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Oct 26

Systematic Covariance Envelopes from Wasserstein Geometry: Evidence from Language-Model Representations

Firm characteristics are commonly represented as fixed vectors, even though evidence about firms' operations arrives as heterogeneous collections of articles reports. We study how distances between distributions of firm characteristics restrict systematic covariance. For given latent exposure laws, quadratic Wasserstein geometry yields sharp covariance endpoints over admissible couplings. Under a common randomized bi-Lipschitz characteristic-to-exposure map, bounded risk-coordinate slack, and a maintained return-covariance bridge, characteristic-side distance yields a conditional interval for the covariance ceiling. Greater separation then leaves less scope for aligned systematic exposures when these assumptions are tight, while a non-negative transport excess term records the gap between realized and maximum-covariance arrangements. The resulting envelope is scenario analysis rather than an expected-return, no-arbitrage, or identified structural model. Empirically, we proxy characteristic distributions with encoder-only language-model embeddings of financial news articles, disclosures, and analyst reports for Nasdaq firms over 2018-2022. In a dyadic regression with symmetric firm effects, greater pairwise article-embedding W2 distance is associated with weaker return co-movement: the coefficient is 1.920, with 95% interval [1.412, 2.468]. The estimate retains the same sign when returns are measured in a later window, although the feature construction is not point-in-time and the evidence remains reduced form.

Can "consciousness" be observed from large language model (LLM) internal states? Dissecting LLM representations obtained from Theory of Mind test with Integrated Information Theory and Span Representation analysis

Integrated Information Theory (IIT) provides a quantitative framework for explaining consciousness phenomenon, positing that conscious systems comprise elements integrated through causal properties. We apply IIT 3.0 and 4.0 -- the latest iterations of this framework -- to sequences of Large Language Model (LLM) representations, analyzing data derived from existing Theory of Mind (ToM) test results. Our study systematically investigates whether the differences of ToM test performances, when presented in the LLM representations, can be revealed by IIT estimates, i.e., Phi^{max} (IIT 3.0), Phi (IIT 4.0), Conceptual Information (IIT 3.0), and Phi-structure (IIT 4.0). Furthermore, we compare these metrics with the Span Representations independent of any estimate for consciousness. This additional effort aims to differentiate between potential "consciousness" phenomena and inherent separations within LLM representational space. We conduct comprehensive experiments examining variations across LLM transformer layers and linguistic spans from stimuli. Our results suggest that sequences of contemporary Transformer-based LLM representations lack statistically significant indicators of observed "consciousness" phenomena but exhibit intriguing patterns under spatio-permutational analyses. The Appendix and code are available as Supplementary Materials at: https://doi.org/10.1016/j.nlp.2025.100163.

  • 1 authors
·
Jun 26, 2025

Reverse Distillation: Consistently Scaling Protein Language Model Representations

Unlike the predictable scaling laws in natural language processing and computer vision, protein language models (PLMs) scale poorly: for many tasks, models within the same family plateau or even decrease in performance, with mid-sized models often outperforming the largest in the family. We introduce Reverse Distillation, a principled framework that decomposes large PLM representations into orthogonal subspaces guided by smaller models of the same family. The resulting embeddings have a nested, Matryoshka-style structure: the first k dimensions of a larger model's embedding are exactly the representation from the smaller model. This ensures that larger reverse-distilled models consistently outperform smaller ones. A motivating intuition is that smaller models, constrained by capacity, preferentially encode broadly-shared protein features. Reverse distillation isolates these shared features and orthogonally extracts additional contributions from larger models, preventing interference between the two. On ProteinGym benchmarks, reverse-distilled ESM-2 variants outperform their respective baselines at the same embedding dimensionality, with the reverse-distilled 15 billion parameter model achieving the strongest performance. Our framework is generalizable to any model family where scaling challenges persist. Code and trained models are available at https://github.com/rohitsinghlab/plm_reverse_distillation.

  • 4 authors
·
Mar 8

The strength of clinical evidence is recoverable from language model representations but not from their stated grades

Large language models (LLMs) increasingly summarize clinical evidence, where a claim's weight depends on how strongly it is supported. Yet these models convey confidence poorly, and properties they never state, such as truth, are often readable from their activations. Whether a clinical model registers evidence strength, distinct from truth, and states it when asked is untested, and any such signal could be lexical. We compiled 45,134 clinical claims from six public sources, harmonized 20,611 into a four-level evidence grade under three independent frameworks, and tested 22 local, open-weight LLMs from several developers (0.6-70 billion parameters; general, medical, and reasoning), with lexical, truth, and cross-framework controls. A linear estimator recovered the grade in every model (median AUROC 71.8), yet decodability did not rise with scale and was weakest in reasoning models. The grade the models stated fell to chance, 25-27 percentage points below the estimator. The recoverable signal was largely lexical and did not transfer across topics or frameworks, yet it was distinct from factual truth and still flagged weakly supported claims (AUROC 69.2). Clinical LLMs thus carry an ordered evidence-strength signal they do not express, so their stated grades fail to convey a claim's support even when it is recoverable from their representations and text.

  • 1 authors
·
Jun 26

Skin-Deep: A Geometric Diagnostic for Alignment Fragility in Large Language Model Representations

Alignment tuning is meant to make harmful-request refusal robust, yet this safety behavior can be erased by a small set of benign fine-tuning examples. This is a deployment risk for open-weight models because a checkpoint can pass refusal tests at release time and later lose refusal under low-cost downstream fine-tuning. Prior work has established these refusal failures, but existing studies do not show how to detect this fragility in the aligned model itself before an attack or fine-tuning intervention is run. We introduce Skin-Deep, a geometric diagnostic that detects alignment fragility directly from the aligned model's hidden-state activations before such an intervention is run and compresses the layer-wise safety geometry into a single scalar, the Geometric Fragility Score (GFS). Applied to twenty-one instruction-tuned models spanning six alignment recipes and 3B--32B parameters, Skin-Deep reveals a recurring low-rank safety subspace across model families. Direction ablations show that removing directions in this subspace weakens harmful-request refusal, providing causal evidence that the recovered geometry underlies refusal behavior. Crucially, GFS identifies, before any fine-tuning, the initially safe model that retains the most refusal after small-scale LoRA fine-tuning. These results establish GFS as a practical pre-deployment diagnostic for flagging fragile refusal behavior without running an attack.

  • 8 authors
·
Jun 20

Portfolio Risk Bounds without Cross-Asset Return Covariances: Distributional Fields from Language-Model Representations

Portfolio risk assessment ordinarily relies on reliable estimates of cross-asset return covariances, which are difficult to obtain in short, high-dimensional panels. We show that firm-level distribution-valued characteristics can instead provide one-sided certificates of portfolio risk. Under maintained links from characteristics to systematic exposures and from exposures to returns, multi-firm Wasserstein-2 dispersion yields a sharp upper bound on systematic portfolio variance and a corresponding bound for standardized returns. A weighted pairwise relaxation produces an objective that is convex under a checkable condition and requires marginal volatility scales but no cross-asset return covariances. With zero firm-specific slack, the common-map scale changes the certified variance reduction but not the normalized allocation, which depends only on observed information geometry. In a 52-firm panel from 2018-2022, an allocation constructed from Qwen3-Embedding-8B news representations lies between the 0.69th and 1.33rd in-sample variance percentiles across four prespecified capped portfolio populations; equal risk weighting lies between the 21.1st and 28.6th percentiles. The lower in-sample variance ranking relative to equal risk also appears across the reported frozen language-model representations. The framework therefore distribution-valued firm information into a coherent risk bound and an implementable allocation rule constructed without cross-asset return covariances.

