory of representation dynamics to detect these moments in real time. Analyzing a passive GMM probe attached to the evolving encoder, we show the onset of structure corresponds to a supercritical pitchfork bifurcation driven by the loss Hessian. The system exhibits a theoretically predictable zero-crossing (β_c) that, compared to the network's current state (β), yields a dynamic ratio β(t)/β_c(t): a universal, label-free phase coordinate for representation dynamics, computable entirely from hidden states. We empirically validate four distinct transition regimes predicted by this coordinate across diverse settings: SAEs on language models (Pythia), SSL (CIFAR), and grokking (modular arithmetic). Crucially, under finite dissipation, macroscopic symmetry-breaking can lag the initial zero-crossing by orders of magnitude, which providing a rigorous dynamical account of the delayed escape observed in grokking. Microscopically, the bifurcation creates a shared unstable subspace, forcing collective symmetry breaking. We term this the "feature lottery" in SAE training: a feature's terminal interpretability becomes predictable remarkably early. By only 5% of training, early atom purity robustly predicts final convergence purity, with top-decile early atoms achieving over 12x the baseline purity at convergence. Beyond explaining concept emergence, β/β_c provides a practical early-warning indicator for training health, detecting the onset of usable structure, the crystallization of feature identity, and representational collapse epochs before downstream metrics react.

  • 1 authors
·
May 21

Atom-Searcher: Enhancing Agentic Deep Research via Fine-Grained Atomic Thought Reward

Large language models (LLMs) exhibit remarkable problem-solving abilities, but struggle with complex tasks due to static internal knowledge. Retrieval-Augmented Generation (RAG) enhances access to external information, yet remains limited in multi-hop reasoning and strategic search due to rigid workflows. Recent advancements in agentic deep research empower LLMs to autonomously reason, search, and synthesize information. However, current approaches relying on outcome-based reinforcement learning (RL) face critical issues such as conflicting gradients and reward sparsity, limiting performance gains and training efficiency. To address these, we first propose Atomic Thought, a novel LLM thinking paradigm that decomposes reasoning into fine-grained functional units. These units are supervised by Reasoning Reward Models (RRMs), which provide Atomic Thought Rewards (ATR) for fine-grained guidance. Building on this, we propose Atom-Searcher, a novel RL framework for agentic deep research that integrates Atomic Thought and ATR. Atom-Searcher uses a curriculum-inspired reward schedule, prioritizing process-level ATR early and transitioning to outcome rewards, accelerating convergence on effective reasoning paths. Experiments on seven benchmarks show consistent improvements over the state-of-the-art. Key advantages include: (1) Atom-Searcher scales computation at test-time. (2) Atomic Thought provides supervision anchors for RRMs, bridging deep research tasks and RRMs. (3) Atom-Searcher exhibits more interpretable, human-like reasoning patterns.

  • 12 authors
·
Aug 18, 2025 2

Can Atomic Step Decomposition Enhance the Self-structured Reasoning of Multimodal Large Models?

In this paper, we address the challenging task of multimodal mathematical reasoning by incorporating the ability of "slow thinking" into multimodal large language models (MLLMs). Our core idea is that different levels of reasoning abilities can be combined dynamically to tackle questions with different complexity. To this end, we propose a paradigm of Self-structured Chain of Thought (SCoT), which is composed of minimal semantic atomic steps. Different from existing methods that rely on structured templates or free-form paradigms, our method can not only generate cognitive CoT structures for various complex tasks but also mitigates the phenomenon of overthinking. To introduce structured reasoning capabilities into visual understanding models, we further design a novel AtomThink framework with four key modules, including (i) a data engine to generate high-quality multimodal reasoning paths; (ii) a supervised fine-tuning process with serialized inference data; (iii) a policy-guided multi-turn inference method; and (iv) an atomic capability metric to evaluate the single step utilization rate. We conduct extensive experiments to show that the proposed AtomThink significantly improves the performance of baseline MLLMs, achieving more than 10\% average accuracy gains on MathVista and MathVerse. Compared to state-of-the-art structured CoT approaches, our method not only achieves higher accuracy but also improves data utilization by 5 times and boosts inference efficiency by 85.3\%. Our code is now public available in https://github.com/Quinn777/AtomThink.

  • 16 authors
·
Mar 8, 2025

ConceptExpress: Harnessing Diffusion Models for Single-image Unsupervised Concept Extraction

While personalized text-to-image generation has enabled the learning of a single concept from multiple images, a more practical yet challenging scenario involves learning multiple concepts within a single image. However, existing works tackling this scenario heavily rely on extensive human annotations. In this paper, we introduce a novel task named Unsupervised Concept Extraction (UCE) that considers an unsupervised setting without any human knowledge of the concepts. Given an image that contains multiple concepts, the task aims to extract and recreate individual concepts solely relying on the existing knowledge from pretrained diffusion models. To achieve this, we present ConceptExpress that tackles UCE by unleashing the inherent capabilities of pretrained diffusion models in two aspects. Specifically, a concept localization approach automatically locates and disentangles salient concepts by leveraging spatial correspondence from diffusion self-attention; and based on the lookup association between a concept and a conceptual token, a concept-wise optimization process learns discriminative tokens that represent each individual concept. Finally, we establish an evaluation protocol tailored for the UCE task. Extensive experiments demonstrate that ConceptExpress is a promising solution to the UCE task. Our code and data are available at: https://github.com/haoosz/ConceptExpress

  • 5 authors
·
Jul 9, 2024

Towards Atoms of Large Language Models

The fundamental units of internal representations in large language models (LLMs) remain undefined, limiting further understanding of their mechanisms. Neurons or features are often regarded as such units, yet neurons suffer from polysemy, while features face concerns of unreliable reconstruction and instability. To address this issue, we propose the Atoms Theory, which defines such units as atoms. We introduce the atomic inner product (AIP) to correct representation shifting, formally define atoms, and prove the conditions that atoms satisfy the Restricted Isometry Property (RIP), ensuring stable sparse representations over atom set and linking to compressed sensing. Under stronger conditions, we further establish the uniqueness and exact ell_1 recoverability of the sparse representations, and provide guarantees that single-layer sparse autoencoders (SAEs) with threshold activations can reliably identify the atoms. To validate the Atoms Theory, we train threshold-activated SAEs on Gemma2-2B, Gemma2-9B, and Llama3.1-8B, achieving 99.9% sparse reconstruction across layers on average, and more than 99.8% of atoms satisfy the uniqueness condition, compared to 0.5% for neurons and 68.2% for features, showing that atoms more faithfully capture intrinsic representations of LLMs. Scaling experiments further reveal the link between SAEs size and recovery capacity. Overall, this work systematically introduces and validates Atoms Theory of LLMs, providing a theoretical framework for understanding internal representations and a foundation for mechanistic interpretability. Code available at https://github.com/ChenhuiHu/towards_atoms.

  • 5 authors
·
Sep 25, 2025

Can we Constrain Concept Bottleneck Models to Learn Semantically Meaningful Input Features?

Concept Bottleneck Models (CBMs) are regarded as inherently interpretable because they first predict a set of human-defined concepts which are used to predict a task label. For inherent interpretability to be fully realised, and ensure trust in a model's output, it's desirable for concept predictions to use semantically meaningful input features. For instance, in an image, pixels representing a broken bone should contribute to predicting a fracture. However, current literature suggests that concept predictions often rely on irrelevant input features. We hypothesise that this occurs when dataset labels include inaccurate concept annotations, or the relationship between input features and concepts is unclear. In general, the effect of dataset labelling on concept representations remains an understudied area. In this paper, we demonstrate that CBMs can learn to map concepts to semantically meaningful input features, by utilising datasets with a clear link between the input features and the desired concept predictions. This is achieved, for instance, by ensuring multiple concepts do not always co-occur and, therefore provide a clear training signal for the CBM to distinguish the relevant input features for each concept. We validate our hypothesis on both synthetic and real-world image datasets, and demonstrate under the correct conditions, CBMs can learn to attribute semantically meaningful input features to the correct concept predictions.

  • 4 authors
·
Feb 1, 2024

Digital Gene: Learning about the Physical World through Analytic Concepts

Reviewing the progress in artificial intelligence over the past decade, various significant advances (e.g. object detection, image generation, large language models) have enabled AI systems to produce more semantically meaningful outputs and achieve widespread adoption in internet scenarios. Nevertheless, AI systems still struggle when it comes to understanding and interacting with the physical world. This reveals an important issue: relying solely on semantic-level concepts learned from internet data (e.g. texts, images) to understand the physical world is far from sufficient -- machine intelligence currently lacks an effective way to learn about the physical world. This research introduces the idea of analytic concept -- representing the concepts related to the physical world through programs of mathematical procedures, providing machine intelligence a portal to perceive, reason about, and interact with the physical world. Except for detailing the design philosophy and providing guidelines for the application of analytic concepts, this research also introduce about the infrastructure that has been built around analytic concepts. I aim for my research to contribute to addressing these questions: What is a proper abstraction of general concepts in the physical world for machine intelligence? How to systematically integrate structured priors with neural networks to constrain AI systems to comply with physical laws?

  • 2 authors
·
Apr 5, 2025

Energy-Based Concept Bottleneck Models: Unifying Prediction, Concept Intervention, and Probabilistic Interpretations

Existing methods, such as concept bottleneck models (CBMs), have been successful in providing concept-based interpretations for black-box deep learning models. They typically work by predicting concepts given the input and then predicting the final class label given the predicted concepts. However, (1) they often fail to capture the high-order, nonlinear interaction between concepts, e.g., correcting a predicted concept (e.g., "yellow breast") does not help correct highly correlated concepts (e.g., "yellow belly"), leading to suboptimal final accuracy; (2) they cannot naturally quantify the complex conditional dependencies between different concepts and class labels (e.g., for an image with the class label "Kentucky Warbler" and a concept "black bill", what is the probability that the model correctly predicts another concept "black crown"), therefore failing to provide deeper insight into how a black-box model works. In response to these limitations, we propose Energy-based Concept Bottleneck Models (ECBMs). Our ECBMs use a set of neural networks to define the joint energy of candidate (input, concept, class) tuples. With such a unified interface, prediction, concept correction, and conditional dependency quantification are then represented as conditional probabilities, which are generated by composing different energy functions. Our ECBMs address both limitations of existing CBMs, providing higher accuracy and richer concept interpretations. Empirical results show that our approach outperforms the state-of-the-art on real-world datasets.

  • 5 authors
·
Jan 25, 2024

Large Concept Models: Language Modeling in a Sentence Representation Space

LLMs have revolutionized the field of artificial intelligence and have emerged as the de-facto tool for many tasks. The current established technology of LLMs is to process input and generate output at the token level. This is in sharp contrast to humans who operate at multiple levels of abstraction, well beyond single words, to analyze information and to generate creative content. In this paper, we present an attempt at an architecture which operates on an explicit higher-level semantic representation, which we name a concept. Concepts are language- and modality-agnostic and represent a higher level idea or action in a flow. Hence, we build a "Large Concept Model". In this study, as proof of feasibility, we assume that a concept corresponds to a sentence, and use an existing sentence embedding space, SONAR, which supports up to 200 languages in both text and speech modalities. The Large Concept Model is trained to perform autoregressive sentence prediction in an embedding space. We explore multiple approaches, namely MSE regression, variants of diffusion-based generation, and models operating in a quantized SONAR space. These explorations are performed using 1.6B parameter models and training data in the order of 1.3T tokens. We then scale one architecture to a model size of 7B parameters and training data of about 2.7T tokens. We perform an experimental evaluation on several generative tasks, namely summarization and a new task of summary expansion. Finally, we show that our model exhibits impressive zero-shot generalization performance to many languages, outperforming existing LLMs of the same size. The training code of our models is freely available.

  • 21 authors
·
Dec 11, 2024 1

Atom of Thoughts for Markov LLM Test-Time Scaling

Large Language Models (LLMs) achieve superior performance through training-time scaling, and test-time scaling further enhances their capabilities by conducting effective reasoning during inference. However, as the scale of reasoning increases, existing test-time scaling methods suffer from accumulated historical information, which not only wastes computational resources but also interferes with effective reasoning. To address this issue, we observe that complex reasoning progress is often achieved by solving a sequence of independent subquestions, each being self-contained and verifiable. These subquestions are essentially atomic questions, relying primarily on their current state rather than accumulated history, similar to the memoryless transitions in a Markov process. Based on this observation, we propose Atom of Thoughts (AoT), where each state transition in the reasoning process consists of decomposing the current question into a dependency-based directed acyclic graph and contracting its subquestions, forming a new atomic question state. This iterative decomposition-contraction process continues until reaching directly solvable atomic questions, naturally realizing Markov transitions between question states. Furthermore, these atomic questions can be seamlessly integrated into existing test-time scaling methods, enabling AoT to serve as a plug-in enhancement for improving reasoning capabilities. Experiments across six benchmarks demonstrate the effectiveness of AoT both as a standalone framework and a plug-in enhancement. Notably, on HotpotQA, when applied to gpt-4o-mini, AoT achieves an 80.6% F1 score, surpassing o3-mini by 3.4% and DeepSeek-R1 by 10.6%. The code will be available at https://github.com/qixucen/atom.