Do LLMs Know What Is Private Internally? Probing and Steering Contextual Privacy Norms in Large Language Model Representations

Large language models (LLMs) are increasingly deployed in high-stakes settings, yet they frequently violate contextual privacy by disclosing private information in situations where humans would exercise discretion. This raises a fundamental question: do LLMs internally encode contextual privacy norms, and if so, why do violations persist? We present the first systematic study of contextual privacy as a structured latent representation in LLMs, grounded in contextual integrity (CI) theory. Probing multiple models, we find that the three norm-determining CI parameters (information type, recipient, and transmission principle) are encoded as linearly separable and functionally independent directions in activation space. Despite this internal structure, models still leak private information in practice, revealing a clear gap between concept representation and model behavior. To bridge this gap, we introduce CI-parametric steering, which independently intervenes along each CI dimension. This structured control reduces privacy violations more effectively and predictably than monolithic steering. Our results demonstrate that contextual privacy failures arise from misalignment between representation and behavior rather than missing awareness, and that leveraging the compositional structure of CI enables more reliable contextual privacy control, shedding light on potential improvement of contextual privacy understanding in LLMs.

  • 3 authors
·
Mar 30

Linear representations in language models can change dramatically over a conversation

Language model representations often contain linear directions that correspond to high-level concepts. Here, we study the dynamics of these representations: how representations evolve along these dimensions within the context of (simulated) conversations. We find that linear representations can change dramatically over a conversation; for example, information that is represented as factual at the beginning of a conversation can be represented as non-factual at the end and vice versa. These changes are content-dependent; while representations of conversation-relevant information may change, generic information is generally preserved. These changes are robust even for dimensions that disentangle factuality from more superficial response patterns, and occur across different model families and layers of the model. These representation changes do not require on-policy conversations; even replaying a conversation script written by an entirely different model can produce similar changes. However, adaptation is much weaker from simply having a sci-fi story in context that is framed more explicitly as such. We also show that steering along a representational direction can have dramatically different effects at different points in a conversation. These results are consistent with the idea that representations may evolve in response to the model playing a particular role that is cued by a conversation. Our findings may pose challenges for interpretability and steering -- in particular, they imply that it may be misleading to use static interpretations of features or directions, or probes that assume a particular range of features consistently corresponds to a particular ground-truth value. However, these types of representational dynamics also point to exciting new research directions for understanding how models adapt to context.

google Google
·
Jan 28 2

Diffusion on language model encodings for protein sequence generation

Protein sequence design has seen significant advances through discrete diffusion and autoregressive approaches, yet the potential of continuous diffusion remains underexplored. Here, we present DiMA, a latent diffusion framework that operates on protein language model representations. Through systematic exploration of architectural choices and diffusion components, we develop a robust methodology that generalizes across multiple protein encoders ranging from 8M to 3B parameters. We demonstrate that our framework achieves consistently high performance across sequence-only (ESM-2, ESMc), dual-decodable (CHEAP), and multimodal (SaProt) representations using the same architecture and training approach. We extensively evaluate existing methods alongside DiMA using multiple metrics across two protein modalities, covering quality, diversity, novelty, and distribution matching of generated proteins. DiMA consistently produces novel, high-quality and diverse protein sequences and achieves strong results compared to baselines such as autoregressive, discrete diffusion and flow matching language models. The model demonstrates versatile functionality, supporting conditional generation tasks including protein family-generation, motif scaffolding and infilling, and fold-specific sequence design. This work provides a universal continuous diffusion framework for protein sequence generation, offering both architectural insights and practical applicability across various protein design scenarios. Code is released at https://github.com/MeshchaninovViacheslav/DiMA{GitHub}.

  • 7 authors
·
Sep 5, 2025

SeLMRoute: Probabilistic Semantic Evidence for Large Language Model Routing

Large language model (LLM) routing aims to select the most suitable model for each incoming query. Most existing routers learn this decision directly from query embeddings, model representations, preference data, or clusters of similar examples. Such approaches can be effective, yet the representation used for routing rarely states what a query actually requires. We introduce SeLMRoute, a routing framework that separates the extraction of candidate-independent semantic evidence from the learning of candidate performance and the application of deployment objectives. A decision model first evaluates a set of interpretable questions about the query, such as its reasoning requirements and use of external knowledge, with each judgment retained as a probability distribution. The resulting probabilistic semantic state is used by a lightweight supervised router to estimate candidate model performance. Routing objectives are applied after performance estimation, which allows the same semantic state to support performance-oriented and cost-aware decisions. On the LLMRouterBench (15 datasets, 20 candidate models, 11,481 queries), SeLMRoute achieves an average accuracy of 72.08% pm 0.45, while grouped five-fold out-of-fold evaluation reaches 72.64%, compared with 69.23% for the strongest fixed candidate. The representation achieves the highest mean performance among the evaluated semantic, dense, lexical, and domain-level representations. In a separate 13-model performance-cost setting, SeLMRoute improves performance in all five grouped splits, with a mean PerfGain of 2.66%. Our code is available at https://github.com/Indigma-Innovations/SeLMRoute.

REMA: A Unified Reasoning Manifold Framework for Interpreting Large Language Model

Understanding how Large Language Models (LLMs) perform complex reasoning and their failure mechanisms is a challenge in interpretability research. To provide a measurable geometric analysis perspective, we define the concept of the Reasoning Manifold, a latent low-dimensional geometric structure formed by the internal representations corresponding to all correctly reasoned generations. This structure can be conceptualized as the embodiment of the effective thinking paths that the model has learned to successfully solve a given task. Based on this concept, we build REMA, a framework that explains the origins of failures by quantitatively comparing the spatial relationships of internal model representations corresponding to both erroneous and correct reasoning samples. Specifically, REMA first quantifies the geometric deviation of each erroneous representation by calculating its k-nearest neighbors distance to the approximated manifold formed by correct representations, thereby providing a unified failure signal. It then localizes the divergence points where these deviations first become significant by tracking this deviation metric across the model's layers and comparing it against a baseline of internal fluctuations from correct representations, thus identifying where the reasoning chain begins to go off-track. Our extensive experiments on diverse language and multimodal models and tasks demonstrate the low-dimensional nature of the reasoning manifold and the high separability between erroneous and correct reasoning representations. The results also validate the effectiveness of the REMA framework in analyzing the origins of reasoning failures. This research connects abstract reasoning failures to measurable geometric deviations in representations, providing new avenues for in-depth understanding and diagnosis of the internal computational processes of black-box models.