  • 6 authors
·
Feb 17, 2025 4

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

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.

Deciphering the "chemical" nature of the exotic isotopes of Hydrogen by the MC-QTAIM analysis: The positively charged Muon and the Muonic Helium as new members of the Periodic Table

This report is a primarily survey on the chemical nature of some exotic species containing the positively charged muon and the muonic Helium, i.e., the negatively charged muon plus helium nucleus, as exotic isotopes of hydrogen, using the newly developed multi-component quantum theory of atoms in molecules (MC-QTAIM) analysis, employing ab initio non-Born-Oppenhiemer wavefunctions. Accordingly, the "atoms in molecules" analysis performed on various asymmetric exotic isotopomers of hydrogen molecule, recently detected experimentally [Science 331, 448 (2011)], demonstrates that both the exotic isotopes are capable of forming atoms in molecules and retaining the identity of hydrogen atom. Various derived properties of atomic basins containing muonic helium cast no doubt that apart from its short life time, it is a heavier isotope of hydrogen while the properties of basins containing the positively charged muon are more remote from those of the orthodox hydrogen basins, capable of appreciable donation of electrons as well as large charge polarization; however, with some tolerance, they may be categorized also as hydrogen basins though with a smaller electronegativity. All in all, present study also clearly demonstrates that the MC-QTAIM analysis is an efficient approach to decipher the chemical nature of species containing exotic constituents, hard to be elucidated by experimental and/or alternative theoretical schemes.

  • 2 authors
·
Nov 25, 2013

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

Concepts in Motion: Temporal Bottlenecks for Interpretable Video Classification

Conceptual models such as Concept Bottleneck Models (CBMs) have driven substantial progress in improving interpretability for image classification by leveraging human-interpretable concepts. However, extending these models from static images to sequences of images, such as video data, introduces a significant challenge due to the temporal dependencies inherent in videos, which are essential for capturing actions and events. In this work, we introduce MoTIF (Moving Temporal Interpretable Framework), an architectural design inspired by a transformer that adapts the concept bottleneck framework for video classification and handles sequences of arbitrary length. Within the video domain, concepts refer to semantic entities such as objects, attributes, or higher-level components (e.g., 'bow', 'mount', 'shoot') that reoccur across time - forming motifs collectively describing and explaining actions. Our design explicitly enables three complementary perspectives: global concept importance across the entire video, local concept relevance within specific windows, and temporal dependencies of a concept over time. Our results demonstrate that the concept-based modeling paradigm can be effectively transferred to video data, enabling a better understanding of concept contributions in temporal contexts while maintaining competitive performance. Code available at github.com/patrick-knab/MoTIF.

  • 5 authors
·
Sep 25, 2025

OmniPrism: Learning Disentangled Visual Concept for Image Generation

Creative visual concept generation often draws inspiration from specific concepts in a reference image to produce relevant outcomes. However, existing methods are typically constrained to single-aspect concept generation or are easily disrupted by irrelevant concepts in multi-aspect concept scenarios, leading to concept confusion and hindering creative generation. To address this, we propose OmniPrism, a visual concept disentangling approach for creative image generation. Our method learns disentangled concept representations guided by natural language and trains a diffusion model to incorporate these concepts. We utilize the rich semantic space of a multimodal extractor to achieve concept disentanglement from given images and concept guidance. To disentangle concepts with different semantics, we construct a paired concept disentangled dataset (PCD-200K), where each pair shares the same concept such as content, style, and composition. We learn disentangled concept representations through our contrastive orthogonal disentangled (COD) training pipeline, which are then injected into additional diffusion cross-attention layers for generation. A set of block embeddings is designed to adapt each block's concept domain in the diffusion models. Extensive experiments demonstrate that our method can generate high-quality, concept-disentangled results with high fidelity to text prompts and desired concepts.

  • 7 authors
·
Dec 16, 2024

Sparse Concept Bottleneck Models: Gumbel Tricks in Contrastive Learning

We propose a novel architecture and method of explainable classification with Concept Bottleneck Models (CBMs). While SOTA approaches to Image Classification task work as a black box, there is a growing demand for models that would provide interpreted results. Such a models often learn to predict the distribution over class labels using additional description of this target instances, called concepts. However, existing Bottleneck methods have a number of limitations: their accuracy is lower than that of a standard model and CBMs require an additional set of concepts to leverage. We provide a framework for creating Concept Bottleneck Model from pre-trained multi-modal encoder and new CLIP-like architectures. By introducing a new type of layers known as Concept Bottleneck Layers, we outline three methods for training them: with ell_1-loss, contrastive loss and loss function based on Gumbel-Softmax distribution (Sparse-CBM), while final FC layer is still trained with Cross-Entropy. We show a significant increase in accuracy using sparse hidden layers in CLIP-based bottleneck models. Which means that sparse representation of concepts activation vector is meaningful in Concept Bottleneck Models. Moreover, with our Concept Matrix Search algorithm we can improve CLIP predictions on complex datasets without any additional training or fine-tuning. The code is available at: https://github.com/Andron00e/SparseCBM.

  • 4 authors
·
Apr 4, 2024

VQ-Atom: Semantic Discretization of Local Atomic Environments for Molecular Representation Learning

Large language models succeed by combining large-scale pretraining with meaningful discrete tokens. In molecular machine learning, SMILES is widely used as a token representation, but it is primarily a linearization format for molecular graphs rather than a semantic decomposition of chemistry. We propose VQ-Atom, a semantic tokenization framework that assigns discrete atom-level tokens based on local chemical environments via vector quantization. Unlike SMILES tokens, VQ-Atom tokens encode graph-local chemical context and are aligned with molecular structure. On protein-cold drug--target interaction prediction using the KIBA dataset, VQ-Atom substantially improves global ranking performance, achieving AUROC of 0.79 while substantially outperforming both SMILES-based and continuous molecular representations under an identical downstream architecture. Furthermore, VQ-Atom enables approximately 3 times faster downstream training than continuous atom-level representations by replacing per-atom continuous features with reusable discrete tokens. These results suggest that molecular tokenization is not merely a preprocessing step, but a central design choice. In particular, well-structured tokens can encode substantial chemical semantics, reducing the burden on downstream learning. VQ-Atom can be interpreted as defining a molecular language, where tokens correspond to chemically meaningful atomic environments, suggesting that token design may constitute an additional axis of machine learning research alongside architecture, objectives, and optimization.