  • 8 authors
·
Sep 26, 2025 2

Persistent Depth Ordering amid Shifting Block-Bypass Responses in Language Model Pretraining

Layer interventions are widely used to probe the internal organization of language models, yet most analyses examine a single training checkpoint even though model representations and computations evolve throughout pretraining. This leaves open which depth-dependent intervention responses reflect persistent organization and which are transient consequences of training. We study this question using single-block identity bypass on fixed teacher-forced contexts across five released trajectories and 11 model-domain combinations. We find that block-bypass responses retain recognizable depth ordering while their magnitudes redistribute: nearby checkpoints preserve stronger rank correspondence than distant ones, and large changes concentrate at positions that recur across text samples and transfer across evaluation domains. Controlled experiments further show that changes in the natural bypass effect cannot be reduced to a single downstream sensitivity: in replicated Pythia runs, local missing-update magnitude grows while the pooled matched downstream response decreases, whereas OLMo-2 7B exhibits a different balance. These matched responses also depend on perturbation strength and direction, without identifying targeted compensation. Together, our results show that longitudinal layer sensitivity is structured but not static, and that single-checkpoint intervention responses should be interpreted in the context of how the underlying perturbation pathway evolves during training.

  • 3 authors
·
Sep 30

ScoutRoute: Efficient Mixture-of-Experts Routing Using Internal Language Model Signals

Efficient expert routing is a fundamental challenge in Mixture-of-Experts (MoE) systems, particularly for heterogeneous collections of independently trained Large Language Mod els (LLMs). Existing routing approaches typically rely on jointly trained gating networks, prompt-based predictors, or computationally expensive multi-model inference, limiting their flexibility and efficiency. This paper presents ScoutRoute, a lightweight post-hoc routing framework that predicts expert competence using internal language model signals extracted from a single forward pass through an inexpensive scout model. Hidden-state representations are used to estimate cross-model competence through lightweight logistic probes, while logit-derived confidence measures are incorporated within a domain-aware routing strategy for efficient expert selec tion without modifying the underlying language models. ScoutRoute isevaluatedon fiveopen-weightlanguagemodels across fourbenchmark datasets covering mathematical reasoning, code generation, commonsense reasoning, and multidis ciplinary knowledge. Experimental results show that ScoutRoute consistently outperforms individual routing signals while requiring only a single scout-model inference. The proposed competence probes also achieve superior calibration compared with conventional confidence measures, demonstrating that internal language model representations provide transferable information for accurate and efficient expert routing across heterogeneous language models

  • 2 authors
·
Oct 15

ICA Lens: Interpreting Language Models Without Training Another Dictionary

Finding interpretable directions in language-model representations is critical for understanding and controlling model behavior. Sparse autoencoders (SAEs) have become the standard tool for this purpose, but using them as the default first lens often requires training, storing, and evaluating large overcomplete dictionaries. This bottleneck limits rapid exploration and raises a fundamental question: how much interpretable structure is already visible from activation geometry before training another neural dictionary? Our intuition is simple: many interpretable directions are selective on tokens, and these directions should look less Gaussian than random directions. We therefore revisit independent component analysis (ICA), a classical method for finding non-Gaussian directions, as a compact lens for language-model interpretability. We find that ICA has been underestimated for LLM interpretability, because prior uses often relied on off-the-shelf ICA implementations that are brittle on LLM activations and lacked systematic tools for inspecting and evaluating the recovered directions. To bridge these gaps, we introduce ICALens, the first practical workflow for stable, efficient, and auditable ICA analysis of LLM representations. It combines an optimized GPU-parallel FastICA pipeline with LLM-specific stability recipes and better fitting diagnostics, enabling efficient and reliable layer-wise analysis. Across GPT-2 Small, Gemma 2 2B, and Qwen 3.5 2B Base, ICALens efficiently recovers compact, human-interpretable directions without per-layer gradient-based dictionary training. On SAEBench, ICA is competitive with public SAEs in sparse probing and outperforms them in targeted probe perturbation under small-to-medium budgets. These results suggest that ICA should not be viewed as a weak baseline, but as an efficient and complementary first lens for exploring language-model representations.

Why Does Reinforcement Learning Generalize? A Feature-Level Mechanistic Study of Post-Training in Large Language Models

Reinforcement learning (RL)-based post-training often improves the reasoning performance of large language models (LLMs) beyond the training domain, while supervised fine-tuning (SFT) frequently leads to general capabilities forgetting. However, the mechanisms underlying this contrast remain unclear. To bridge this gap, we present a feature-level mechanistic analysis methodology to probe RL generalization using a controlled experimental setup, where RL- and SFT-tuned models are trained from the same base model on identical data. Leveraging our interpretability framework, we align internal activations across models within a shared feature space and analyze how features evolve during post-training. We find that SFT rapidly introduces many highly specialized features that stabilize early in training, whereas RL induces more restrained and continually evolving feature changes that largely preserve base models' representations. Focusing on samples where RL succeeds but the base model fails, we identify a compact, task-agnostic set of features that directly mediate generalization across diverse tasks. Feature-level interventions confirm their causal role: disabling these features significantly degrades RL models' generalization performance, while amplifying them improves base models' performance. The code is available at https://github.com/danshi777/RL-generalization.

  • 6 authors
·
Apr 26

Making MLLM Latents Matter: Factor-Aware Predictive Learning for Cinematic Video Generation

Cinematic video generation requires both temporal inference from limited inputs (i.e., sparse rather than frame-by-frame guidance) and factor-aware control of character, scene, action, and camera. Multimodal large language models (MLLMs) offer useful priors for both capabilities, but their representations are not automatically actionable for video generation: a Video Diffusion Transformer (DiT) may bypass them through native conditioning pathways, and using them does not ensure either factor-aware control or generation-compatible temporal prediction. We propose Factor-Aware Predictive Learning (FAPL), which establishes effective MLLM latent use as a shared prerequisite and then targets the two capabilities with complementary learning signals. First, latent-only generator grounding trains the DiT with a frozen MLLM and connector, strengthening the DiT's use of MLLM latents for generation. Second, for factor-aware control, paired videos specify a target-factor change and non-target preservation, and factor-span replacement trains the DiT to realize this relationship in its output. Third, for temporal inference, text-only and text-plus-complete-video observations share a video target, and the trained DiT is then frozen while the MLLM and connector are optimized through it. This final stage trains limited-input representations for generation while retaining complete-observation reconstruction as a complementary training mode. Extensive experiments demonstrate our consistently better performance on three cinematic video generation tasks (i.e., sparse-to-video, factor-aware editing, and multi-shot generation) over baselines and validate FAPL's contributions to MLLM feature use, temporal control, and factor coordination.

tencent Tencent
·
Oct 22 2

Learning What to Forget: Distributional Unlearning for LLM Representation Spaces

Machine learning systems increasingly face the need to remove the influence of entire data domains, such as toxic language, harmful behavior, or topical content, rather than isolated records. Recent work formalizes this problem as distributional unlearning: selecting a subset of a forget domain whose removal moves the training distribution away from an unwanted population while preserving proximity to the desired one. However, existing analyses often impose parametric assumptions to obtain tractable selection rules. These assumptions may be poorly suited to high-dimensional language-model representations. We introduce Mamushi, a framework for non-parametric distributional unlearning that ranks forget examples using a probabilistic classifier whose Bayes-optimal logit equals the forget-to-retain log-density ratio (up to an additive class-prior constant). We show that thresholding the population log-density ratio yields the optimal fixed-budget selection rule for our removal--preservation objective and establish a non-asymptotic transfer guarantee relating score-estimation and threshold-calibration errors to degradation from the population-optimal selection rule. Our empirical evaluation spans real-world datasets on toxic-language removal and topical-domain removal regimes using different representations, with Mamushi achieving a more favorable removal--preservation trade-off than other baselines. Our work shows that Mamushi can serve as an efficient selection approach for downstream machine unlearning procedures, reducing the number of forget examples required to reach a fixed forgetting target.

  • 4 authors
·
Sep 29

Mind the Shift: Decoding Monetary Policy Stance from FOMC Statements with Large Language Models

Federal Open Market Committee (FOMC) statements are a major source of monetary-policy information, and even subtle changes in their wording can move global financial markets. A central task is therefore to measure the hawkish--dovish stance conveyed in these texts. Existing approaches typically treat stance detection as a standard classification problem, labeling each statement in isolation. However, the interpretation of monetary-policy communication is inherently relative: market reactions depend not only on the tone of a statement, but also on how that tone shifts across meetings. We introduce Delta-Consistent Scoring (DCS), an annotation-free framework that maps frozen large language model (LLM) representations to continuous stance scores by jointly modeling absolute stance and relative inter-meeting shifts. Rather than relying on manual hawkish--dovish labels, DCS uses consecutive meetings as a source of self-supervision. It learns an absolute stance score for each statement and a relative shift score between consecutive statements. A delta-consistency objective encourages changes in absolute scores to align with the relative shifts. This allows DCS to recover a temporally coherent stance trajectory without manual labels. Across four LLM backbones, DCS consistently outperforms supervised probes and LLM-as-judge baselines, achieving up to 71.1% accuracy on sentence-level hawkish--dovish classification. The resulting meeting-level scores are also economically meaningful: they correlate strongly with inflation indicators and are significantly associated with Treasury yield movements. Overall, the results suggest that LLM representations encode monetary-policy signals that can be recovered through relative temporal structure.

FinanceMTEB FinMTEB
·
Mar 15 2

Contrastive Search Is What You Need For Neural Text Generation

Generating text with autoregressive language models (LMs) is of great importance to many natural language processing (NLP) applications. Previous solutions for this task often produce text that contains degenerative expressions or lacks semantic consistency. Recently, Su et al. introduced a new decoding method, contrastive search, based on the isotropic representation space of the language model and obtained new state of the art on various benchmarks. Additionally, Su et al. argued that the representations of autoregressive LMs (e.g. GPT-2) are intrinsically anisotropic which is also shared by previous studies. Therefore, to ensure the language model follows an isotropic distribution, Su et al. proposed a contrastive learning scheme, SimCTG, which calibrates the language model's representations through additional training. In this study, we first answer the question: "Are autoregressive LMs really anisotropic?". To this end, we extensively evaluate the isotropy of LMs across 16 major languages. Surprisingly, we find that the anisotropic problem only exists in the two specific English GPT-2-small/medium models. On the other hand, all other evaluated LMs are naturally isotropic which is in contrast to the conclusion drawn by previous studies. Based on our findings, we further assess the contrastive search decoding method using off-the-shelf LMs on four generation tasks across 16 languages. Our experimental results demonstrate that contrastive search significantly outperforms previous decoding methods without any additional training. More notably, on 12 out of the 16 evaluated languages, contrastive search performs comparably with human-level performances as judged by human evaluations. Our code and other related resources are publicly available at https://github.com/yxuansu/Contrastive_Search_Is_What_You_Need.

  • 2 authors
·
Oct 25, 2022

Matryoshka attribution: Learning to attribute language model outputs to representations and weights

Attributing language model outputs to their internal computations is an open problem in interpretability. Existing methods, which use causal interventions, gradients, or learnable masks, either are infeasibly expensive or struggle to identify actual causally-important internal computations. We propose framing attribution as the problem of identifying nested subsets of internal components which minimise a downstream loss. To learn this task, we introduce Matryoshka Attribution (MAttr), a mask learning method that parametrises the mask with a simple differentiable sigmoid top-k operator. We supervise training over all sparsities simultaneously by randomising k over training, resulting in a learned ordering of components by attribution score. MAttr achieves number 1 on the official leaderboard of the Mechanistic Interpretability Benchmark (Mueller et al., 2025); our method identifies sparse and task-transferrable circuits across varying circuit bases. As a practical application, we show that MAttr can be trained with reinforcement learning to identify weight changes responsible for downstream behaviours in LLM finetuning. We train MAttr on refusal judge scores and find that restoring 1% of Llama 3.1 8B Instruct's weights to their base model state is sufficient to remove refusals while maintaining capabilities. We view MAttr as a successful formulation of interpretability into a learnable objective that we can tackle with gradient descent, and encourage future work along these lines.

  • 7 authors
·
Sep 21

Neuron Patching: Semantic-based Neuron-level Language Model Repair for Code Generation

Language Models (LMs) have become widely used in software engineering, especially for tasks such as code generation, where they are referred to as code LMs. These models have proven effective in generating code, making it easier for developers to automate coding activities. However, research has highlighted a significant limitation: despite their effectiveness, LMs often produce code that is incorrect, buggy, or not fully functional. Updating these models with limited data can be prohibitively challenging, yet it is essential to maximize their utility. This may require hot-fix techniques (updating models with limited data) to resolve. In this paper, we propose Model Improvement via Neuron Targeting (MINT), a novel approach for repairing code LMs. MINT leverages the semantic property of language models to perform neuron-level repairs in a novel way. Further, by analyzing the relationships between the model's latent representations, the incorrect outputs, and the desired outputs, MINT determines which neurons are worth updating. This approach ensures that only the neurons crucial to the model's failure are targeted, avoiding unnecessary changes and allowing for a more efficient and precise repair process. MINT is effective, efficient, and reliable, capable of correcting a neural model by patching a minimum number of neurons (usually one or two neurons). Our approach is evaluated on three coding tasks: line-level code generation, shellcode generation, and intent-to-bash translation. The experimental results demonstrate that the proposed approach significantly outperforms the state-of-the-art in both effectiveness and efficiency measures. In addition, we analyze and discuss the side effects of model repair techniques, including the balance between generalization and specificity, and the performance after multiple repairs in succession.