  • 1 authors
·
Jun 7

Verified LLM-Driven Synthesis for Concept Design

Concept Design structures software systems around concepts: user-facing, self-contained units of functionality with a focused purpose. Concepts are composed into applications using synchronization rules called reactions, which specify how actions in one concept trigger actions in others. This paper first gives a formal semantics for concepts and reactions, enabling automatic verification of safety invariants in applications developed with this methodology. It then presents a CEGIS-style, LLM-driven synthesis procedure for generating reaction designs that satisfy such invariants. Because many different designs can satisfy the same invariant, we study two ways of steering synthesis toward the user's intended design: natural-language prompts and positive/negative scenarios. We also propose an LLM-driven scenario elicitation technique to support early design exploration. In an evaluation on three applications and twelve design variants using one LLM configuration, invariant-only synthesis reached verified designs quickly but often produced inconsistent designs across runs, some of which were implausible, showing that invariants alone underconstrain the design task. Scenario-guided synthesis recovered intended designs more consistently than natural-language prompting, although minimal scenarios can lead to overfitting. LLM-driven scenario elicitation, where the user classifies proposed scenarios rather than authoring them from scratch, recovered the intended designs in most variants when enough scenarios were elicited, but missed behaviors and non-determinism prevented reliable coverage in all cases.

  • 1 authors
·
Jul 16

Concept Conductor: Orchestrating Multiple Personalized Concepts in Text-to-Image Synthesis

The customization of text-to-image models has seen significant advancements, yet generating multiple personalized concepts remains a challenging task. Current methods struggle with attribute leakage and layout confusion when handling multiple concepts, leading to reduced concept fidelity and semantic consistency. In this work, we introduce a novel training-free framework, Concept Conductor, designed to ensure visual fidelity and correct layout in multi-concept customization. Concept Conductor isolates the sampling processes of multiple custom models to prevent attribute leakage between different concepts and corrects erroneous layouts through self-attention-based spatial guidance. Additionally, we present a concept injection technique that employs shape-aware masks to specify the generation area for each concept. This technique injects the structure and appearance of personalized concepts through feature fusion in the attention layers, ensuring harmony in the final image. Extensive qualitative and quantitative experiments demonstrate that Concept Conductor can consistently generate composite images with accurate layouts while preserving the visual details of each concept. Compared to existing baselines, Concept Conductor shows significant performance improvements. Our method supports the combination of any number of concepts and maintains high fidelity even when dealing with visually similar concepts. The code and models are available at https://github.com/Nihukat/Concept-Conductor.

  • 4 authors
·
Aug 7, 2024

ConceptSeg-R1: Segment Any Concept via Meta-Reinforcement Learning

Recent progress in promptable segmentation has shifted visual perception from object-level localization toward concept-level understanding. However, the notion of a concept remains under-specified, making it unclear whether current methods truly generalize beyond category recognition. In this work, we formalize generalized concept segmentation through a three-level taxonomy consisting of context-independent (CI), context-dependent (CD), and context-reasoning (CR) concepts, which reveals a clear capability gap across increasing levels of cognitive complexity. To address this challenge, we propose ConceptSeg-R1, a unified framework that reformulates concept segmentation as rule-induced concept grounding. At the core of our method is Meta-GRPO, a meta-reinforcement learning mechanism that learns transferable task rules from visual demonstrations and verifies them through proxy reasoning. The inferred reasoning states are then translated into segmentation-ready concept prompts via a lightweight concept translation module, enabling deductive application to target images. A shortcut routing strategy further preserves the native efficiency of segmentation models on simple cases. To systematically evaluate generalized concept segmentation, we conduct extensive experiments across diverse CI, CD, and CR concept segmentation benchmarks spanning natural, industrial, medical and reasoning-intensive domains. Without bells and whistles, ConceptSeg-R1 achieves strong performance across the full concept hierarchy while maintaining the native capability of promptable segmentation backbones. As an initial step toward segmenting any concept, we hope ConceptSeg-R1 can serve as a practical baseline for advancing segmentation from object-level prediction toward concept-level understanding.

  • 13 authors
·
May 18

ConceptMoE: Adaptive Token-to-Concept Compression for Implicit Compute Allocation

Large language models allocate uniform computation across all tokens, ignoring that some sequences are trivially predictable while others require deep reasoning. We introduce ConceptMoE, which dynamically merges semantically similar tokens into concept representations, performing implicit token-level compute allocation. A learnable chunk module identifies optimal boundaries by measuring inter-token similarity, compressing sequences by a target ratio R before they enter the compute-intensive concept model. Crucially, the MoE architecture enables controlled evaluation: we reallocate saved computation to match baseline activated FLOPs (excluding attention map computation) and total parameters, isolating genuine architectural benefits. Under these conditions, ConceptMoE consistently outperforms standard MoE across language and vision-language tasks, achieving +0.9 points on language pretraining, +2.3 points on long context understanding, and +0.6 points on multimodal benchmarks. When converting pretrained MoE during continual training with layer looping, gains reach +5.5 points, demonstrating practical applicability. Beyond performance, ConceptMoE reduces attention computation by up to R^2times and KV cache by Rtimes. At R=2, empirical measurements show prefill speedups reaching 175\% and decoding speedups up to 117\% on long sequences. The minimal architectural modifications enable straightforward integration into existing MoE, demonstrating that adaptive concept-level processing fundamentally improves both effectiveness and efficiency of large language models.

Can MLLMs Decode the Creative Leap? Introducing C4 for Cross-Concept Understanding

Creative capabilities of MLLMs matter in design, communication, education, and human--AI collaboration, yet remain difficult to evaluate because explicit targets and reward signals are scarce compared with accuracy-oriented tasks. Cross-concept understanding is a core cognitive capacity underlying receptive creativity. It enables a perceiver to recover intended meaning from non-obvious but meaningful conceptual relations. We operationalize item construction as cross-concept encoding and model inference as cross-concept decoding. We introduce C4, a cognition-inspired evaluation framework for Chengyu (Chinese idiom)-based Cross-Concept Creativity. Its encoding component maps target slots to imageable substitute concepts along bridge paths in a manually annotated and third-party-reviewed cross-concept network, enabling batch generation with explicit structure, difficulty indexed by bridge count and depth, and exact answers. Using this framework, we instantiate the C4 Evaluation Set (C4-Eval), comprising 184 synthetic items and 37 human-created cross-concept chengyu figures collected from online sources. We manually construct and review cross-concept relations, bridge paths, and reasoning processes for the collected figures. Each C4-Eval item is instantiated in five task settings, yielding 884 primary answer-recovery cases. Across ten evaluated MLLMs, the strongest closed models reach 50.7% and 48.0% primary accuracy, while open-source models remain substantially lower. Candidate constraints improve accuracy sharply, but bridge hints and explanation requests provide only modest gains. These results expose a substantial gap in how current MLLMs decode creatively encoded meaning through cross-concept relations. The code is in the supplementary material.

kinamind KinaMind
·
Aug 5 2

How Do Large Language Models Learn Concepts During Continual Pre-Training?