  • 4 authors
·
Dec 8, 2023

How's it going? Reinforcement learning in language models recruits a functional welfare axis

How does reinforcement learning shape a language model's internal representations? We present evidence that RL recruits a pre-existing representation of functional welfare: an estimate of how well or badly the system is doing, relative to its goals. We train several language models in a novel, semantically neutral maze environment. We then extract concept vectors for rewarded and punished trajectories, and evaluate those vectors in settings unrelated to the maze environment. The punishment vector behaves like a representation of negative welfare: it promotes failure and impossibility tokens, it aligns with negative emotion concepts, it negatively tracks goal-achievement, and steering with it induces negative self-reports, pathological backtracking, refusal, and uncertainty. The positive reward vector behaves as the mirror image, and the two are nearly antiparallel. These effects are robust when controlling for tile-to-reward mapping, scale, instruct tuning, RL training algorithm, model family, and LoRA versus full-finetuning, and largely persist when we replace RL with supervised fine-tuning. Importantly, the vectors are effective in models before they have undergone maze training. Combined with observations that the effects also appear in pretrain-only models, we therefore argue that this functional welfare axis pre-exists post-training: it is recruited, rather than created, by post-training. While we make no claims about any experience of welfare, the axis offers a demonstration that minimal reward signals can broadly affect model behavior by recruiting pre-existing welfare-like representations, with implications for interpretability, post-training dynamics, and alignment.

  • 3 authors
·
May 27

SpatialVLA: Exploring Spatial Representations for Visual-Language-Action Model

In this paper, we claim that spatial understanding is the keypoint in robot manipulation, and propose SpatialVLA to explore effective spatial representations for the robot foundation model. Specifically, we introduce Ego3D Position Encoding to inject 3D information into the input observations of the visual-language-action model, and propose Adaptive Action Grids to represent spatial robot movement actions with adaptive discretized action grids, facilitating learning generalizable and transferrable spatial action knowledge for cross-robot control. SpatialVLA is first pre-trained on top of a vision-language model with 1.1 Million real-world robot episodes, to learn a generalist manipulation policy across multiple robot environments and tasks. After pre-training, SpatialVLA is directly applied to perform numerous tasks in a zero-shot manner. The superior results in both simulation and real-world robots demonstrate its advantage of inferring complex robot motion trajectories and its strong in-domain multi-task generalization ability. We further show the proposed Adaptive Action Grids offer a new and effective way to fine-tune the pre-trained SpatialVLA model for new simulation and real-world setups, where the pre-learned action grids are re-discretized to capture robot-specific spatial action movements of new setups. The superior results from extensive evaluations demonstrate the exceptional in-distribution generalization and out-of-distribution adaptation capability, highlighting the crucial benefit of the proposed spatial-aware representations for generalist robot policy learning. All the details and codes will be open-sourced.

  • 11 authors
·
Jan 27, 2025 1

Reading and Steering Representations of Materials-Science Mechanisms in an Open-Weight Language Model

Large language models can answer scientific questions, yet a correct output does not reveal whether the model represents or uses the governing physics. Here we show that materials science mechanism information in the open-weight google/gemma-4-E4B-it model has three experimentally separable forms: concepts are readable in individual hidden states, constitutive orientation is carried by controlled transformations between states, and selected internal representations causally control engineering answers. We combine matched direct and Jacobian vocabulary readouts, option-free state geometry, a 60-law counterfactual benchmark and causal interventions. In 50 held-out materials descriptions, three independently fitted Jacobian lenses reproduced concept ranks, and target-free word sets from both readouts enabled blinded identification of 9 of 10 mechanism families. A separate 72-prompt benchmark produced mechanism-specific hidden-state neighborhoods, but an exact graph audit showed that this apparent physical organization was equally explained by numerical comparison. We therefore compared otherwise identical prompts in which only the direction of the physical input was reversed, asking whether the resulting hidden-state movement followed the supplied constitutive law. These state transformations ordered direct, physically neutral and inverse laws across 60 frozen relations and correctly oriented 39 of 40 directional laws, whereas lexical controls were near chance. Bidirectional interventions shifted answer probabilities toward or away from the physically appropriate outcome across all 12 matched cases, while counterfactual state patches transferred opposing decision signals across mechanisms and answer formats. Physical relationships were therefore more visible in controlled state changes than in absolute states alone.

FireRedAudio: A General-Purpose Audio Language Model with Decoupled Continuous Representations for Understanding and Generation

A unified audio model must recognize and understand linguistic, paralinguistic, and environmental information while supporting speech synthesis and editing. A key challenge is representation: understanding favors compact features suited to long-context modeling, whereas speech generation requires reconstructible features that preserve fine-grained acoustic detail. We introduce FireRedAudio, a general-purpose audio language model with a shared 9B-parameter LLM. To the best of our knowledge, it is the first publicly disclosed unified audio-language model to provide separate continuous input representations for understanding and generation within a single trainable autoregressive LLM. Audio to be recognized or analyzed is processed by a dedicated Audio Encoder, while speech inputs for generation use a RedAE-based pathway. The LLM directly generates text or conditions a flow-matching DiT to produce continuous acoustic latents. Through progressive multitask training, FireRedAudio supports ASR and audio understanding, with the latter extending to recordings of up to one hour, as well as zero-shot TTS, Instruct TTS, and semantic and acoustic speech editing. Its structured organization of long-form audio achieves second-level timestamp accuracy. Across comprehensive evaluations, FireRedAudio achieves competitive or leading performance in audio understanding and multilingual ASR, strong content accuracy and speaker preservation in zero-shot TTS, leading instruction following in Instruct TTS, and substantial improvements over Ming-UniAudio-Edit in both semantic and acoustic speech editing. These results demonstrate the viability of decoupled continuous input representations for unifying audio understanding and continuous-latent speech generation in a model of moderate scale. Our code is available at https://github.com/FireRedTeam/FireRedAudio.

  • 16 authors
·
Aug 24

Your Language Model is Its Own Critic: Reinforcement Learning with Value Estimation from Actor's Internal States

Reinforcement learning with verifiable rewards (RLVR) for Large Reasoning Models hinges on baseline estimation for variance reduction, but existing approaches pay a heavy price: PPO requires a policy-model scale critic, while GRPO needs multiple rollouts per prompt to keep its empirical group mean stable. We introduce Policy Optimization with Internal State Value Estimation), which obtains a baseline at negligible cost by using the policy model's internal signals already computed during the policy forward pass. A lightweight probe predicts the expected verifiable reward from the hidden states of the prompt and generated trajectory, as well as token-entropy statistics, and is trained online alongside the policy. To preserve gradient unbiasedness despite using trajectory-conditioned features, we introduce a cross-rollout construction that predicts each rollout's value from an independent rollout's internal states. Because POISE estimates prompt value using only a single rollout, it enables higher prompt diversity for a fixed compute budget during training. This reduces gradient variance for more stable learning and also eliminates the compute overhead of sampling costs for detecting zero-advantage prompts. On Qwen3-4B and DeepSeek-R1-Distill-Qwen-1.5B across math reasoning benchmarks, POISE matches DAPO while requiring less compute. Moreover, its value estimator shows similar performance to a separate LLM-scale value model and generalizes to various verifiable tasks. By leveraging the model's own internal representations, POISE enables more stable and efficient policy optimization.

Item-Language Model for Conversational Recommendation

Large-language Models (LLMs) have been extremely successful at tasks like complex dialogue understanding, reasoning and coding due to their emergent abilities. These emergent abilities have been extended with multi-modality to include image, audio, and video capabilities. Recommender systems, on the other hand, have been critical for information seeking and item discovery needs. Recently, there have been attempts to apply LLMs for recommendations. One difficulty of current attempts is that the underlying LLM is usually not trained on the recommender system data, which largely contains user interaction signals and is often not publicly available. Another difficulty is user interaction signals often have a different pattern from natural language text, and it is currently unclear if the LLM training setup can learn more non-trivial knowledge from interaction signals compared with traditional recommender system methods. Finally, it is difficult to train multiple LLMs for different use-cases, and to retain the original language and reasoning abilities when learning from recommender system data. To address these three limitations, we propose an Item-Language Model (ILM), which is composed of an item encoder to produce text-aligned item representations that encode user interaction signals, and a frozen LLM that can understand those item representations with preserved pretrained knowledge. We conduct extensive experiments which demonstrate both the importance of the language-alignment and of user interaction knowledge in the item encoder.

  • 7 authors
·
Jun 4, 2024 1

Bioformer: an efficient transformer language model for biomedical text mining

Pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art performance in natural language processing (NLP) tasks. Recently, BERT has been adapted to the biomedical domain. Despite the effectiveness, these models have hundreds of millions of parameters and are computationally expensive when applied to large-scale NLP applications. We hypothesized that the number of parameters of the original BERT can be dramatically reduced with minor impact on performance. In this study, we present Bioformer, a compact BERT model for biomedical text mining. We pretrained two Bioformer models (named Bioformer8L and Bioformer16L) which reduced the model size by 60% compared to BERTBase. Bioformer uses a biomedical vocabulary and was pre-trained from scratch on PubMed abstracts and PubMed Central full-text articles. We thoroughly evaluated the performance of Bioformer as well as existing biomedical BERT models including BioBERT and PubMedBERT on 15 benchmark datasets of four different biomedical NLP tasks: named entity recognition, relation extraction, question answering and document classification. The results show that with 60% fewer parameters, Bioformer16L is only 0.1% less accurate than PubMedBERT while Bioformer8L is 0.9% less accurate than PubMedBERT. Both Bioformer16L and Bioformer8L outperformed BioBERTBase-v1.1. In addition, Bioformer16L and Bioformer8L are 2-3 fold as fast as PubMedBERT/BioBERTBase-v1.1. Bioformer has been successfully deployed to PubTator Central providing gene annotations over 35 million PubMed abstracts and 5 million PubMed Central full-text articles. We make Bioformer publicly available via https://github.com/WGLab/bioformer, including pre-trained models, datasets, and instructions for downstream use.

  • 5 authors
·
Feb 3, 2023

iCLP: Large Language Model Reasoning with Implicit Cognition Latent Planning

Large language models (LLMs), when guided by explicit textual plans, can perform reliable step-by-step reasoning during problem-solving. However, generating accurate and effective textual plans remains challenging due to LLM hallucinations and the high diversity of task-specific questions. To address this, we draw inspiration from human Implicit Cognition (IC), the subconscious process by which decisions are guided by compact, generalized patterns learned from past experiences without requiring explicit verbalization. We propose iCLP, a novel framework that enables LLMs to adaptively generate latent plans (LPs), which are compact encodings of effective reasoning instructions. iCLP first distills explicit plans from existing step-by-step reasoning trajectories. It then learns discrete representations of these plans via a vector-quantized autoencoder coupled with a codebook. Finally, by fine-tuning LLMs on paired latent plans and corresponding reasoning steps, the models learn to perform implicit planning during reasoning. Experimental results on mathematical reasoning and code generation tasks demonstrate that, with iCLP, LLMs can plan in latent space while reasoning in language space. This approach yields significant improvements in both accuracy and efficiency and, crucially, demonstrates strong cross-domain generalization while preserving the interpretability of chain-of-thought reasoning.

  • 2 authors
·
Dec 30, 2025

Distilling Large Vision-Language Model with Out-of-Distribution Generalizability

Large vision-language models have achieved outstanding performance, but their size and computational requirements make their deployment on resource-constrained devices and time-sensitive tasks impractical. Model distillation, the process of creating smaller, faster models that maintain the performance of larger models, is a promising direction towards the solution. This paper investigates the distillation of visual representations in large teacher vision-language models into lightweight student models using a small- or mid-scale dataset. Notably, this study focuses on open-vocabulary out-of-distribution (OOD) generalization, a challenging problem that has been overlooked in previous model distillation literature. We propose two principles from vision and language modality perspectives to enhance student's OOD generalization: (1) by better imitating teacher's visual representation space, and carefully promoting better coherence in vision-language alignment with the teacher; (2) by enriching the teacher's language representations with informative and finegrained semantic attributes to effectively distinguish between different labels. We propose several metrics and conduct extensive experiments to investigate their techniques. The results demonstrate significant improvements in zero-shot and few-shot student performance on open-vocabulary out-of-distribution classification, highlighting the effectiveness of our proposed approaches. Code released at https://github.com/xuanlinli17/large_vlm_distillation_ood

  • 6 authors
·
Jul 6, 2023

PUMGPT: A Large Vision-Language Model for Product Understanding

Recent developments of multi-modal large language models have demonstrated its strong ability in solving vision-language tasks. In this paper, we focus on the product understanding task, which plays an essential role in enhancing online shopping experience. Product understanding task includes a variety of sub-tasks, which require models to respond diverse queries based on multi-modal product information. Traditional methods design distinct model architectures for each sub-task. On the contrary, we present PUMGPT, a large vision-language model aims at unifying all product understanding tasks under a singular model structure. To bridge the gap between vision and text representations, we propose Layer-wise Adapters (LA), an approach that provides enhanced alignment with fewer visual tokens and enables parameter-efficient fine-tuning. Moreover, the inherent parameter-efficient fine-tuning ability allows PUMGPT to be readily adapted to new product understanding tasks and emerging products. We design instruction templates to generate diverse product instruction datasets. Simultaneously, we utilize open-domain datasets during training to improve the performance of PUMGPT and its generalization ability. Through extensive evaluations, PUMGPT demonstrates its superior performance across multiple product understanding tasks, including product captioning, category question-answering, attribute extraction, attribute question-answering, and even free-form question-answering about products.