Human beings primarily understand the world through concepts (e.g., dog), abstract mental representations that structure perception, reasoning, and learning. However, how large language models (LLMs) acquire, retain, and forget such concepts during continual pretraining remains poorly understood. In this work, we study how individual concepts are acquired and forgotten, as well as how multiple concepts interact through interference and synergy. We link these behavioral dynamics to LLMs' internal concept circuits, computational subgraphs associated with specific concepts, and incorporate graph metrics to characterize circuit topology. Our analysis reveals: (1) LLMs concept circuits provide a non-trivial, consistent signal of concept learning and forgetting; (2) concept circuits exhibit a stage-wise temporal pattern during continual pretraining, with an early increase followed by gradual decrease and stabilization; (3) concepts with larger learning gains tend to exhibit greater forgetting under subsequent training; (4) semantically similar concepts induce stronger interference than weakly related ones; (5) conceptual knowledge differs in their transferability, with some significantly facilitating the learning of others. Together, our findings provide a circuit-level view of concept learning dynamics and motivate concept-aware training strategies, such as Circuit-aware Experience Replay, which uses circuit topology to prioritize concepts vulnerable to forgetting.

  • 7 authors
·
Aug 16 3

Interactive Medical Image Analysis with Concept-based Similarity Reasoning

The ability to interpret and intervene model decisions is important for the adoption of computer-aided diagnosis methods in clinical workflows. Recent concept-based methods link the model predictions with interpretable concepts and modify their activation scores to interact with the model. However, these concepts are at the image level, which hinders the model from pinpointing the exact patches the concepts are activated. Alternatively, prototype-based methods learn representations from training image patches and compare these with test image patches, using the similarity scores for final class prediction. However, interpreting the underlying concepts of these patches can be challenging and often necessitates post-hoc guesswork. To address this issue, this paper introduces the novel Concept-based Similarity Reasoning network (CSR), which offers (i) patch-level prototype with intrinsic concept interpretation, and (ii) spatial interactivity. First, the proposed CSR provides localized explanation by grounding prototypes of each concept on image regions. Second, our model introduces novel spatial-level interaction, allowing doctors to engage directly with specific image areas, making it an intuitive and transparent tool for medical imaging. CSR improves upon prior state-of-the-art interpretable methods by up to 4.5\% across three biomedical datasets. Our code is released at https://github.com/tadeephuy/InteractCSR.

  • 10 authors
·
Mar 9, 2025

Beyond Heuristic Prompting: A Concept-Guided Bayesian Framework for Zero-Shot Image Recognition

Vision-Language Models (VLMs), such as CLIP, have significantly advanced zero-shot image recognition. However, their performance remains limited by suboptimal prompt engineering and poor adaptability to target classes. While recent methods attempt to improve prompts through diverse class descriptions, they often rely on heuristic designs, lack versatility, and are vulnerable to outlier prompts. This paper enhances prompt by incorporating class-specific concepts. By treating concepts as latent variables, we rethink zero-shot image classification from a Bayesian perspective, casting prediction as marginalization over the concept space, where each concept is weighted by a prior and a test-image conditioned likelihood. This formulation underscores the importance of both a well-structured concept proposal distribution and the refinement of concept priors. To construct an expressive and efficient proposal distribution, we introduce a multi-stage concept synthesis pipeline driven by LLMs to generate discriminative and compositional concepts, followed by a Determinantal Point Process to enforce diversity. To mitigate the influence of outlier concepts, we propose a training-free, adaptive soft-trim likelihood, which attenuates their impact in a single forward pass. We further provide robustness guarantees and derive multi-class excess risk bounds for our framework. Extensive experiments demonstrate that our method consistently outperforms state-of-the-art approaches, validating its effectiveness in zero-shot image classification. Our code is available at https://github.com/less-and-less-bugs/CGBC.

  • 6 authors
·
Mar 8

AtomicRAG: Atom-Entity Graphs for Retrieval-Augmented Generation

Recent GraphRAG methods integrate graph structures into text indexing and retrieval, using knowledge graph triples to connect text chunks, thereby improving retrieval coverage and precision. However, we observe that treating text chunks as the basic unit of knowledge representation rigidly groups multiple atomic facts together, limiting the flexibility and adaptability needed to support diverse retrieval scenarios. Additionally, triple-based entity linking is sensitive to relation-extraction errors, which can lead to missing or incorrect reasoning paths and ultimately hurt retrieval accuracy. To address these issues, we propose the Atom-Entity Graph, a more precise and reliable architecture for knowledge representation and indexing. In our approach, knowledge is stored as knowledge atoms, namely individual, self-contained units of factual information, rather than coarse-grained text chunks. This allows knowledge elements to be flexibly reassembled without mutual interference, thereby enabling seamless alignment with diverse query perspectives. Edges between entities simply indicate whether a relationship exists. By combining personalized PageRank with relevance-based filtering, we maintain accurate entity connections and improve the reliability of reasoning. Theoretical analysis and experiments on five public benchmarks show that the proposed AtomicRAG algorithm outperforms strong RAG baselines in retrieval accuracy and reasoning robustness. Code: https://github.com/7HHHHH/AtomicRAG.

  • 8 authors
·
Feb 9

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

Soft Thinking: Unlocking the Reasoning Potential of LLMs in Continuous Concept Space

Human cognition typically involves thinking through abstract, fluid concepts rather than strictly using discrete linguistic tokens. Current reasoning models, however, are constrained to reasoning within the boundaries of human language, processing discrete token embeddings that represent fixed points in the semantic space. This discrete constraint restricts the expressive power and upper potential of such reasoning models, often causing incomplete exploration of reasoning paths, as standard Chain-of-Thought (CoT) methods rely on sampling one token per step. In this work, we introduce Soft Thinking, a training-free method that emulates human-like "soft" reasoning by generating soft, abstract concept tokens in a continuous concept space. These concept tokens are created by the probability-weighted mixture of token embeddings, which form the continuous concept space, enabling smooth transitions and richer representations that transcend traditional discrete boundaries. In essence, each generated concept token encapsulates multiple meanings from related discrete tokens, implicitly exploring various reasoning paths to converge effectively toward the correct answer. Empirical evaluations on diverse mathematical and coding benchmarks consistently demonstrate the effectiveness and efficiency of Soft Thinking, improving pass@1 accuracy by up to 2.48 points while simultaneously reducing token usage by up to 22.4% compared to standard CoT. Qualitative analysis further reveals that Soft Thinking outputs remain highly interpretable and readable, highlighting the potential of Soft Thinking to break the inherent bottleneck of discrete language-based reasoning. Code is available at https://github.com/eric-ai-lab/Soft-Thinking.