  • 7 authors
·
Aug 18, 2023 1

Expediting and Elevating Large Language Model Reasoning via Hidden Chain-of-Thought Decoding

Large language models (LLMs) have demonstrated remarkable capabilities in tasks requiring reasoning and multi-step problem-solving through the use of chain-of-thought (CoT) prompting. However, generating the full CoT process results in significantly longer output sequences, leading to increased computational costs and latency during inference. To address this challenge, we propose a novel approach to compress the CoT process through semantic alignment, enabling more efficient decoding while preserving the benefits of CoT reasoning. Our method introduces an auxiliary CoT model that learns to generate and compress the full thought process into a compact special token representation semantically aligned with the original CoT output. This compressed representation is then integrated into the input of the Hidden Chain-of-Thought (HCoT) model. The training process follows a two-stage procedure: First, the CoT model is optimized to generate the compressed token representations aligned with the ground-truth CoT outputs using a contrastive loss. Subsequently, with the CoT model parameters frozen, the HCoT model is fine-tuned to generate accurate subsequent predictions conditioned on the prefix instruction and the compressed CoT representations from the CoT model. Extensive experiments across three challenging domains - mathematical reasoning, agent invocation, and question answering - demonstrate that our semantic compression approach achieves competitive or improved performance compared to the full CoT baseline, while providing significant speedups of at least 1.5x in decoding time. Moreover, incorporating contrastive learning objectives further enhances the quality of the compressed representations, leading to better CoT prompting and improved task accuracy. Our work paves the way for more efficient exploitation of multi-step reasoning capabilities in LLMs across a wide range of applications.

  • 5 authors
·
Sep 13, 2024 2

Long-context Protein Language Model

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

  • 7 authors
·
Oct 29, 2024

SecureBERT 2.0: Advanced Language Model for Cybersecurity Intelligence

Effective analysis of cybersecurity and threat intelligence data demands language models that can interpret specialized terminology, complex document structures, and the interdependence of natural language and source code. Encoder-only transformer architectures provide efficient and robust representations that support critical tasks such as semantic search, technical entity extraction, and semantic analysis, which are key to automated threat detection, incident triage, and vulnerability assessment. However, general-purpose language models often lack the domain-specific adaptation required for high precision. We present SecureBERT 2.0, an enhanced encoder-only language model purpose-built for cybersecurity applications. Leveraging the ModernBERT architecture, SecureBERT 2.0 introduces improved long-context modeling and hierarchical encoding, enabling effective processing of extended and heterogeneous documents, including threat reports and source code artifacts. Pretrained on a domain-specific corpus more than thirteen times larger than its predecessor, comprising over 13 billion text tokens and 53 million code tokens from diverse real-world sources, SecureBERT 2.0 achieves state-of-the-art performance on multiple cybersecurity benchmarks. Experimental results demonstrate substantial improvements in semantic search for threat intelligence, semantic analysis, cybersecurity-specific named entity recognition, and automated vulnerability detection in code within the cybersecurity domain.

  • 4 authors
·
Sep 30, 2025

GAMA: A Large Audio-Language Model with Advanced Audio Understanding and Complex Reasoning Abilities

Perceiving and understanding non-speech sounds and non-verbal speech is essential to making decisions that help us interact with our surroundings. In this paper, we propose GAMA, a novel General-purpose Large Audio-Language Model (LALM) with Advanced Audio Understanding and Complex Reasoning Abilities. We build GAMA by integrating an LLM with multiple types of audio representations, including features from a custom Audio Q-Former, a multi-layer aggregator that aggregates features from multiple layers of an audio encoder. We fine-tune GAMA on a large-scale audio-language dataset, which augments it with audio understanding capabilities. Next, we propose CompA-R (Instruction-Tuning for Complex Audio Reasoning), a synthetically generated instruction-tuning (IT) dataset with instructions that require the model to perform complex reasoning on the input audio. We instruction-tune GAMA with CompA-R to endow it with complex reasoning abilities, where we further add a soft prompt as input with high-level semantic evidence by leveraging event tags of the input audio. Finally, we also propose CompA-R-test, a human-labeled evaluation dataset for evaluating the capabilities of LALMs on open-ended audio question-answering that requires complex reasoning. Through automated and expert human evaluations, we show that GAMA outperforms all other LALMs in literature on diverse audio understanding tasks by margins of 1%-84%. Further, GAMA IT-ed on CompA-R proves to be superior in its complex reasoning and instruction following capabilities.

  • 9 authors
·
Jun 17, 2024 1

Controlling Large Language Model Agents with Entropic Activation Steering

The generality of pretrained large language models (LLMs) has prompted increasing interest in their use as in-context learning agents. To be successful, such agents must form beliefs about how to achieve their goals based on limited interaction with their environment, resulting in uncertainty about the best action to take at each step. In this paper, we study how LLM agents form and act on these beliefs by conducting experiments in controlled sequential decision-making tasks. To begin, we find that LLM agents are overconfident: They draw strong conclusions about what to do based on insufficient evidence, resulting in inadequately explorative behavior. We dig deeper into this phenomenon and show how it emerges from a collapse in the entropy of the action distribution implied by sampling from the LLM. We then demonstrate that existing token-level sampling techniques are by themselves insufficient to make the agent explore more. Motivated by this fact, we introduce Entropic Activation Steering (EAST), an activation steering method for in-context LLM agents. EAST computes a steering vector as an entropy-weighted combination of representations, and uses it to manipulate an LLM agent's uncertainty over actions by intervening on its activations during the forward pass. We show that EAST can reliably increase the entropy in an LLM agent's actions, causing more explorative behavior to emerge. Finally, EAST modifies the subjective uncertainty an LLM agent expresses, paving the way to interpreting and controlling how LLM agents represent uncertainty about their decisions.

  • 3 authors
·
May 31, 2024

Improving Multi-modal Large Language Model through Boosting Vision Capabilities

We focus on improving the visual understanding capability for boosting the vision-language models. We propose Arcana, a multiModal language model, which introduces two crucial techniques. First, we present Multimodal LoRA (MM-LoRA), a module designed to enhance the decoder. Unlike traditional language-driven decoders, MM-LoRA consists of two parallel LoRAs -- one for vision and one for language -- each with its own parameters. This disentangled parameters design allows for more specialized learning in each modality and better integration of multimodal information. Second, we introduce the Query Ladder adapter (QLadder) to improve the visual encoder. QLadder employs a learnable ``ladder'' structure to deeply aggregates the intermediate representations from the frozen pretrained visual encoder (e.g., CLIP image encoder). This enables the model to learn new and informative visual features, as well as remaining the powerful capabilities of the pretrained visual encoder. These techniques collectively enhance Arcana's visual perception power, enabling it to leverage improved visual information for more accurate and contextually relevant outputs across various multimodal scenarios. Extensive experiments and ablation studies demonstrate the effectiveness and generalization capability of our Arcana. The code and re-annotated data are available at https://arcana-project-page.github.io.

  • 8 authors
·
Oct 17, 2024

GP-GPT: Large Language Model for Gene-Phenotype Mapping

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.

  • 18 authors
·
Sep 15, 2024

MLA: A Multisensory Language-Action Model for Multimodal Understanding and Forecasting in Robotic Manipulation

Vision-language-action models (VLAs) have shown generalization capabilities in robotic manipulation tasks by inheriting from vision-language models (VLMs) and learning action generation. Most VLA models focus on interpreting vision and language to generate actions, whereas robots must perceive and interact within the spatial-physical world. This gap highlights the need for a comprehensive understanding of robotic-specific multisensory information, which is crucial for achieving complex and contact-rich control. To this end, we introduce a multisensory language-action (MLA) model that collaboratively perceives heterogeneous sensory modalities and predicts future multisensory objectives to facilitate physical world modeling. Specifically, to enhance perceptual representations, we propose an encoder-free multimodal alignment scheme that innovatively repurposes the large language model itself as a perception module, directly interpreting multimodal cues by aligning 2D images, 3D point clouds, and tactile tokens through positional correspondence. To further enhance MLA's understanding of physical dynamics, we design a future multisensory generation post-training strategy that enables MLA to reason about semantic, geometric, and interaction information, providing more robust conditions for action generation. For evaluation, the MLA model outperforms the previous state-of-the-art 2D and 3D VLA methods by 12% and 24% in complex, contact-rich real-world tasks, respectively, while also demonstrating improved generalization to unseen configurations. Project website: https://sites.google.com/view/open-mla

  • 13 authors
·
Sep 30, 2025

DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA

Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn generalizable representations of diverse DNA elements, potentially enabling various genomic prediction, interpretation and design tasks. Despite their potential, existing benchmarks do not adequately assess the capabilities of DNALMs on key downstream applications involving an important class of non-coding DNA elements critical for regulating gene activity. In this study, we introduce DART-Eval, a suite of representative benchmarks specifically focused on regulatory DNA to evaluate model performance across zero-shot, probed, and fine-tuned scenarios against contemporary ab initio models as baselines. Our benchmarks target biologically meaningful downstream tasks such as functional sequence feature discovery, predicting cell-type specific regulatory activity, and counterfactual prediction of the impacts of genetic variants. We find that current DNALMs exhibit inconsistent performance and do not offer compelling gains over alternative baseline models for most tasks, while requiring significantly more computational resources. We discuss potentially promising modeling, data curation, and evaluation strategies for the next generation of DNALMs. Our code is available at https://github.com/kundajelab/DART-Eval.

  • 6 authors
·
Dec 6, 2024

ASCIIBench: Evaluating Language-Model-Based Understanding of Visually-Oriented Text

Large language models (LLMs) have demonstrated several emergent behaviors with scale, including reasoning and fluency in long-form text generation. However, they continue to struggle with tasks requiring precise spatial and positional reasoning. ASCII art, a symbolic medium where characters encode structure and form, provides a unique probe of this limitation. We introduce ASCIIBench, a novel benchmark for evaluating both the generation and classification of ASCII-text images. ASCIIBench consists of a filtered dataset of 5,315 class-labeled ASCII images and is, to our knowledge, the first publicly available benchmark of its kind. Alongside the dataset, we release weights for a fine-tuned CLIP model adapted to capture ASCII structure, enabling the evaluation of LLM-generated ASCII art. Our analysis shows that cosine similarity over CLIP embeddings fails to separate most ASCII categories, yielding chance-level performance even for low-variance classes. In contrast, classes with high internal mean similarity exhibit clear discriminability, revealing that the bottleneck lies in representation rather than generational variance. These findings position ASCII art as a stress test for multimodal representations and motivate the development of new embedding methods or evaluation metrics tailored to symbolic visual modalities. All resources are available at https://github.com/ASCIIBench/ASCIIBench.

  • 9 authors
·
Dec 1, 2025

A Unified Graph Language Model for Multi-Domain Multi-Task Graph Alignment Instruction Tuning

Leveraging Graph Neural Networks (GNNs) as graph encoders and aligning the resulting representations with Large Language Models (LLMs) through alignment instruction tuning has become a mainstream paradigm for constructing Graph Language Models (GLMs), combining the generalization ability of LLMs with the structural modeling capacity of GNNs. However, existing GLMs that adopt GNNs as graph encoders largely overlook the problem of aligning GNN-encoded representations across domains and tasks with the LLM token space to obtain unified graph tokens, thereby limiting their ability to generalize across diverse graph data. To bridge this gap, we aim to incorporate a multi-domain, multi-task GNN encoder into GLMs and align its representations with LLMs to enable multi-domain, multi-task graph alignment instruction tuning. This alignment problem remains underexplored and poses two key challenges: 1) learning GNN-encoded representations that are simultaneously generalizable across domains and tasks and well aligned with textual semantics is difficult, due to substantial variations in graph structures, feature distributions, and supervision signals, together with the lack of textual-semantic alignment guidance in task-specific GNN training; 2) diverse graph data and task-specific instructions can exhibit different degrees of compatibility with the LLM token space during instruction tuning, leading to varying alignment difficulty and rendering a fixed alignment strategy suboptimal. To tackle these challenges, we propose UniGraphLM, a Unified Graph Language Model that incorporates a multi-domain, multi-task GNN encoder to learn generalizable graph representations aligned with textual semantics, and then adaptively aligns these representations with the LLM.

  • 5 authors
·
May 11

Multimodal LLMs Can Learn to Read Brain Signals: A Vision--Language Model for Unified Multi-Task EEG Decoding

Learning EEG representations that generalize across cognitive tasks, subjects, and recording conditions remains a key challenge in electroencephalography (EEG) decoding. Recent advances in foundation models have improved EEG decoding performance, yet a fundamental open question remains: how to effectively interface neural signals with these models to enable multi-task learning across datasets. To investigate this question, we introduce BraVista, a visual-language framework that encodes multichannel EEG signals as structured images and enables multi-task learning through instruction-conditioned vision-language models (VLMs). Our approach relies on continued post-training of a general-domain VLM, leveraging its visual and linguistic priors to adapt to neural signals without a separate large-scale EEG-specific pretraining stage. We evaluate BraVista on four datasets spanning sleep staging, emotion recognition, cognitive workload classification, and abnormal EEG detection, showing strong performance across these tasks. Further analyses show that the choice of EEG-to-image representation is critical to performance. Moreover, through controlled perturbations of the EEG signal, we observe a gradual performance degradation under increasing noise, suggesting that the model relies on EEG-relevant information rather than superficial visual patterns. Together, these findings establish structured visual representations as an effective and scalable interface between neural signals and general-domain foundation models for unified multi-task EEG decoding.

  • 3 authors
·
Oct 6

LEMON: LanguagE ModeL for Negative Sampling of Knowledge Graph Embeddings

Knowledge Graph Embedding models have become an important area of machine learning.Those models provide a latent representation of entities and relations in a knowledge graph which can then be used in downstream machine learning tasks such as link prediction. The learning process of such models can be performed by contrasting positive and negative triples. While all triples of a KG are considered positive, negative triples are usually not readily available. Therefore, the choice of the sampling method to obtain the negative triples play a crucial role in the performance and effectiveness of Knowledge Graph Embedding models. Most of the current methods fetch negative samples from a random distribution of entities in the underlying Knowledge Graph which also often includes meaningless triples. Other known methods use adversarial techniques or generative neural networks which consequently reduce the efficiency of the process. In this paper, we propose an approach for generating informative negative samples considering available complementary knowledge about entities. Particularly, Pre-trained Language Models are used to form neighborhood clusters by utilizing the distances between entities to obtain representations of symbolic entities via their textual information. Our comprehensive evaluations demonstrate the effectiveness of the proposed approach on benchmark Knowledge Graphs with textual information for the link prediction task.

  • 5 authors
·
Mar 9, 2022