ucsbai UCSB AI Group
·
May 21, 2025 3

Concept-Based Explainable Artificial Intelligence: Metrics and Benchmarks

Concept-based explanation methods, such as concept bottleneck models (CBMs), aim to improve the interpretability of machine learning models by linking their decisions to human-understandable concepts, under the critical assumption that such concepts can be accurately attributed to the network's feature space. However, this foundational assumption has not been rigorously validated, mainly because the field lacks standardised metrics and benchmarks to assess the existence and spatial alignment of such concepts. To address this, we propose three metrics: the concept global importance metric, the concept existence metric, and the concept location metric, including a technique for visualising concept activations, i.e., concept activation mapping. We benchmark post-hoc CBMs to illustrate their capabilities and challenges. Through qualitative and quantitative experiments, we demonstrate that, in many cases, even the most important concepts determined by post-hoc CBMs are not present in input images; moreover, when they are present, their saliency maps fail to align with the expected regions by either activating across an entire object or misidentifying relevant concept-specific regions. We analyse the root causes of these limitations, such as the natural correlation of concepts. Our findings underscore the need for more careful application of concept-based explanation techniques especially in settings where spatial interpretability is critical.

  • 3 authors
·
Jan 31, 2025

Discover-then-Name: Task-Agnostic Concept Bottlenecks via Automated Concept Discovery

Concept Bottleneck Models (CBMs) have recently been proposed to address the 'black-box' problem of deep neural networks, by first mapping images to a human-understandable concept space and then linearly combining concepts for classification. Such models typically require first coming up with a set of concepts relevant to the task and then aligning the representations of a feature extractor to map to these concepts. However, even with powerful foundational feature extractors like CLIP, there are no guarantees that the specified concepts are detectable. In this work, we leverage recent advances in mechanistic interpretability and propose a novel CBM approach -- called Discover-then-Name-CBM (DN-CBM) -- that inverts the typical paradigm: instead of pre-selecting concepts based on the downstream classification task, we use sparse autoencoders to first discover concepts learnt by the model, and then name them and train linear probes for classification. Our concept extraction strategy is efficient, since it is agnostic to the downstream task, and uses concepts already known to the model. We perform a comprehensive evaluation across multiple datasets and CLIP architectures and show that our method yields semantically meaningful concepts, assigns appropriate names to them that make them easy to interpret, and yields performant and interpretable CBMs. Code available at https://github.com/neuroexplicit-saar/discover-then-name.

  • 4 authors
·
Jul 19, 2024

CHAMP: A Competition-level Dataset for Fine-Grained Analyses of LLMs' Mathematical Reasoning Capabilities

Recent large language models (LLMs) have shown indications of mathematical reasoning ability. However it has not been clear how they would fare on more challenging competition-level problems. And while self-generated verbalizations of intermediate reasoning steps (i.e., chain-of-thought prompting) have been shown to be helpful, whether LLMs can make use of helpful side information such as problem-specific hints has not been investigated before. In this paper, we propose a challenging benchmark dataset for enabling such analyses. The Concept and Hint-Annotated Math Problems (CHAMP) consists of high school math competition problems, annotated with concepts, or general math facts, and hints, or problem-specific tricks. These annotations allow us to explore the effects of additional information, such as relevant hints, misleading concepts, or related problems. This benchmark is difficult, with the best model only scoring 58.1% in standard settings. With concepts and hints, performance sometimes improves, indicating that some models can make use of such side information. We further annotate model-generated solutions for their correctness. Using this corpus, we find that models often arrive at the correct final answer through wrong reasoning steps. In addition, we test whether models are able to verify these solutions, and find that most models struggle. The dataset and code are available on the project website.

  • 3 authors
·
Jan 12, 2024

TPE: Towards Better Compositional Reasoning over Conceptual Tools with Multi-persona Collaboration

Large language models (LLMs) have demonstrated exceptional performance in planning the use of various functional tools, such as calculators and retrievers, particularly in question-answering tasks. In this paper, we expand the definition of these tools, centering on conceptual tools within the context of dialogue systems. A conceptual tool specifies a cognitive concept that aids systematic or investigative thought. These conceptual tools play important roles in practice, such as multiple psychological or tutoring strategies being dynamically applied in a single turn to compose helpful responses. To further enhance the reasoning and planning capability of LLMs with these conceptual tools, we introduce a multi-persona collaboration framework: Think-Plan-Execute (TPE). This framework decouples the response generation process into three distinct roles: Thinker, Planner, and Executor. Specifically, the Thinker analyzes the internal status exhibited in the dialogue context, such as user emotions and preferences, to formulate a global guideline. The Planner then generates executable plans to call different conceptual tools (e.g., sources or strategies), while the Executor compiles all intermediate results into a coherent response. This structured approach not only enhances the explainability and controllability of responses but also reduces token redundancy. We demonstrate the effectiveness of TPE across various dialogue response generation tasks, including multi-source (FoCus) and multi-strategy interactions (CIMA and PsyQA). This reveals its potential to handle real-world dialogue interactions that require more complicated tool learning beyond just functional tools. The full code and data will be released for reproduction.

  • 9 authors
·
Sep 27, 2023

ConceptMaster: Multi-Concept Video Customization on Diffusion Transformer Models Without Test-Time Tuning

Text-to-video generation has made remarkable advancements through diffusion models. However, Multi-Concept Video Customization (MCVC) remains a significant challenge. We identify two key challenges in this task: 1) the identity decoupling problem, where directly adopting existing customization methods inevitably mix attributes when handling multiple concepts simultaneously, and 2) the scarcity of high-quality video-entity pairs, which is crucial for training such a model that represents and decouples various concepts well. To address these challenges, we introduce ConceptMaster, an innovative framework that effectively tackles the critical issues of identity decoupling while maintaining concept fidelity in customized videos. Specifically, we introduce a novel strategy of learning decoupled multi-concept embeddings that are injected into the diffusion models in a standalone manner, which effectively guarantees the quality of customized videos with multiple identities, even for highly similar visual concepts. To further overcome the scarcity of high-quality MCVC data, we carefully establish a data construction pipeline, which enables systematic collection of precise multi-concept video-entity data across diverse concepts. A comprehensive benchmark is designed to validate the effectiveness of our model from three critical dimensions: concept fidelity, identity decoupling ability, and video generation quality across six different concept composition scenarios. Extensive experiments demonstrate that our ConceptMaster significantly outperforms previous approaches for this task, paving the way for generating personalized and semantically accurate videos across multiple concepts.

  • 9 authors
·
Jan 8, 2025 2

The Future of AI: Exploring the Potential of Large Concept Models

The field of Artificial Intelligence (AI) continues to drive transformative innovations, with significant progress in conversational interfaces, autonomous vehicles, and intelligent content creation. Since the launch of ChatGPT in late 2022, the rise of Generative AI has marked a pivotal era, with the term Large Language Models (LLMs) becoming a ubiquitous part of daily life. LLMs have demonstrated exceptional capabilities in tasks such as text summarization, code generation, and creative writing. However, these models are inherently limited by their token-level processing, which restricts their ability to perform abstract reasoning, conceptual understanding, and efficient generation of long-form content. To address these limitations, Meta has introduced Large Concept Models (LCMs), representing a significant shift from traditional token-based frameworks. LCMs use concepts as foundational units of understanding, enabling more sophisticated semantic reasoning and context-aware decision-making. Given the limited academic research on this emerging technology, our study aims to bridge the knowledge gap by collecting, analyzing, and synthesizing existing grey literature to provide a comprehensive understanding of LCMs. Specifically, we (i) identify and describe the features that distinguish LCMs from LLMs, (ii) explore potential applications of LCMs across multiple domains, and (iii) propose future research directions and practical strategies to advance LCM development and adoption.

  • 2 authors
·
Jan 8, 2025

Retrieval-Infused Reasoning Sandbox: A Benchmark for Decoupling Retrieval and Reasoning Capabilities

Despite strong performance on existing benchmarks, it remains unclear whether large language models can reason over genuinely novel scientific information. Most evaluations score end-to-end RAG pipelines, where reasoning is confounded with retrieval and toolchain choices, and the signal is further contaminated by parametric memorization and open-web volatility. We introduce DeR2, a controlled deep-research sandbox that isolates document-grounded reasoning while preserving core difficulties of deep search: multi-step synthesis, denoising, and evidence-based conclusion making. DeR2 decouples evidence access from reasoning via four regimes--Instruction-only, Concepts (gold concepts without documents), Related-only (only relevant documents), and Full-set (relevant documents plus topically related distractors)--yielding interpretable regime gaps that operationalize retrieval loss vs. reasoning loss and enable fine-grained error attribution. To prevent parametric leakage, we apply a two-phase validation that requires parametric failure without evidence while ensuring oracle-concept solvability. To ensure reproducibility, each instance provides a frozen document library (drawn from 2023-2025 theoretical papers) with expert-annotated concepts and validated rationales. Experiments across a diverse set of state-of-the-art foundation models reveal substantial variation and significant headroom: some models exhibit mode-switch fragility, performing worse with the Full-set than with Instruction-only, while others show structural concept misuse, correctly naming concepts but failing to execute them as procedures.

Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation

The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally matter engineering -- generally denoted as inverse design -- was based massively on human intuition and high-throughput virtual screening. The last few years have seen the emergence of significant interest in computer-inspired designs based on evolutionary or deep learning methods. The major challenge here is that the standard strings molecular representation SMILES shows substantial weaknesses in that task because large fractions of strings do not correspond to valid molecules. Here, we solve this problem at a fundamental level and introduce SELFIES (SELF-referencIng Embedded Strings), a string-based representation of molecules which is 100\% robust. Every SELFIES string corresponds to a valid molecule, and SELFIES can represent every molecule. SELFIES can be directly applied in arbitrary machine learning models without the adaptation of the models; each of the generated molecule candidates is valid. In our experiments, the model's internal memory stores two orders of magnitude more diverse molecules than a similar test with SMILES. Furthermore, as all molecules are valid, it allows for explanation and interpretation of the internal working of the generative models.

  • 5 authors
·
May 31, 2019

Multi-Concept T2I-Zero: Tweaking Only The Text Embeddings and Nothing Else

Recent advances in text-to-image diffusion models have enabled the photorealistic generation of images from text prompts. Despite the great progress, existing models still struggle to generate compositional multi-concept images naturally, limiting their ability to visualize human imagination. While several recent works have attempted to address this issue, they either introduce additional training or adopt guidance at inference time. In this work, we consider a more ambitious goal: natural multi-concept generation using a pre-trained diffusion model, and with almost no extra cost. To achieve this goal, we identify the limitations in the text embeddings used for the pre-trained text-to-image diffusion models. Specifically, we observe concept dominance and non-localized contribution that severely degrade multi-concept generation performance. We further design a minimal low-cost solution that overcomes the above issues by tweaking (not re-training) the text embeddings for more realistic multi-concept text-to-image generation. Our Correction by Similarities method tweaks the embedding of concepts by collecting semantic features from most similar tokens to localize the contribution. To avoid mixing features of concepts, we also apply Cross-Token Non-Maximum Suppression, which excludes the overlap of contributions from different concepts. Experiments show that our approach outperforms previous methods in text-to-image, image manipulation, and personalization tasks, despite not introducing additional training or inference costs to the diffusion steps.

  • 5 authors
·
Oct 11, 2023

Knowledge Graph in Astronomical Research with Large Language Models: Quantifying Driving Forces in Interdisciplinary Scientific Discovery

Identifying and predicting the factors that contribute to the success of interdisciplinary research is crucial for advancing scientific discovery. However, there is a lack of methods to quantify the integration of new ideas and technological advancements in astronomical research and how these new technologies drive further scientific breakthroughs. Large language models, with their ability to extract key concepts from vast literature beyond keyword searches, provide a new tool to quantify such processes. In this study, we extracted concepts in astronomical research from 297,807 publications between 1993 and 2024 using large language models, resulting in a set of 24,939 concepts. These concepts were then used to form a knowledge graph, where the link strength between any two concepts was determined by their relevance through the citation-reference relationships. By calculating this relevance across different time periods, we quantified the impact of numerical simulations and machine learning on astronomical research. The knowledge graph demonstrates two phases of development: a phase where the technology was integrated and another where the technology was explored in scientific discovery. The knowledge graph reveals that despite machine learning has made much inroad in astronomy, there is currently a lack of new concept development at the intersection of AI and Astronomy, which may be the current bottleneck preventing machine learning from further transforming the field of astronomy.

  • 6 authors
·
Jun 3, 2024

Exploring Concept Depth: How Large Language Models Acquire Knowledge at Different Layers?

Large language models (LLMs) have shown remarkable performances across a wide range of tasks. However, the mechanisms by which these models encode tasks of varying complexities remain poorly understood. In this paper, we explore the hypothesis that LLMs process concepts of varying complexities in different layers, introducing the idea of "Concept Depth" to suggest that more complex concepts are typically acquired in deeper layers. Specifically, we categorize concepts based on their level of abstraction, defining them in the order of increasing complexity within factual, emotional, and inferential tasks. We conduct extensive probing experiments using layer-wise representations across various LLM families (Gemma, LLaMA, QWen) on various datasets spanning the three domains of tasks. Our findings reveal that models could efficiently conduct probing for simpler tasks in shallow layers, and more complex tasks typically necessitate deeper layers for accurate understanding. Additionally, we examine how external factors, such as adding noise to the input and quantizing the model weights, might affect layer-wise representations. Our findings suggest that these factors can impede the development of a conceptual understanding of LLMs until deeper layers are explored. We hope that our proposed concept and experimental insights will enhance the understanding of the mechanisms underlying LLMs. Our codes are available at https://github.com/Luckfort/CD.

  • 13 authors
·
Apr 10, 2024

A Holistic Approach to Unifying Automatic Concept Extraction and Concept Importance Estimation

In recent years, concept-based approaches have emerged as some of the most promising explainability methods to help us interpret the decisions of Artificial Neural Networks (ANNs). These methods seek to discover intelligible visual 'concepts' buried within the complex patterns of ANN activations in two key steps: (1) concept extraction followed by (2) importance estimation. While these two steps are shared across methods, they all differ in their specific implementations. Here, we introduce a unifying theoretical framework that comprehensively defines and clarifies these two steps. This framework offers several advantages as it allows us: (i) to propose new evaluation metrics for comparing different concept extraction approaches; (ii) to leverage modern attribution methods and evaluation metrics to extend and systematically evaluate state-of-the-art concept-based approaches and importance estimation techniques; (iii) to derive theoretical guarantees regarding the optimality of such methods. We further leverage our framework to try to tackle a crucial question in explainability: how to efficiently identify clusters of data points that are classified based on a similar shared strategy. To illustrate these findings and to highlight the main strategies of a model, we introduce a visual representation called the strategic cluster graph. Finally, we present https://serre-lab.github.io/Lens, a dedicated website that offers a complete compilation of these visualizations for all classes of the ImageNet dataset.

  • 8 authors
·
Jun 11, 2023

UniCTokens: Boosting Personalized Understanding and Generation via Unified Concept Tokens

Personalized models have demonstrated remarkable success in understanding and generating concepts provided by users. However, existing methods use separate concept tokens for understanding and generation, treating these tasks in isolation. This may result in limitations for generating images with complex prompts. For example, given the concept langle borangle, generating "langle borangle wearing its hat" without additional textual descriptions of its hat. We call this kind of generation \textbf{personalized attribute-reasoning generation}. To address the limitation, we present UniCTokens, a novel framework that effectively integrates personalized information into a unified vision language model (VLM) for understanding and generation. UniCTokens trains a set of unified concept tokens to leverage complementary semantics, boosting two personalized tasks. Moreover, we propose a progressive training strategy with three stages: understanding warm-up, bootstrapping generation from understanding, and deepening understanding from generation to enhance mutual benefits between both tasks. To quantitatively evaluate the unified VLM personalization, we present UnifyBench, the first benchmark for assessing concept understanding, concept generation, and attribute-reasoning generation. Experimental results on UnifyBench indicate that UniCTokens shows competitive performance compared to leading methods in concept understanding, concept generation, and achieving state-of-the-art results in personalized attribute-reasoning generation. Our research demonstrates that enhanced understanding improves generation, and the generation process can yield valuable insights into understanding. Our code and dataset will be released at: https://github.com/arctanxarc/UniCTokens{https://github.com/arctanxarc/UniCTokens}.

  • 13 authors
·
May 20, 2025

Overlooked factors in concept-based explanations: Dataset choice, concept learnability, and human capability

Concept-based interpretability methods aim to explain deep neural network model predictions using a predefined set of semantic concepts. These methods evaluate a trained model on a new, "probe" dataset and correlate model predictions with the visual concepts labeled in that dataset. Despite their popularity, they suffer from limitations that are not well-understood and articulated by the literature. In this work, we analyze three commonly overlooked factors in concept-based explanations. First, the choice of the probe dataset has a profound impact on the generated explanations. Our analysis reveals that different probe datasets may lead to very different explanations, and suggests that the explanations are not generalizable outside the probe dataset. Second, we find that concepts in the probe dataset are often less salient and harder to learn than the classes they claim to explain, calling into question the correctness of the explanations. We argue that only visually salient concepts should be used in concept-based explanations. Finally, while existing methods use hundreds or even thousands of concepts, our human studies reveal a much stricter upper bound of 32 concepts or less, beyond which the explanations are much less practically useful. We make suggestions for future development and analysis of concept-based interpretability methods. Code for our analysis and user interface can be found at https://github.com/princetonvisualai/OverlookedFactors

  • 4 authors
·
Jul 19, 2022

ResearchStudio-Idea: An Evidence-Grounded Research-Ideation Skill Suite from ML Conference Outcomes

Large language models have made research ideation increasingly accessible, yet effective idea development requires more than generating candidate directions. Researchers must ground a problem in current literature, identify meaningful bottlenecks, differentiate from existing solutions, and evaluate risks before committing to implementation. We present ResearchStudio-Idea as a reusable skill suite for this first mile of research ideation. The suite includes Paper-Search, a standalone multi-source literature search skill; Scoop-Check, a standalone prior-art collision checker for novelty claims; and IdeaSpark, the end-to-end skill that composes evidence grounding, pattern-guided generation, collision retrieval, audit, and idea-card rendering into one workflow. IdeaSpark is constructed from a corpus of 1,947 machine learning conference papers collected from ICLR, ICML, and NeurIPS between 2021 and 2025, including Oral papers, a separately tracked high-citation subset, and rejected submissions. Analysis of these outcomes reveals 31 recurring ideation sub-patterns, consolidated into 15 reusable ideation patterns. Each pattern is operationalized as a structured card containing research contexts, bottleneck types, differentiation strategies, supporting precedents, and common failure modes. Given a research problem and an evidence bundle, IdeaSpark evaluates evidence readiness, reconstructs the surrounding research context, identifies unresolved bottlenecks, selects relevant patterns, instantiates one candidate direction, retrieves potentially conflicting prior work, and performs outcome-informed auditing. This workflow transforms reusable ideation patterns into traceable research proposals. Blind automated-judge evaluations show that IdeaSpark consistently produces stronger research proposals than no-skill and generic-skill baselines while maintaining competitive novelty.

microsoft Microsoft
·
Jul 4 3

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